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  • 1.
    Chen, Jian
    et al.
    Fudan Univ, Shanghai Publ Hlth Clin Ctr, Sci Res Ctr, Shanghai 201508, Peoples R China..
    Yang, Yi-feng
    ShanghaiTech Univ, Shanghai Inst Adv Immunochem Studies, Shanghai 201210, Peoples R China..
    Chen, Jun
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Zhou, Xiaohui
    Fudan Univ, Shanghai Publ Hlth Clin Ctr, Sci Res Ctr, Shanghai 201508, Peoples R China..
    Dong, Zhaoguang
    Fudan Univ, Shanghai Publ Hlth Clin Ctr, Sci Res Ctr, Shanghai 201508, Peoples R China..
    Chen, Tianyue
    Fudan Univ, Shanghai Publ Hlth Clin Ctr, Sci Res Ctr, Shanghai 201508, Peoples R China..
    Yang, Yu
    Fudan Univ, Shanghai Publ Hlth Clin Ctr, Sci Res Ctr, Shanghai 201508, Peoples R China..
    Zou, Peng
    Fudan Univ, Shanghai Publ Hlth Clin Ctr, Sci Res Ctr, Shanghai 201508, Peoples R China..
    Jiang, Biao
    ShanghaiTech Univ, Shanghai Inst Adv Immunochem Studies, Shanghai 201210, Peoples R China..
    Hu, Yunwen
    Fudan Univ, Shanghai Publ Hlth Clin Ctr, Sci Res Ctr, Shanghai 201508, Peoples R China..
    Lu, Lu
    Fudan Univ, Shanghai Publ Hlth Clin Ctr, Sci Res Ctr, Shanghai 201508, Peoples R China..
    Zhang, Xiaoyan
    Fudan Univ, Shanghai Publ Hlth Clin Ctr, Sci Res Ctr, Shanghai 201508, Peoples R China.;Fudan Univ, Minist Educ Hlth, Key Lab Med Mol Virol, Inst Biomed Sci, Shanghai 200032, Peoples R China..
    Liu, Jia
    ShanghaiTech Univ, Shanghai Inst Adv Immunochem Studies, Shanghai 201210, Peoples R China..
    Xu, Jianqing
    Fudan Univ, Shanghai Publ Hlth Clin Ctr, Sci Res Ctr, Shanghai 201508, Peoples R China.;Fudan Univ, Minist Educ Hlth, Key Lab Med Mol Virol, Inst Biomed Sci, Shanghai 200032, Peoples R China..
    Zhu, Tongyu
    Fudan Univ, Shanghai Publ Hlth Clin Ctr, Sci Res Ctr, Shanghai 201508, Peoples R China.;Fudan Univ, Zhongshan Hosp, Dept Urol, Shanghai 200032, Peoples R China.;Fudan Univ, Zhongshan Hosp, Shanghai Key Lab Organ Transplantat, Shanghai 200032, Peoples R China..
    Zika virus infects renal proximal tubular epithelial cells with prolonged persistency and cytopathic effects2017In: EMERGING MICROBES & INFECTIONS, ISSN 2222-1751, Vol. 6, article id e77Article in journal (Refereed)
    Abstract [en]

    Zika virus (ZIKV) infection can cause fetal developmental abnormalities and Guillain-Barre syndrome in adults. Although progress has been made in understanding the link between ZIKV infection and microcephaly, the pathology of ZIKV, particularly the viral reservoirs in human, remains poorly understood. Several studies have shown that compared to serum samples, patients' urine samples often have a longer duration of ZIKV persistency and higher viral load. This finding suggests that an independent viral reservoir may exist in the human urinary system. Despite the clinical observations, the host cells of ZIKV in the human urinary system are poorly characterized. In this study, we demonstrate that ZIKV can infect renal proximal tubular epithelial cells (RPTEpiCs) in immunodeficient mice in vivo and in both immortalized and primary human renal proximal tubular epithelial cells (hRPTEpiCs) in vitro. Importantly, ZIKV infection in mouse kidneys caused caspase-3-mediated apoptosis of renal cells. Similarly, in vitro infection of immortalized and primary hRPTEpiCs resulted in notable cytopathic effects. Consistent with the clinical observations, we found that ZIKV infection can persist with prolonged duration in hRPTEpiCs. RNA-Seq analyses of infected hRPTEpiCs revealed a large number of transcriptional changes in response to ZIKV infection, including type I interferon signaling genes and anti-viral response genes. Our results suggest that hRPTEpiCs are a potential reservoir of ZIKV in the human urinary system, providing a possible explanation for the prolonged persistency of ZIKV in patients' urine.

