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  • 1.
    Alvarez, Laura
    et al.
    Umeå University, Faculty of Medicine, Department of Molecular Biology (Faculty of Medicine). Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid—Consejo Superior de Investigaciones Científicas, Madrid, Spain.
    Quintáns, Nieves G.
    Blesa, Alba
    Baquedano, Ignacio
    Mencía, Mario
    Bricio, Carlos
    Berenguer, José
    Hierarchical control of nitrite respiration by transcription factors encoded within mobile gene clusters of Thermus thermophilus2017In: Genes, ISSN 2073-4425, E-ISSN 2073-4425, Vol. 8, no 12, article id 361Article in journal (Refereed)
    Abstract [en]

    Denitrification in Thermus thermophilus is encoded by the nitrate respiration conjugative element (NCE) and nitrite and nitric oxide respiration (nic) gene clusters. A tight coordination of each cluster's expression is required to maximize anaerobic growth, and to avoid toxicity by intermediates, especially nitric oxides (NO). Here, we study the control of the nitrite reductases (Nir) and NO reductases (Nor) upon horizontal acquisition of the NCE and nic clusters by a formerly aerobic host. Expression of the nic promoters PnirS, PnirJ, and PnorC, depends on the oxygen sensor DnrS and on the DnrT protein, both NCE-encoded. NsrR, a nic-encoded transcription factor with an iron-sulfur cluster, is also involved in Nir and Nor control. Deletion of nsrR decreased PnorC and PnirJ transcription, and activated PnirS under denitrification conditions, exhibiting a dual regulatory role never described before for members of the NsrR family. On the basis of these results, a regulatory hierarchy is proposed, in which under anoxia, there is a pre-activation of the nic promoters by DnrS and DnrT, and then NsrR leads to Nor induction and Nir repression, likely as a second stage of regulation that would require NO detection, thus avoiding accumulation of toxic levels of NO. The whole system appears to work in remarkable coordination to function only when the relevant nitrogen species are present inside the cell.

  • 2. Ameur, Adam
    et al.
    Che, Huiwen
    Martin, Marcel
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Bunikis, Ignas
    Dahlberg, Johan
    Höijer, Ida
    Häggqvist, Susana
    Vezzi, Francesco
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Nordlund, Jessica
    Olason, Pall
    Feuk, Lars
    Gyllensten, Ulf
    De Novo Assembly of Two Swedish Genomes Reveals Missing Segments from the Human GRCh38 Reference and Improves Variant Calling of Population-Scale Sequencing Data2018In: Genes, ISSN 2073-4425, E-ISSN 2073-4425, Vol. 9, no 10, article id 486Article in journal (Refereed)
    Abstract [en]

    The current human reference sequence (GRCh38) is a foundation for large-scale sequencing projects. However, recent studies have suggested that GRCh38 may be incomplete and give a suboptimal representation of specific population groups. Here, we performed a de novo assembly of two Swedish genomes that revealed over 10 Mb of sequences absent from the human GRCh38 reference in each individual. Around 6 Mb of these novel sequences (NS) are shared with a Chinese personal genome. The NS are highly repetitive, have an elevated GC-content, and are primarily located in centromeric or telomeric regions. Up to 1 Mb of NS can be assigned to chromosome Y, and large segments are also missing from GRCh38 at chromosomes 14, 17, and 21. Inclusion of NS into the GRCh38 reference radically improves the alignment and variant calling from short-read whole-genome sequencing data at several genomic loci. A re-analysis of a Swedish population-scale sequencing project yields > 75,000 putative novel single nucleotide variants (SNVs) and removes > 10,000 false positive SNV calls per individual, some of which are located in protein coding regions. Our results highlight that the GRCh38 reference is not yet complete and demonstrate that personal genome assemblies from local populations can improve the analysis of short-read whole-genome sequencing data.