  • 2.
    Chen, Jian
    et al.
    Fudan Univ, Shanghai Publ Hlth Clin Ctr, Sci Res Ctr, Shanghai, Peoples R China.;Fudan Univ, Inst Biomed Sci, Key Lab Med Mol Virol, Minist Educ Hlth,Shanghai Med Coll, Shanghai, Peoples R China..
    Yang, Yi-feng
    ShanghaiTech Univ, Shanghai Inst Adv Immunochem Studies, Shanghai, Peoples R China..
    Yang, Yu
    Fudan Univ, Shanghai Publ Hlth Clin Ctr, Sci Res Ctr, Shanghai, Peoples R China.;Fudan Univ, Inst Biomed Sci, Key Lab Med Mol Virol, Minist Educ Hlth,Shanghai Med Coll, Shanghai, Peoples R China..
    Zou, Peng
    Fudan Univ, Shanghai Publ Hlth Clin Ctr, Sci Res Ctr, Shanghai, Peoples R China.;Fudan Univ, Inst Biomed Sci, Key Lab Med Mol Virol, Minist Educ Hlth,Shanghai Med Coll, Shanghai, Peoples R China..
    Chen, Jun
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    He, Yongquan
    Fudan Univ, Shanghai Publ Hlth Clin Ctr, Sci Res Ctr, Shanghai, Peoples R China.;Fudan Univ, Inst Biomed Sci, Key Lab Med Mol Virol, Minist Educ Hlth,Shanghai Med Coll, Shanghai, Peoples R China..
    Shui, Sai-lan
    ShanghaiTech Univ, Shanghai Inst Adv Immunochem Studies, Shanghai, Peoples R China..
    Cui, Yan-ru
    ShanghaiTech Univ, Shanghai Inst Adv Immunochem Studies, Shanghai, Peoples R China..
    Bai, Ru
    Fudan Univ, Shanghai Publ Hlth Clin Ctr, Sci Res Ctr, Shanghai, Peoples R China.;Fudan Univ, Inst Biomed Sci, Key Lab Med Mol Virol, Minist Educ Hlth,Shanghai Med Coll, Shanghai, Peoples R China..
    Liang, Ya-jun
    ShanghaiTech Univ, Shanghai Inst Adv Immunochem Studies, Shanghai, Peoples R China..
    Hu, Yunwen
    Fudan Univ, Shanghai Publ Hlth Clin Ctr, Sci Res Ctr, Shanghai, Peoples R China.;Fudan Univ, Inst Biomed Sci, Key Lab Med Mol Virol, Minist Educ Hlth,Shanghai Med Coll, Shanghai, Peoples R China..
    Jiang, Biao
    ShanghaiTech Univ, Shanghai Inst Adv Immunochem Studies, Shanghai, Peoples R China..
    Lu, Lu
    Fudan Univ, Shanghai Publ Hlth Clin Ctr, Sci Res Ctr, Shanghai, Peoples R China.;Fudan Univ, Inst Biomed Sci, Key Lab Med Mol Virol, Minist Educ Hlth,Shanghai Med Coll, Shanghai, Peoples R China..
    Zhang, Xiaoyan
    Fudan Univ, Shanghai Publ Hlth Clin Ctr, Sci Res Ctr, Shanghai, Peoples R China.;Fudan Univ, Inst Biomed Sci, Key Lab Med Mol Virol, Minist Educ Hlth,Shanghai Med Coll, Shanghai, Peoples R China.;China Ctr Dis Control & Prevent, State Key Lab Infect Dis Prevent & Control, Beijing, Peoples R China..
    Liu, Jia
    ShanghaiTech Univ, Shanghai Inst Adv Immunochem Studies, Shanghai, Peoples R China..
    Xu, Jianqing
    Fudan Univ, Shanghai Publ Hlth Clin Ctr, Sci Res Ctr, Shanghai, Peoples R China.;Fudan Univ, Inst Biomed Sci, Key Lab Med Mol Virol, Minist Educ Hlth,Shanghai Med Coll, Shanghai, Peoples R China.;China Ctr Dis Control & Prevent, State Key Lab Infect Dis Prevent & Control, Beijing, Peoples R China..
    AXL promotes Zika virus infection in astrocytes by antagonizing type I interferon signalling2018In: Nature Microbiology, E-ISSN 2058-5276, Vol. 3, no 3, p. 302-309Article in journal (Refereed)
    Abstract [en]

    Zika virus (ZIKV) is associated with neonatal microcephaly and Guillain-Barre syndrome(1,2). While progress has been made in understanding the causal link between ZIKV infection and microcephaly(3-9), the life cycle and pathogenesis of ZIKV are less well understood. In particular, there are conflicting reports on the role of AXL, a TAM family kinase receptor that was initially described as the entry receptor for ZIKV(10-22). Here, we show that while genetic ablation of AXL protected primary human astrocytes and astrocytoma cell lines from ZIKV infection, AXL knockout did not block the entry of ZIKV. We found, instead, that the presence of AXL attenuated the ZIKV-induced activation of type I interferon (IFN) signalling genes, including several type I IFNs and IFN-stimulating genes. Knocking out type I IFN receptor alpha chain (IFNAR1) restored the vulnerability of AXL knockout astrocytes to ZIKV infection. Further experiments suggested that AXL regulates the expression of SOCS1, a known type I IFN signalling suppressor, in a STAT1/STAT2-dependent manner. Collectively, our results demonstrate that AXL is unlikely to function as an entry receptor for ZIKV and may instead promote ZIKV infection in human astrocytes by antagonizing type I IFN signalling.

  • 3.
    Chen, Jun
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Conifer Evolution, from Demography and Local Adaptation to Evolutionary Rates: Examples from the Picea genus2012Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Evolutionary process can be inferred at three different levels: the species level, the population level and the molecular level. In this thesis, I applied approaches at these three levels and aimed to get a comprehensive picture of conifer evolution, from speciation and demography to geographic variation and local adaptation, and then to the molecular evolution of proteins and small regulatory RNAs.

    Spruce species have been observed to possess a large number of trans-species shared polymorphisms. Using an “Isolation with migration” model, we found that the large effective population size of spruce retained these shared polymorphisms, inheriting them from the common ancestor. Post-divergence gene flow only existed between Picea abies and P. glauca, and between P. wilsonii and P. schrenkiana. The combination of Tajima’s D and Fay & Wu’s H at most of loci suggested an ancient and severe bottleneck for most species except P. breweriana.

    Furthermore, I investigated the effect of local selection in two parallel clines, which is one of the major forces that can cause divergence or even speciation. The timing of bud set and growth cessation was found correlated with latitude in populations of P. abies and P. obovata. Using allele frequency spectrum analyses we identified three genes under local selection in both species including two circadian-clock genes GI and PRR7, and one photoperiodic gene FTL2. This indicated that parallel evolution could occur through groups of genes within related pathways. Clinal variation at expression level provided stronger evidence of selection in FTL2, which has previously been associated with bud set in P. abies.

    Finally we focused on the molecular evolution of mRNA and small regulatory RNAs in P. abies. With the help of Next-Generation sequencing, we have achieved in spruce the first de novel assembly of the needle transcriptome and a preliminary characterization of sRNA populations. Along with features common in plants, spruce also exhibited novelties in many aspects including lower substitution rate and protein evolutionary rate, dominance of 21-nt sRNA, and a large proportion of TIR-NBS-LRR genes as sRNA sources and targets.

  • 4.
    Chen, Jun
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Glemin, Sylvain
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab. Univ Montpellier, CNRS, IRD, Inst Sci Evolut,EPHE,UMR 5554, Montpellier, France..
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Genetic Diversity and the Efficacy of Purifying Selection across Plant and Animal Species2017In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 34, no 6, p. 1417-1428Article in journal (Refereed)
    Abstract [en]

    A central question in evolutionary biology is why some species have more genetic diversity than others and a no less important question is why selection efficacy varies among species. Although these questions have started to be tackled in animals, they have not been addressed to the same extent in plants. Here, we estimated nucleotide diversity at synonymous, pi(S), and nonsynonymous sites, pi(N), and a measure of the efficacy of selection, the ratio pi(N)/pi(S), in 34 animal and 28 plant species using full genome data. We then evaluated the relationship of nucleotide diversity and selection efficacy with effective population size, the distribution of fitness effect and life history traits. In animals, our data confirm that longevity and propagule size are the variables that best explain the variation in pi(S) among species. In plants longevity also plays a major role as well as mating system. As predicted by the nearly neutral theory of molecular evolution, the log of pi(N)/pi(S) decreased linearly with the log of pi(S) but the slope was weaker in plants than in animals. This appears to be due to a higher mutation rate in long lived plants, and the difference disappears when pi(S) is rescaled by the mutation rate. Differences in the distribution of fitness effect of new mutations also contributed to variation in pi(N)/pi(S) among species.

  • 5.
    Chen, Jun
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Källman, Thomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Ma, Xiaofei
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Gyllenstrand, Niclas
    Zaina, Giusi
    Morgante, Michele
    Bousquet, Jean
    Eckert, Andrew
    Wegrzyn, Jill
    Neale, David
    Lagercrantz, Ulf
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Disentangling the Roles of History and Local Selection in Shaping Clinal Variation of Allele Frequencies and Gene Expression in Norway Spruce (Picea abies)2012In: Genetics, ISSN 0016-6731, E-ISSN 1943-2631, Vol. 191, no 3, p. 865-881Article in journal (Refereed)
    Abstract [en]

    Understanding the genetic basis of local adaptation is challenging due to the subtle balance among conflicting evolutionary forces that are involved in its establishment and maintenance. One system with which to tease apart these difficulties is clines in adaptive characters. Here we analyzed genetic and phenotypic variation in bud set, a highly heritable and adaptive trait, among 18 populations of Norway spruce (Picea abies), arrayed along a latitudinal gradient ranging from 47°N to 68°N. We confirmed that variation in bud set is strongly clinal, using a subset of five populations. Genotypes for 137 single-nucleotide polymorphisms (SNPs) chosen from 18 candidate genes putatively affecting bud set and 308 control SNPs chosen from 264 random genes were analyzed for patterns of genetic structure and correlation to environment. Population genetic structure was low (F(ST) = 0.05), but latitudinal patterns were apparent among Scandinavian populations. Hence, part of the observed clinal variation should be attributable to population demography. Conditional on patterns of genetic structure, there was enrichment of SNPs within candidate genes for correlations with latitude. Twenty-nine SNPs were also outliers with respect to F(ST). The enrichment for clinal variation at SNPs within candidate genes (i.e., SNPs in PaGI, PaPhyP, PaPhyN, PaPRR7, and PaFTL2) indicated that local selection in the 18 populations, and/or selection in the ancestral populations from which they were recently derived, shaped the observed cline. Validation of these genes using expression studies also revealed that PaFTL2 expression is significantly associated with latitude, thereby confirming the central role played by this gene in the control of phenology in plants.

  • 6.
    Chen, Jun
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Källman, Thomas
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Ma, Xiao-Fei
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Chinese Acad Sci, Key Lab Stress Physiol & Ecol Cold & Arid Reg, Lanzhou, Peoples R China..
    Zaina, Giusi
    Univ Udine, Dept Agr Food Environm & Anim Sci, I-33100 Udine, Italy..
    Morgante, Michele
    Univ Udine, Dept Agr Food Environm & Anim Sci, I-33100 Udine, Italy..
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Identifying Genetic Signatures of Natural Selection Using Pooled Population Sequencing in Picea abies2016In: G3: Genes, Genomes, Genetics, ISSN 2160-1836, E-ISSN 2160-1836, Vol. 6, no 7, p. 1979-1989Article in journal (Refereed)
    Abstract [en]

    The joint inference of selection and past demography remain a costly and demanding task. We used next generation sequencing of two pools of 48 Norway spruce mother trees, one corresponding to the Fennoscandian domain, and the other to the Alpine domain, to assess nucleotide polymorphism at 88 nuclear genes. These genes are candidate genes for phenological traits, and most belong to the photoperiod pathway. Estimates of population genetic summary statistics from the pooled data are similar to previous estimates, suggesting that pooled sequencing is reliable. The nonsynonymous SNPs tended to have both lower frequency differences and lower F-ST values between the two domains than silent ones. These results suggest the presence of purifying selection. The divergence between the two domains based on synonymous changes was around 5 million yr, a time similar to a recent phylogenetic estimate of 6 million yr, but much larger than earlier estimates based on isozymes. Two approaches, one of them novel and that considers both F-ST and difference in allele frequencies between the two domains, were used to identify SNPs potentially under diversifying selection. SNPs from around 20 genes were detected, including genes previously identified as main target for selection, such as PaPRR3 and PaGI.

  • 7.
    Chen, Jun
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Li, Lili
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Milesi, Pascal
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Jansson, Gunnar
    Forestry Res Inst Sweden Skogforsk, Uppsala, Sweden.
    Berlin, Mats
    Forestry Res Inst Sweden Skogforsk, Uppsala, Sweden.
    Karlsson, Bo
    Forestry Res Inst Sweden Skogforsk, Ekebo, Sweden.
    Aleksic, Jelena
    Univ Belgrade, Inst Mol Genet & Genet Engn, Belgrade, Serbia.
    Vendramin, Giovanni G.
    CNR, Natl Res Council IBBR, Div Florence, Inst Biosci & BioResources, Sesto Fiorentino, Italy.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Genomic data provide new insights on the demographic history and the extent of recent material transfers in Norway spruce2019In: Evolutionary Applications, ISSN 1752-4571, E-ISSN 1752-4571, Vol. 12, no 8, p. 1539-1551Article in journal (Refereed)
    Abstract [en]