  • 3.
    Ameur, Adam
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Che, Huiwen
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Martin, Marcel
    Stockholm Univ, DBB, Sci Life Lab, S-11419 Stockholm, Sweden.
    Bunikis, Ignas
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology. Uppsala Univ, Dept Immunol Genet & Pathol, Sci Life Lab, S-75236 Uppsala, Sweden.
    Dahlberg, Johan
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Molecular Medicine. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Höijer, Ida
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Häggqvist, Susana
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Vezzi, Francesco
    Stockholm Univ, DBB, Sci Life Lab, S-11419 Stockholm, Sweden.
    Nordlund, Jessica
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Molecular Medicine. Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala Univ, Dept Med Sci, Sci Life Lab, Mol Med, S-75236 Uppsala, Sweden.
    Olason, Pall
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Feuk, Lars
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Medicinsk genetik och genomik.
    Gyllensten, Ulf B.
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Medicinsk genetik och genomik.
    De Novo Assembly of Two Swedish Genomes Reveals Missing Segments from the Human GRCh38 Reference and Improves Variant Calling of Population-Scale Sequencing Data2018In: Genes, ISSN 2073-4425, E-ISSN 2073-4425, Vol. 9, no 10, article id 486Article in journal (Refereed)
    Abstract [en]

    The current human reference sequence (GRCh38) is a foundation for large-scale sequencing projects. However, recent studies have suggested that GRCh38 may be incomplete and give a suboptimal representation of specific population groups. Here, we performed a de novo assembly of two Swedish genomes that revealed over 10 Mb of sequences absent from the human GRCh38 reference in each individual. Around 6 Mb of these novel sequences (NS) are shared with a Chinese personal genome. The NS are highly repetitive, have an elevated GC-content, and are primarily located in centromeric or telomeric regions. Up to 1 Mb of NS can be assigned to chromosome Y, and large segments are also missing from GRCh38 at chromosomes 14, 17, and 21. Inclusion of NS into the GRCh38 reference radically improves the alignment and variant calling from short-read whole-genome sequencing data at several genomic loci. A re-analysis of a Swedish population-scale sequencing project yields > 75,000 putative novel single nucleotide variants (SNVs) and removes > 10,000 false positive SNV calls per individual, some of which are located in protein coding regions. Our results highlight that the GRCh38 reference is not yet complete and demonstrate that personal genome assemblies from local populations can improve the analysis of short-read whole-genome sequencing data.

  • 4.
    Boman, Jesper
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Frankl-Vilches, Carolina
    Max Planck Inst Ornithol, Dept Behav Neurobiol, D-82319 Seewiesen, Germany.
    dos Santos, Michelly da Silva
    Inst Evandro Chagas, SAMAM, Lab Cultura Tecidos & Citogenet, Ananindeua, Para, Brazil;Univ Fed Para, Fac Ciencias Nat ICEN, BR-66075110 Belem, Para, Brazil.
    de Oliveira, Edivaldo H. C.
    Inst Evandro Chagas, SAMAM, Lab Cultura Tecidos & Citogenet, Ananindeua, Para, Brazil;Univ Fed Para, Fac Ciencias Nat ICEN, BR-66075110 Belem, Para, Brazil.
    Gahr, Manfred
    Max Planck Inst Ornithol, Dept Behav Neurobiol, D-82319 Seewiesen, Germany.
    Suh, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    The Genome of Blue-Capped Cordon-Bleu Uncovers Hidden Diversity of LTR Retrotransposons in Zebra Finch2019In: Genes, ISSN 2073-4425, E-ISSN 2073-4425, Vol. 10, no 4, article id 301Article in journal (Refereed)
    Abstract [en]

    Avian genomes have perplexed researchers by being conservative in both size and rearrangements, while simultaneously holding the blueprints for a massive species radiation during the last 65 million years (My). Transposable elements (TEs) in bird genomes are relatively scarce but have been implicated as important hotspots for chromosomal inversions. In zebra finch (Taeniopygia guttata), long terminal repeat (LTR) retrotransposons have proliferated and are positively associated with chromosomal breakpoint regions. Here, we present the genome, karyotype and transposons of blue-capped cordon-bleu (Uraeginthus cyanocephalus), an African songbird that diverged from zebra finch at the root of estrildid finches 10 million years ago (Mya). This constitutes the third linked-read sequenced genome assembly and fourth in-depth curated TE library of any bird. Exploration of TE diversity on this brief evolutionary timescale constitutes a considerable increase in resolution for avian TE biology and allowed us to uncover 4.5 Mb more LTR retrotransposons in the zebra finch genome. In blue-capped cordon-bleu, we likewise observed a recent LTR accumulation indicating that this is a shared feature of Estrildidae. Curiously, we discovered 25 new endogenous retrovirus-like LTR retrotransposon families of which at least 21 are present in zebra finch but were previously undiscovered. This highlights the importance of studying close relatives of model organisms.

  • 5. Chyleński, Maciej
    et al.
    Ehler, Edvard
    Somel, Mehmet
    Yaka, Reyhan
    Krzewińska, Maja
    Stockholm University, Faculty of Humanities, Department of Archaeology and Classical Studies.
    Dabert, Miroslawa
    Juras, Anna
    Marciniak, Arkadiusz
    Ancient Mitochondrial Genomes Reveal the Absence of Maternal Kinship in the Burials of catalhoyuk People and Their Genetic Affinities2019In: Genes, ISSN 2073-4425, E-ISSN 2073-4425, Vol. 10, no 3, article id 207Article in journal (Refereed)
    Abstract [en]

    Çatalhöyük is one of the most widely recognized and extensively researched Neolithic settlements. The site has been used to discuss a wide range of aspects associated with the spread of the Neolithic lifestyle and the social organization of Neolithic societies. Here, we address both topics using newly generated mitochondrial genomes, obtained by direct sequencing and capture-based enrichment of genomic libraries, for a group of individuals buried under a cluster of neighboring houses from the classical layer of the site's occupation. Our data suggests a lack of maternal kinship between individuals interred under the floors of Çatalhöyük buildings. The findings could potentially be explained either by a high variability of maternal lineages within a larger kin group, or alternatively, an intentional selection of individuals for burial based on factors other than biological kinship. Our population analyses shows that Neolithic Central Anatolian groups, including Çatalhöyük, share the closest affinity with the population from the Marmara Region and are, in contrast, set further apart from the Levantine populations. Our findings support the hypothesis about the emergence and the direction of spread of the Neolithic within Anatolian Peninsula and beyond, emphasizing a significant role of Central Anatolia in this process.

  • 6.
    Dalen, Love
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Lagerholm, Vendela K.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Nylander, Johan A. A.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Barton, Nick
    Bochenski, Zbigniew M.
    Tomek, Teresa
    Rudling, David
    Ericson, Per G. P.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics. Swedish Museum of Natural History, Research Division.
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Stewart, John R.
    Identifying Bird Remains Using Ancient DNA Barcoding2017In: Genes, ISSN 2073-4425, E-ISSN 2073-4425, Vol. 8, no 6, article id 169Article in journal (Refereed)
  • 7. Dalén, Love
    et al.
    Kempe Lagerholm, Vendela
    Stockholm University, Faculty of Science, Department of Zoology. Swedish Museum of Natural History, Sweden; University of St Andrews, UK.
    Nylander, Johan A. A.
    Barton, Nick
    Bochenski, Zbigniew M.
    Tomek, Teresa
    Rudling, David
    Ericson, Per G. P.
    Irestedt, Martin
    Stewart, John R.
    Identifying Bird Remains Using Ancient DNA Barcoding2017In: Genes, ISSN 2073-4425, E-ISSN 2073-4425, Vol. 8, no 6, article id 169Article in journal (Refereed)
    Abstract [en]

    Bird remains that are difficult to identify taxonomically using morphological methods, are common in the palaeontological record. Other types of challenging avian material include artefacts and food items from endangered taxa, as well as remains from aircraft strikes. We here present a DNA-based method that enables taxonomic identification of bird remains, even from material where the DNA is heavily degraded. The method is based on the amplification and sequencing of two short variable parts of the 16S region in the mitochondrial genome. To demonstrate the applicability of this approach, we evaluated the method on a set of Holocene and Late Pleistocene postcranial bird bones from several palaeontological and archaeological sites in Europe with good success.