    Primeval forests are today exceedingly rare in Europe, and transfer of forest reproductive material for afforestation and improvement has been very common, especially over the last two centuries. This can be a serious impediment when inferring past population movements in response to past climate changes such as the last glacial maximum (LGM), some 18,000 years ago. In the present study, we genotyped 1,672 individuals from three Picea species (P. abies, P. obovata, and P. omorika) at 400K SNPs using exome capture to infer the past demographic history of Norway spruce (P. abies) and estimate the amount of recent introduction used to establish the Norway spruce breeding program in southern Sweden. Most of these trees belong to P. abies and originate from the base populations of the Swedish breeding program. Others originate from populations across the natural ranges of the three species. Of the 1,499 individuals stemming from the breeding program, a large proportion corresponds to recent introductions from mainland Europe. The split of P. omorika occurred 23 million years ago (mya), while the divergence between P. obovata and P. abies began 17.6 mya. Demographic inferences retrieved the same main clusters within P. abies than previous studies, that is, a vast northern domain ranging from Norway to central Russia, where the species is progressively replaced by Siberian spruce (P. obovata) and two smaller domains, an Alpine domain and a Carpathian one, but also revealed further subdivision and gene flow among clusters. The three main domains divergence was ancient (15 mya), and all three went through a bottleneck corresponding to the LGM. Approximately 17% of P. abies Nordic domain migrated from P. obovata ~103K years ago, when both species had much larger effective population sizes. Our analysis of genomewide polymorphism data thus revealed the complex demographic history of Picea genus in Western Europe and highlighted the importance of material transfer in Swedish breeding program.

  • 8.
    Chen, Jun
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Tsuda, Yoshiaki
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Stocks, Michael
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Kallman, Thomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Xu, Nannan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Karkkainen, Katri
    Huotari, Tea
    Semerikov, Vladimir L.
    Vendramin, Giovanni G.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Clinal Variation at Phenology-Related Genes in Spruce: Parallel Evolution in FTL2 and Gigantea?2014In: Genetics, ISSN 0016-6731, E-ISSN 1943-2631, Vol. 197, no 3, p. 1025-1038Article in journal (Refereed)
    Abstract [en]

    Parallel clines in different species, or in different geographical regions of the same species, are an important source of information on the genetic basis of local adaptation. We recently detected latitudinal clines in SNPs frequencies and gene expression of candidate genes for growth cessation in Scandinavian populations of Norway spruce (Picea abies). Here we test whether the same clines are also present in Siberian spruce (P. obovata), a close relative of Norway spruce with a different Quaternary history. We sequenced nine candidate genes and 27 control loci and genotyped 14 SSR loci in six populations of P. obovata located along the Yenisei river from latitude 56 N to latitude 67 N. In contrast to Scandinavian Norway spruce that both departs from the standard neutral model (SNM) and shows a clear population structure, Siberian spruce populations along the Yenisei do not depart from the SNM and are genetically unstructured. Nonetheless, as in Norway spruce, growth cessation is significantly clinal. Polymorphisms in photoperiodic (FTL2) and circadian clock (Gigantea, GI, PRR3) genes also show significant clinal variation and/or evidence of local selection. In GI, one of the variants is the same as in Norway spruce. Finally, a strong cline in gene expression is observed for FTL2, but not for GI. These results, together with recent physiological studies, confirm the key role played by FTL2 and circadian clock genes in the control of growth cessation in spruce species and suggest the presence of parallel adaptation in these two species.

  • 9.
    Chen, Jun
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Uebbing, Severin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Gyllenstrand, Niclas
    Department of Plant Biology and Forest Genetics, Swedish University of Agriculture Science.
    Lagercrantz, Ulf
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Källman, Thomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Sequencing of the needle transcriptome from Norway spruce (Picea abies Karst L.) reveals lower substitution rates, but similar selective constraints in gymnosperms compared to angiosperms2012In: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 13, p. 589-Article in journal (Other academic)
    Abstract [en]

    Background: A detailed knowledge about which genes are expressed in which tissues and at which developmental stage is important for understanding both the function of genes and their evolution. For the vast majority of species, transcriptomes are still largely uncharacterized and even in those where substantial information is available it is often in the form of partially sequenced transcriptomes. With the development of next generation sequencing, a single experiment can now give both a snap-shot of the transcribed part of a species genome and simultaneously estimate levels of gene expression.

    Results: mRNA from actively growing needles of Norway spruce (Picea abies) was sequenced using next generation sequencing technology. In total, close to 70 million fragments with a length of 76 bp were sequenced resulting in 5 Gbp of raw data. A de novo assembly of these reads were, together with publicly available expressed sequence tag (EST) data from Norway spruce, used to create a reference transcriptome. Of the 38,419 PUTs (putative unique transcripts) longer than 150 bp in this reference assembly, 59% show similarity to ESTs from other spruce species and of the remaining PUTs, 3,704 show similarity to protein sequences from other plant species, leaving 4,167 PUTs with limited similarity to currently available plant proteins. By predicting coding frames and comparing not only the Norway spruce PUTs, but also PUTs from the close relatives Picea glauca and Picea sitchensis to both Pinus taeda and Taxus mairei, we obtained estimates of synonymous and non-synonymous divergence among conifer species. In addition, we detected close to 15,000 SNPs of high quality and estimated gene expression difference between samples collected during dark and light conditions.

    Conclusions: Our study yielded a large number of single nucleotide polymorphisms as well as estimates of gene expression on transcriptome scale. In agreement with a recent study we find that the synonymous substitution rate per year (0.6 × 10-09 and 1.1 × 10-09) is an order of magnitude smaller than values reported for angiosperm herbs, but if one takes generation time in to account, most of this difference disappear. The estimates of the non-synonymous over the synonymous divergence (dN/dS ratio) reported here is in general much lower than 1 and only a few genes showed a ratio larger than 1.