  • 8. Dussex, Nicolas
    et al.
    von Seth, Johanna
    Stockholm University, Faculty of Science, Department of Zoology. Swedish Museum of Natural History, Sweden.
    Robertson, Bruce C.
    Dalen, Love
    Full Mitogenomes in the Critically Endangered Kakapo Reveal Major Post-Glacial and Anthropogenic Effects on Neutral Genetic Diversity2018In: Genes, ISSN 2073-4425, E-ISSN 2073-4425, Vol. 9, no 4, article id 220Article in journal (Refereed)
    Abstract [en]

    Understanding how species respond to population declines is a central question in conservation and evolutionary biology. Population declines are often associated with loss of genetic diversity, inbreeding and accumulation of deleterious mutations, which can lead to a reduction in fitness and subsequently contribute to extinction. Using temporal approaches can help us understand the effects of population declines on genetic diversity in real time. Sequencing pre-decline as well as post-decline mitogenomes representing all the remaining mitochondrial diversity, we estimated the loss of genetic diversity in the critically endangered kakapo (Strigops habroptilus). We detected a signal of population expansion coinciding with the end of the Pleistocene last glacial maximum (LGM). Also, we found some evidence for northern and southern lineages, supporting the hypothesis that the species may have been restricted to isolated northern and southern refugia during the LGM. We observed an important loss of neutral genetic diversity associated with European settlement in New Zealand but we could not exclude a population decline associated with Polynesian settlement in New Zealand. However, we did not find evidence for fixation of deleterious mutations. We argue that despite high pre-decline genetic diversity, a rapid and range-wide decline combined with the lek mating system, and life-history traits of kakapo contributed to a rapid loss of genetic diversity following severe population declines.

  • 9.
    Fogelholm, Jesper
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Inkabi, Samuel
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Höglund, Andrey
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Abbey-Lee, Robin
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Johnsson, Martin
    Univ Edinburgh, Scotland; Swedish Univ Agr Sci, Sweden.
    Jensen, Per
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Henriksen, Rie
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Wright, Dominic
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Genetical Genomics of Tonic Immobility in the Chicken2019In: Genes, ISSN 2073-4425, E-ISSN 2073-4425, Vol. 10, no 5, article id 341Article in journal (Refereed)
    Abstract [en]

    Identifying the molecular mechanisms of animal behaviour is an enduring goal for researchers. Gaining insight into these mechanisms enables us to gain a greater understanding of behaviour and their genetic control. In this paper, we perform Quantitative Trait Loci (QTL) mapping of tonic immobility behaviour in an advanced intercross line between wild and domestic chickens. Genes located within the QTL interval were further investigated using global expression QTL (eQTL) mapping from hypothalamus tissue, as well as causality analysis. This identified five candidate genes, with the genes PRDX4 and ACOT9 emerging as the best supported candidates. In addition, we also investigated the connection between tonic immobility, meat pH and struggling behaviour, as the two candidate genes PRDX4 and ACOT9 have previously been implicated in controlling muscle pH at slaughter. We did not find any phenotypic correlations between tonic immobility, struggling behaviour and muscle pH in a smaller additional cohort, despite these behaviours being repeatable within-test.