  • 10.
    Kryvokhyzha, Dmytro
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Holm, Karl
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Chen, Jun
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Cornille, Amandine
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Glemin, Sylvain
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Univ Montpellier, CNRS IRD EPHE, ISEM UMR 5554, Inst Sci Evolut, Pl Eugene Bataillon, F-34075 Montpellier, France..
    Wright, Stephen I.
    Univ Toronto, Dept Ecol & Evolut, 25 Willcocks St, Toronto, ON M5S 3B2, Canada..
    Lagercrantz, Ulf
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    The influence of population structure on gene expression and flowering time variation in the ubiquitous weed Capsella bursa-pastoris (Brassicaceae)2016In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 25, no 5, p. 1106-1121Article in journal (Refereed)
    Abstract [en]

    Population structure is a potential problem when testing for adaptive phenotypic differences among populations. The observed phenotypic differences among populations can simply be due to genetic drift, and if the genetic distance between them is not considered, the differentiation may be falsely interpreted as adaptive. Conversely, adaptive and demographic processes might have been tightly associated and correcting for the population structure may lead to false negatives. Here, we evaluated this problem in the cosmopolitan weed Capsella bursa-pastoris. We used RNA-Seq to analyse gene expression differences among 24 accessions, which belonged to a much larger group that had been previously characterized for flowering time and circadian rhythm and were genotyped using genotyping-by-sequencing (GBS) technique. We found that clustering of accessions for gene expression retrieved the same three clusters that were obtained with GBS data previously, namely Europe, the Middle East and Asia. Moreover, the three groups were also differentiated for both flowering time and circadian rhythm variation. Correction for population genetic structure when analysing differential gene expression analysis removed all differences among the three groups. This may suggest that most differences are neutral and simply reflect population history. However, geographical variation in flowering time and circadian rhythm indicated that the distribution of adaptive traits might be confounded by population structure. To bypass this confounding effect, we compared gene expression differentiation between flowering ecotypes within the genetic groups. Among the differentially expressed genes, FLOWERING LOCUS C was the strongest candidate for local adaptation in regulation of flowering time.

  • 11.
    Kryvokhyzha, Dmytro
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Salcedo, Adriana
    Univ Toronto, Dept Ecol & Evolut, Toronto, ON, Canada.
    Eriksson, Mimmi C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab. Univ Gothenburg, Dept Biol & Environm Sci, Gothenburg, Sweden.
    Duan, Tianlin
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Tawari, Nilesh
    ASTAR, Genome Inst Singapore, Computat & Syst Biol Grp, Singapore, Singapore.
    Chen, Jun
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Guerrina, Maria
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Kreiner, Julia M.
    Univ Toronto, Dept Ecol & Evolut, Toronto, ON, Canada.
    Kent, Tyler V.
    Univ Toronto, Dept Ecol & Evolut, Toronto, ON, Canada.
    Lagercrantz, Ulf
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Stinchcombe, John R.
    Univ Toronto, Dept Ecol & Evolut, Toronto, ON, Canada.
    Glemin, Sylvain
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab. Univ Rennes 1, CNRS, UMR 6553, ECOBIO,Ecosyst,Biodivers,Evolut, F-35000 Rennes, France.
    Wright, Stephen I.
    Univ Toronto, Dept Ecol & Evolut, Toronto, ON, Canada.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Parental legacy, demography, and admixture influenced the evolution of the two subgenomes of the tetraploid Capsella bursa-pastoris (Brassicaceae)2019In: PLoS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 15, no 2, article id e1007949Article in journal (Refereed)
    Abstract [en]

    Allopolyploidy is generally perceived as a major source of evolutionary novelties and as an instantaneous way to create isolation barriers. However, we do not have a clear understanding of how two subgenomes evolve and interact once they have fused in an allopolyploid species nor how isolated they are from their relatives. Here, we address these questions by analyzing genomic and transcriptomic data of allotetraploid Capsella bursa-pastoris in three differentiated populations, Asia, Europe, and the Middle East. We phased the two subgenomes, one descended from the outcrossing and highly diverse Capsella grandiflora (Cbp(Cg)) and the other one from the selfing and genetically depauperate Capsella orientalis (Cbp(Co)). For each subgenome, we assessed its relationship with the diploid relatives, temporal changes of effective population size (N-e), signatures of positive and negative selection, and gene expression patterns. In all three regions, N-e of the two subgenomes decreased gradually over time and the Cbp(Co) subgenome accumulated more deleterious changes than Cbp(Cg). There were signs of widespread admixture between C. bursa-pastoris and its diploid relatives. The two subgenomes were impacted differentially depending on geographic region suggesting either strong interploidy gene flow or multiple origins of C. bursa-pastoris. Selective sweeps were more common on the Cbp(Cg) subgenome in Europe and the Middle East, and on the Cbp(Co) subgenome in Asia. In contrast, differences in expression were limited with the Cbp(Cg) subgenome slightly more expressed than Cbp(Co) in Europe and the Middle-East. In summary, after more than 100,000 generations of co-existence, the two subgenomes of C. bursa-pastoris still retained a strong signature of parental legacy but their evolutionary trajectory strongly varied across geographic regions. Author summary Allopolyploid species have two or more sets of chromosomes that originate from hybridization of different species. It remains largely unknown how the two genomes evolve in the same organism and how strongly their evolutionary trajectory depends on the initial differences between the two parental species and the specific demographic history of the newly formed allopolyploid species. To address these questions, we analyzed the genomic and gene expression variation of the shepherd's purse, a recent allopolyploid species, in three regions of its natural range. After approximate to 100,000 generations of co-existence within the same species, the two subgenomes had still retained part of the initial difference between the two parental species in the number of deleterious mutations reflecting a history of mating system differences. This difference, as well as differences in patterns of positive selection and levels of gene expression, also strongly depended on the specific histories of the three regions considered. Most strikingly, and unexpectedly, the allopolyploid species showed signs of hybridization with different diploid relatives or multiple origins in different parts of its range. Regardless if it was hybridization or multiple origins, this profoundly altered the relationship between the two subgenomes in different regions. Hence, our study illustrates how both the genomic structure and ecological arena interact to determine the evolutionary trajectories of allopolyploid species.

  • 12.
    Li, Lili
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Chen, Jun
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Clinal variation in growth cessation and FTL2 expression in Siberian spruce2019In: Tree Genetics & Genomes, ISSN 1614-2942, E-ISSN 1614-2950, Vol. 15, no 82Article in journal (Refereed)
    Abstract [en]

    Forest trees exhibit strong patterns of local adaptation in phenological traits along latitudinal gradients. Previous studies in spruce have shown that variation at genes from the photoperiodic pathway and the circadian clock are associated to these clines but it has been difficult to find solid evidence of selection for some of these genes. Here, we used growth cessation, gene expression, and single nucleotide polymorphism (SNP) data at two major candidate loci, FLOWERING LOCUS T/TERMINAL FLOWER1-Like2 (FTL2) and GIGANTEA (GI), as well as at background loci from a latitudinal gradient in Siberian spruce (Picea obovata) populations along the Ob River to test for clinal variation in growth cessation and at the two candidate genes. As in previous studies, there was a strong latitudinal cline in growth cessation that was accompanied by a significant cline in the expression of FTL2. Expression of FTL2 was significantly associated with allele frequencies at some of the GI’s SNPs. However, the cline in allele frequency at candidate genes was not as steep as in a Norway spruce cline and in a parallel Siberian spruce cline studied previously and nonsignificant when a correction for population structure was applied. A McDonald-Kreitman test did not detect decisive evidence of selection on GI (p value = 0.07) and could not be applied to FTL2 because of limited polymorphism. Nonetheless, polymorphisms contributed more to the increased neutrality index of PoGI than to that of control loci. Finally, comparing the results of two previously published studies to our new dataset led to the identification of strong candidate SNPs for local adaptation in FTL2 promoter and GI.