  • 10.
    Grabherr, Manfred
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala Univ, Natl Bioinformat Infrastruct Sweden, S-75236 Uppsala, Sweden.
    Kaminska, Bozena
    Polish Acad Sci, Nencki Inst Expt Biol, PL-02093 Warsaw, Poland;Guangzhou Med Univ, Affiliated Canc Hosp & Inst, Guangzhou 510095, Guangdong, Peoples R China.
    Komorowski, Jan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology. Polish Acad Sci, Inst Comp Sci, PL-02093 Warsaw, Poland.
    Special Issue Introduction: The Wonders and Mysteries Next Generation Sequencing Technologies Help Reveal2018In: Genes, ISSN 2073-4425, E-ISSN 2073-4425, Vol. 9, no 10, article id 505Article in journal (Other academic)
  • 11.
    Hestand, Matthew S.
    et al.
    Cincinnati Childrens Hosp Med Ctr, Div Human Genet, Cincinnati, OH 45202 USA;Univ Cincinnati, Coll Med, Dept Pediat, Cincinnati, OH 45202 USA.
    Ameur, Adam
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology. Uppsala University, Science for Life Laboratory, SciLifeLab. Monash Univ, Dept Epidemiol & Prevent Med, Melbourne, Vic 32901, Australia.
    The Versatility of SMRT Sequencing2019In: Genes, ISSN 2073-4425, E-ISSN 2073-4425, Vol. 10, no 1, article id 24Article in journal (Other academic)
  • 12.
    Hitte, Christophe
    et al.
    Univ Rennes, CNRS, IGDR, UMR 6290, F-35000 Rennes, France.
    Le Beguec, Celine
    Univ Rennes, CNRS, IGDR, UMR 6290, F-35000 Rennes, France.
    Cadieu, Edouard
    Univ Rennes, CNRS, IGDR, UMR 6290, F-35000 Rennes, France.
    Wucher, Valentin
    Barcelona Inst Sci & Technol, Ctr Genom Regulat CRG, Dr Aiguader 88, Barcelona 08003, Spain.
    Primot, Aline
    Univ Rennes, CNRS, IGDR, UMR 6290, F-35000 Rennes, France.
    Prouteau, Pings
    Univ Rennes, CNRS, IGDR, UMR 6290, F-35000 Rennes, France.
    Botherel, Nadine
    Univ Rennes, CNRS, IGDR, UMR 6290, F-35000 Rennes, France.
    Hedan, Benoit
    Univ Rennes, CNRS, IGDR, UMR 6290, F-35000 Rennes, France.
    Lindblad-Toh, Kerstin
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab. Broad Inst MIT & Harvard, Cambridge, MA 02142 USA.
    Andre, Catherine
    Univ Rennes, CNRS, IGDR, UMR 6290, F-35000 Rennes, France.
    Derrien, Thomas
    Univ Rennes, CNRS, IGDR, UMR 6290, F-35000 Rennes, France.
    Genome-Wide Analysis of Long Non-Coding RNA Profiles in Canine Oral Melanomas2019In: Genes, ISSN 2073-4425, E-ISSN 2073-4425, Vol. 10, no 6, article id 477Article in journal (Refereed)
    Abstract [en]

    Mucosal melanomas (MM) are rare aggressive cancers in humans, and one of the most common forms of oral cancers in dogs. Similar biological and histological features are shared between MM in both species, making dogs a powerful model for comparative oncology studies of melanomas. Although exome sequencing recently identified recurrent coding mutations in canine MM, little is known about changes in non-coding gene expression, and more particularly, in canine long non-coding RNAs (lncRNAs), which are commonly dysregulated in human cancers. Here, we sampled a large cohort (n = 52) of canine normal/tumor oral MM from three predisposed breeds (poodles, Labrador retrievers, and golden retrievers), and used deep transcriptome sequencing to identify more than 400 differentially expressed (DE) lncRNAs. We further prioritized candidate lncRNAs by comparative genomic analysis to pinpoint 26 dog-human conserved DE lncRNAs, including SOX21-AS, ZEB2-AS, and CASC15 lncRNAs. Using unsupervised co-expression network analysis with coding genes, we inferred the potential functions of the DE lncRNAs, suggesting associations with cancer-related genes, cell cycle, and carbohydrate metabolism Gene Ontology (GO) terms. Finally, we exploited our multi-breed design to identify DE lncRNAs within breeds. This study provides a unique transcriptomic resource for studying oral melanoma in dogs, and highlights lncRNAs that may potentially be diagnostic or therapeutic targets for human and veterinary medicine.

  • 13.
    Hutter, Sonja
    et al.
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Neuro-Oncology.
    Bolin, Sara
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Neuro-Oncology.
    Weishaupt, Holger
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Neuro-Oncology.
    Johansson, Fredrik K.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Neuro-Oncology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Modeling and Targeting MYC Genes in Childhood Brain Tumors2017In: Genes, ISSN 2073-4425, E-ISSN 2073-4425, Vol. 8, no 4, article id 107Article, review/survey (Refereed)
    Abstract [en]

    Brain tumors are the second most common group of childhood cancers, accounting for about 20%-25% of all pediatric tumors. Deregulated expression of the MYC family of transcription factors, particularly c-MYC and MYCN genes, has been found in many of these neoplasms, and their expression levels are often correlated with poor prognosis. Elevated c-MYC/MYCN initiates and drives tumorigenesis in many in vivo model systems of pediatric brain tumors. Therefore, inhibition of their oncogenic function is an attractive therapeutic target. In this review, we explore the roles of MYC oncoproteins and their molecular targets during the formation, maintenance, and recurrence of childhood brain tumors. We also briefly summarize recent progress in the development of therapeutic approaches for pharmacological inhibition of MYC activity in these tumors.

  • 14.
    Laxman, Navya
    et al.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab). Uppsala University, Sweden.
    Mallmin, Hans
    Nilsson, Olle
    Kindmark, Andreas
    miR-203 and miR-320 Regulate Bone Morphogenetic Protein-2-Induced Osteoblast Differentiation by Targeting Distal-Less Homeobox 5 (Dlx5)2017In: Genes, ISSN 2073-4425, E-ISSN 2073-4425, Vol. 8, no 1, article id 4Article in journal (Refereed)
    Abstract [en]

    MicroRNAs (miRNAs) are a family of small, non-coding RNAs (17-24 nucleotides), which regulate gene expression either by the degradation of the target mRNAs or inhibiting the translation of genes. Recent studies have indicated that miRNA plays an important role in regulating osteoblast differentiation. In this study, we identified miR-203 and miR-320b as important miRNAs modulating osteoblast differentiation. We identified Dlx5 as potential common target by prediction algorithms and confirmed this by knock-down and over expression of the miRNAs and assessing Dlx5 at mRNA and protein levels and specificity was verified by luciferase reporter assays. We examined the effect of miR-203 and miR-320b on osteoblast differentiation by transfecting with pre- and anti-miRs. Over-expression of miR-203 and miR-320b inhibited osteoblast differentiation, whereas inhibition of miR-203 and miR-320b stimulated alkaline phosphatase activity and matrix mineralization. We show that miR-203 and miR-320b negatively regulate BMP-2-induced osteoblast differentiation by suppressing Dlx5, which in turn suppresses the downstream osteogenic master transcription factor Runx2 and Osx and together they suppress osteoblast differentiation. Taken together, we propose a role for miR-203 and miR-320b in modulating bone metabolism.

  • 15.
    Laxman, Navya
    et al.
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Endocrinology and mineral metabolism.
    Mallmin, Hans
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Surgical Sciences, Orthopaedics.
    Nilsson, Olle
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Surgical Sciences, Orthopaedics.
    Kindmark, Andreas
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Endocrinology and mineral metabolism. Uppsala University, Science for Life Laboratory, SciLifeLab.
    miR-203 and miR-320 regulate Bone Morphogenetic Protein-2-induced osteoblast differentiation by targeting Distal-less Homeobox 5 (Dlx5)2017In: Genes, ISSN 2073-4425, E-ISSN 2073-4425, Vol. 8, no 1, article id E4Article in journal (Refereed)
    Abstract [en]

    MicroRNAs (miRNAs) are a family of small, non-coding RNAs (17–24 nucleotides), which regulate gene expression either by the degradation of the target mRNAs or inhibiting the translation of genes. Recent studies have indicated that miRNA plays an important role in regulating osteoblast differentiation. In this study, we identified miR-203 and miR-320b as important miRNAs modulating osteoblast differentiation. We identified Dlx5 as potential common target by prediction algorithms and confirmed this by knock-down and over expression of the miRNAs and assessing Dlx5 at mRNA and protein levels and specificity was verified by luciferase reporter assays. We examined the effect of miR-203 and miR-320b on osteoblast differentiation by transfecting with pre- and anti-miRs. Over-expression of miR-203 and miR-320b inhibited osteoblast differentiation, whereas inhibition of miR-203 and miR-320b stimulated alkaline phosphatase activity and matrix mineralization. We show that miR-203 and miR-320b negatively regulate BMP-2-induced osteoblast differentiation by suppressing Dlx5, which in turn suppresses the downstream osteogenic master transcription factor Runx2 and Osx and together they suppress osteoblast differentiation. Taken together, we propose a role for miR-203 and miR-320b in modulating bone metabolism.