  • 13. Lind, Marten
    et al.
    Kallman, Thomas
    Chen, Jun
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Ma, Xiao-Fei
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Bousquet, Jean
    Morgante, Michele
    Zaina, Giusi
    Karlsson, Bo
    Elfstrand, Malin
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Stenlid, Jan
    A Picea abies Linkage Map Based on SNP Markers Identifies QTLs for Four Aspects of Resistance to Heterobasidion parviporum Infection2014In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 9, no 7, p. e101049-Article in journal (Refereed)
    Abstract [en]

    A consensus linkage map of Picea abies, an economically important conifer, was constructed based on the segregation of 686 SNP markers in a F-1 progeny population consisting of 247 individuals. The total length of 1889.2 cM covered 96.5% of the estimated genome length and comprised 12 large linkage groups, corresponding to the number of haploid P. abies chromosomes. The sizes of the groups (from 5.9 to 9.9% of the total map length) correlated well with previous estimates of chromosome sizes (from 5.8 to 10.8% of total genome size). Any locus in the genome has a 97% probability to be within 10 cM from a mapped marker, which makes the map suited for QTL mapping. Infecting the progeny trees with the root rot pathogen Heterobasidion parviporum allowed for mapping of four different resistance traits: lesion length at the inoculation site, fungal spread within the sapwood, exclusion of the pathogen from the host after initial infection, and ability to prevent the infection from establishing at all. These four traits were associated with two, four, four and three QTL regions respectively of which none overlapped between the traits. Each QTL explained between 4.6 and 10.1% of the respective traits phenotypic variation. Although the QTL regions contain many more genes than the ones represented by the SNP markers, at least four markers within the confidence intervals originated from genes with known function in conifer defence; a leucoanthocyanidine reductase, which has previously been shown to upregulate during H. parviporum infection, and three intermediates of the lignification process; a hydroxycinnamoyl CoA shikimate/quinate hydroxycinnamoyltransferase, a 4-coumarate CoA ligase, and a R2R3-MYB transcription factor.

  • 14.
    Milesi, Pascal
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Berlin, Mats
    The Forestry Research Institute of Sweden (Skogforsk), Uppsala, Sweden.
    Chen, Jun
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Orsucci, Marion
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Li, Lili
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Jansson, Gunnar
    The Forestry Research Institute of Sweden (Skogforsk), Uppsala, Sweden.
    Karlsson, Bo
    The Forestry Research Institute of Sweden (Skogforsk), Ekebo, Sweden.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Assessing the potential for assisted gene flow using past introduction of Norway spruce in southern Sweden: Local adaptation and genetic basis of quantitative traits in trees2019In: Evolutionary Applications, ISSN 1752-4571, E-ISSN 1752-4571, Vol. 12, no 10, p. 1946-1959Article in journal (Refereed)
    Abstract [en]

    Norway spruce (Picea abies) is a dominant conifer species of major economic importance in northern Europe. Extensive breeding programs were established to improve phenotypic traits of economic interest. In southern Sweden, seeds used to create progeny tests were collected on about 3,000 trees of outstanding phenotype (‘plus’ trees) across the region. In a companion paper, we showed that some were of local origin but many were recent introductions from the rest of the natural range. The mixed origin of the trees together with partial sequencing of the exome of >1,500 of these trees and phenotypic data retrieved from the Swedish breeding program offered a unique opportunity to dissect the genetic basis of local adaptation of three quantitative traits (height, diameter and bud-burst) and assess the potential of assisted gene flow. Through a combination of multivariate analyses and genome-wide association studies, we showed that there was a very strong effect of geographical origin on growth (height and diameter) and phenology (bud-burst) with trees from southern origins outperforming local provenances. Association studies revealed that growth traits were highly polygenic and bud-burst somewhat less. Hence, our results suggest that assisted gene flow and genomic selection approaches could help to alleviate the effect of climate change on P. abies breeding programs in Sweden.

  • 15.
    Plomion, Christophe
    et al.
    Univ Bordeaux, BIOGECO, INRA, Cestas, France.
    Aury, Jean-Marc
    CEA, Genoscope, Inst Biol Francois Jacob, Evry, France.
    Amselem, Joelle
    Univ ParisSaclay, URGI, INRA, Versailles, France.
    Leroy, Thibault
    Univ Bordeaux, BIOGECO, INRA, Cestas, France.
    Murat, Florent
    INRA UCA, GDEC, Clermont Ferrand, France.
    Duplessis, Sebastien
    Univ Lorraine, IAM, INRA, Champenoux, France.
    Faye, Sebastien
    CEA, Genoscope, Inst Biol Francois Jacob, Evry, France.
    Francillonne, Nicolas
    Univ ParisSaclay, URGI, INRA, Versailles, France.
    Labadie, Karine
    CEA, Genoscope, Inst Biol Francois Jacob, Evry, France.
    Le Provost, Gregoire
    Univ Bordeaux, BIOGECO, INRA, Cestas, France.
    Lesur, Isabelle
    Univ Bordeaux, BIOGECO, INRA, Cestas, France;HelixVenture, Merignac, France.
    Bartholome, Jerome
    Univ Bordeaux, BIOGECO, INRA, Cestas, France.
    Faivre-Rampant, Patricia
    Univ Paris Saclay, INRA, US EPGV 1279, Evry, France.
    Kohler, Annegret
    Univ Lorraine, IAM, INRA, Champenoux, France.
    Leple, Jean-Charles
    INRA, BIOFORA, Orleans, France.
    Chantret, Nathalie
    Univ Montpellier, AGAP, CIRAD, INRA,Montpellier SupAgro, Montpellier, France.
    Chen, Jun
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Dievart, Anne
    CIRAD, UMR AGAP, Montpellier, France;Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France.
    Alaeitabar, Tina
    Univ ParisSaclay, URGI, INRA, Versailles, France.
    Barbe, Valerie
    CEA, Genoscope, Inst Biol Francois Jacob, Evry, France.
    Belser, Caroline
    CEA, Genoscope, Inst Biol Francois Jacob, Evry, France.
    Berges, Helene
    INRA, CNRGV, Castanet Tolosan, France.
    Bodenes, Catherine
    Univ Bordeaux, BIOGECO, INRA, Cestas, France.
    Bogeat-Triboulot, Marie-Beatrice
    Univ Lorraine, UMR Silva, INRA, AgroPariTech, Nancy, France.
    Bouffaud, Marie-Lara
    UFZ Helmholtz Ctr Environm Res, Dept Soil Ecol, Halle, Germany.
    Brachi, Benjamin
    Univ Bordeaux, BIOGECO, INRA, Cestas, France.
    Chancerel, Emilie
    Univ Bordeaux, BIOGECO, INRA, Cestas, France.
    Cohen, David
    Univ Lorraine, UMR Silva, INRA, AgroPariTech, Nancy, France.
    Couloux, Arnaud
    CEA, Genoscope, Inst Biol Francois Jacob, Evry, France.
    Da Silva, Corinne
    CEA, Genoscope, Inst Biol Francois Jacob, Evry, France.
    Dossat, Carole
    CEA, Genoscope, Inst Biol Francois Jacob, Evry, France.
    Ehrenmann, Francois
    Univ Bordeaux, BIOGECO, INRA, Cestas, France.
    Gaspin, Christine
    INRA, Plateforme Bioinformat Toulouse Midi Pyrenees, Auzeville Castanet Tolos, Germany.
    Grima-Pettenati, Jacqueline
    Univ Toulouse, CNRS, UMR 5546, LRSV, Castanet Tolosan, France.
    Guichoux, Erwan
    Univ Bordeaux, BIOGECO, INRA, Cestas, France.
    Hecker, Arnaud
    Univ Lorraine, IAM, INRA, Champenoux, France.
    Herrmann, Sylvie
    German Ctr Integrat Res IDiv, Leipzig, Germany.
    Hugueney, Philippe
    Univ Strasbourg, SVQV, INRA, Colmar, France.
    Hummel, Irene
    Univ Lorraine, UMR Silva, INRA, AgroPariTech, Nancy, France.
    Klopp, Christophe
    INRA, Plateforme Bioinformat Toulouse Midi Pyrenees, Auzeville Castanet Tolos, Germany.
    Lalanne, Celine
    Univ Bordeaux, BIOGECO, INRA, Cestas, France.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Lasserre, Eric
    Univ Perpignan, UMR 5096, Perpignan, France.
    Lemainque, Arnaud
    CEA, Genoscope, Inst Biol Francois Jacob, Evry, France.
    Desprez-Loustau, Marie-Laure
    Univ Bordeaux, BIOGECO, INRA, Cestas, France.
    Luyten, Isabelle
    Univ ParisSaclay, URGI, INRA, Versailles, France.
    Madoui, Mohammed-Amin
    CEA, Genoscope, Inst Biol Francois Jacob, Evry, France.
    Mangenot, Sophie
    CEA, Genoscope, Inst Biol Francois Jacob, Evry, France.
    Marchal, Clemence
    Univ Lorraine, IAM, INRA, Champenoux, France.
    Maumus, Florian
    Univ ParisSaclay, URGI, INRA, Versailles, France.
    Mercier, Jonathan
    CEA, Genoscope, Inst Biol Francois Jacob, Evry, France.
    Michotey, Celia
    Univ ParisSaclay, URGI, INRA, Versailles, France.
    Panaud, Olivier
    Univ Perpignan, UMR 5096, Perpignan, France.
    Picault, Nathalie
    Univ Perpignan, UMR 5096, Perpignan, France.
    Rouhier, Nicolas
    Univ Lorraine, IAM, INRA, Champenoux, France.
    Rue, Olivier
    INRA, Plateforme Bioinformat Toulouse Midi Pyrenees, Auzeville Castanet Tolos, Germany.
    Rustenholz, Camille
    Univ Strasbourg, SVQV, INRA, Colmar, France.
    Salin, Franck
    Univ Bordeaux, BIOGECO, INRA, Cestas, France.
    Soler, Marcal
    Univ Toulouse, CNRS, UMR 5546, LRSV, Castanet Tolosan, France;Univ Girona, Lab Suro, Girona, Spain.
    Tarkka, Mika
    UFZ Helmholtz Ctr Environm Res, Dept Soil Ecol, Halle, Germany.
    Velt, Amandine
    Univ Strasbourg, SVQV, INRA, Colmar, France.
    Zanne, Amy E.
    George Washington Univ, Dept Biol Sci, Washington, DC 20052 USA.
    Martin, Francis
    Univ Lorraine, IAM, INRA, Champenoux, France.
    Wincker, Patrick
    Univ Paris Saclay, Genom Metab, Genoscope, Inst Biol Francois Jacob,CEA,CNRS,Univ Evry, Evry, France.
    Quesneville, Hadi
    Univ ParisSaclay, URGI, INRA, Versailles, France.
    Kremer, Antoine
    Univ Bordeaux, BIOGECO, INRA, Cestas, France.
    Salse, Jerome
    INRA UCA, GDEC, Clermont Ferrand, France.
    Oak genome reveals facets of long lifespan2018In: NATURE PLANTS, ISSN 2055-026X, Vol. 4, no 7, p. 440-452Article in journal (Refereed)
    Abstract [en]

    Oaks are an important part of our natural and cultural heritage. Not only are they ubiquitous in our most common landscapes' but they have also supplied human societies with invaluable services, including food and shelter, since prehistoric times(2). With 450 species spread throughout Asia, Europe and America(3), oaks constitute a critical global renewable resource. The longevity of oaks (several hundred years) probably underlies their emblematic cultural and historical importance. Such long-lived sessile organisms must persist in the face of a wide range of abiotic and biotic threats over their lifespans. We investigated the genomic features associated with such a long lifespan by sequencing, assembling and annotating the oak genome. We then used the growing number of whole-genome sequences for plants (including tree and herbaceous species) to investigate the parallel evolution of genomic characteristics potentially underpinning tree longevity. A further consequence of the long lifespan of trees is their accumulation of somatic mutations during mitotic divisions of stem cells present in the shoot apical meristems. Empirical(4) and modelling(5) approaches have shown that intra-organismal genetic heterogeneity can be selected for(6) and provides direct fitness benefits in the arms race with short-lived pests and pathogens through a patchwork of intra-organismal phenotypes(7). However, there is no clear proof that large-statured trees consist of a genetic mosaic of clonally distinct cell lineages within and between branches. Through this case study of oak, we demonstrate the accumulation and transmission of somatic mutations and the expansion of disease-resistance gene families in trees.

  • 16.
    Svedberg, Jesper
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Hosseini, Sara
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Chen, Jun
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Vogan, Aaron A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Mozgova, Iva
    Swedish Univ Agr Sci, Dept Plant Biol, POB 7080, SE-75007 Uppsala, Sweden;Swedish Univ Agr Sci, Linnean Ctr Plant Biol, POB 7080, SE-75007 Uppsala, Sweden;Czech Acad Sci, Inst Microbiol, Ctr Algatech, CZ-37981 Trebon, Czech Republic.
    Hennig, Lars
    Swedish Univ Agr Sci, Dept Plant Biol, POB 7080, SE-75007 Uppsala, Sweden;Swedish Univ Agr Sci, Linnean Ctr Plant Biol, POB 7080, SE-75007 Uppsala, Sweden.
    Manitchotpisit, Pennapa
    Illinois State Univ, Sch Biol Sci, Normal, IL 61790 USA.
    Abusharekh, Anna
    Illinois State Univ, Sch Biol Sci, Normal, IL 61790 USA.
    Hammond, Thomas M.
    Illinois State Univ, Sch Biol Sci, Normal, IL 61790 USA.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Johannesson, Hanna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Convergent evolution of complex genomic rearrangements in two fungal meiotic drive elements2018In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 9, article id 4242Article in journal (Refereed)
    Abstract [en]

    Meiotic drive is widespread in nature. The conflict it generates is expected to be an important motor for evolutionary change and innovation. In this study, we investigated the genomic consequences of two large multi-gene meiotic drive elements, Sk-2 and Sk-3, found in the filamentous ascomycete Neurospora intermedia. Using long-read sequencing, we generated the first complete and well-annotated genome assemblies of large, highly diverged, non-recombining regions associated with meiotic drive elements. Phylogenetic analysis shows that, even though Sk-2 and Sk-3 are located in the same chromosomal region, they do not form sister clades, suggesting independent origins or at least a long evolutionary separation. We conclude that they have in a convergent manner accumulated similar patterns of tandem inversions and dense repeat clusters, presumably in response to similar needs to create linkage between genes causing drive and resistance.

  • 17.
    Tsuda, Yoshiaki
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. CNR, Inst Biosci & Bioresources, Via Madonna del Piano 10, I-50019 Florence, Italy..
    Chen, Jun
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Stocks, Michael
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Källman, Thomas
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Sonstebo, Jorn Henrik
    Norwegian Inst Bioecon Res, Post Box 115, N-1431 As, Norway..
    Parducci, Laura
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Semerikov, Vladimir
    Russian Acad Sci, Inst Plant & Anim Ecol, Urals Div, 8 Marta Str,202, Ekaterinburg 620144, Russia..
    Sperisen, Christoph
    Swiss Fed Res Inst Forest, Snow & Landscape Res WSL, Zurcherstr 111, CH-8903 Birmensdorf, Switzerland..
    Politov, Dmitry
    Russian Acad Sci, Vavilov Inst Gen Genet, Gubkin Str 3, Moscow 119991, Russia..
    Ronkainen, Tiina
    Univ Helsinki, Dept Environm Sci, Environm Change Res Unit, POB 65, FI-00014 Helsinki, Finland..
    Valiranta, Minna
    Univ Helsinki, Dept Environm Sci, Environm Change Res Unit, POB 65, FI-00014 Helsinki, Finland..
    Vendramin, Giovanni Giuseppe
    CNR, Inst Biosci & Bioresources, Via Madonna del Piano 10, I-50019 Florence, Italy..
    Tollefsrud, Mari Mette
    Norwegian Inst Bioecon Res, Post Box 115, N-1431 As, Norway..
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    The extent and meaning of hybridization and introgression between Siberian spruce (Picea obovata) and Norway spruce (Picea abies): cryptic refugia as stepping stones to the west?2016In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 25, no 12, p. 2773-2789Article in journal (Refereed)
    Abstract [en]

    Boreal species were repeatedly exposed to ice ages and went through cycles of contraction and expansion while sister species alternated periods of contact and isolation. The resulting genetic structure is consequently complex, and demographic inferences are intrinsically challenging. The range of Norway spruce (Picea abies) and Siberian spruce (Picea obovata) covers most of northern Eurasia; yet their geographical limits and histories remain poorly understood. To delineate the hybrid zone between the two species and reconstruct their joint demographic history, we analysed variation at nuclear SSR and mitochondrial DNA in 102 and 88 populations, respectively. The dynamics of the hybrid zone was analysed with approximate Bayesian computation (ABC) followed by posterior predictive STRUCTURE plot reconstruction and the presence of barriers across the range tested with estimated effective migration surfaces. To estimate the divergence time between the two species, nuclear sequences from two well-separated populations of each species were analysed with ABC. Two main barriers divide the range of the two species: one corresponds to the hybrid zone between them, and the other separates the southern and northern domains of Norway spruce. The hybrid zone is centred on the Urals, but the genetic impact of Siberian spruce extends further west. The joint distribution of mitochondrial and nuclear variation indicates an introgression of mitochondrial DNA from Norway spruce into Siberian spruce. Overall, our data reveal a demographic history where the two species interacted frequently and where migrants originating from the Urals and the West Siberian Plain recolonized northern Russia and Scandinavia using scattered refugial populations of Norway spruce as stepping stones towards the west.

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