  • 16.
    Megquier, Kate
    et al.
    Broad Inst MIT & Harvard, Vertebrate Genom, Cambridge, MA 02142 USA.
    Genereux, Diane P.
    Broad Inst MIT & Harvard, Vertebrate Genom, Cambridge, MA 02142 USA.
    Hekman, Jessica
    Broad Inst MIT & Harvard, Vertebrate Genom, Cambridge, MA 02142 USA.
    Swofford, Ross
    Broad Inst MIT & Harvard, Vertebrate Genom, Cambridge, MA 02142 USA.
    Turner-Maier, Jason
    Broad Inst MIT & Harvard, Vertebrate Genom, Cambridge, MA 02142 USA.
    Johnson, Jeremy
    Broad Inst MIT & Harvard, Vertebrate Genom, Cambridge, MA 02142 USA.
    Alonso, Jacob
    Broad Inst MIT & Harvard, Vertebrate Genom, Cambridge, MA 02142 USA.
    Li, Xue
    Broad Inst MIT & Harvard, Vertebrate Genom, Cambridge, MA 02142 USA;Univ Massachusetts, Bioinformat & Integrat Biol, Med Sch, Worcester, MA 01655 USA.
    Morrill, Kathleen
    Broad Inst MIT & Harvard, Vertebrate Genom, Cambridge, MA 02142 USA;Univ Massachusetts, Bioinformat & Integrat Biol, Med Sch, Worcester, MA 01655 USA.
    Anguish, Lynne J.
    Cornell Univ, Coll Vet Med, Baker Inst Anim Hlth, Ithaca, NY 14853 USA.
    Koltookian, Michele
    Broad Inst MIT & Harvard, Vertebrate Genom, Cambridge, MA 02142 USA.
    Logan, Brittney
    Univ Massachusetts, Bioinformat & Integrat Biol, Med Sch, Worcester, MA 01655 USA.
    Sharp, Claire R.
    Murdoch Univ, Coll Vet Med, Sch Vet & Life Sci, Murdoch, WA 6150, Australia.
    Ferrer, Lluis
    Univ Autonoma Barcelona, Dept Med & Cirurgia Anim, Vet Sch, E-08193 Barcelona, Spain.
    Lindblad-Toh, Kerstin
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab. Broad Inst MIT & Harvard, Vertebrate Genom, Cambridge, MA 02142 USA.
    Meyers-Wallen, Vicki N.
    Cornell Univ, Coll Vet Med, Baker Inst Anim Hlth, Ithaca, NY 14850 USA;Cornell Univ, Coll Vet Med, Dept Biomed Sci, Ithaca, NY 14850 USA.
    Hoffman, Andrew
    Univ Penn, Sch Vet Med, Philadelphia, PA 19104 USA;Tufts Univ, Cummings Sch Vet Med, Grafton, MA 01536 USA.
    Karlsson, Elinor K.
    Broad Inst MIT & Harvard, Vertebrate Genom, Cambridge, MA 02142 USA;Univ Massachusetts, Bioinformat & Integrat Biol, Med Sch, Worcester, MA 01655 USA;Univ Massachusetts, Med Sch, Program Mol Med, Worcester, MA 01655 USA.
    BarkBase: Epigenomic Annotation of Canine Genomes2019In: Genes, ISSN 2073-4425, E-ISSN 2073-4425, Vol. 10, no 6, article id 433Article in journal (Refereed)
    Abstract [en]

    Dogs are an unparalleled natural model for investigating the genetics of health and disease, particularly for complex diseases like cancer. Comprehensive genomic annotation of regulatory elements active in healthy canine tissues is crucial both for identifying candidate causal variants and for designing functional studies needed to translate genetic associations into disease insight. Currently, canine geneticists rely primarily on annotations of the human or mouse genome that have been remapped to dog, an approach that misses dog-specific features. Here, we describe BarkBase, a canine epigenomic resource available at barkbase.org. BarkBase hosts data for 27 adult tissue types, with biological replicates, and for one sample of up to five tissues sampled at each of four carefully staged embryonic time points. RNA sequencing is complemented with whole genome sequencing and with assay for transposase-accessible chromatin using sequencing (ATAC-seq), which identifies open chromatin regions. By including replicates, we can more confidently discern tissue-specific transcripts and assess differential gene expression between tissues and timepoints. By offering data in easy-to-use file formats, through a visual browser modeled on similar genomic resources for human, BarkBase introduces a powerful new resource to support comparative studies in dogs and humans.

  • 17.
    Milani, Diogo
    et al.
    UNESP Univ Estadual Paulista, Dept Biol, IB, BR-01049010 Rio Claro, SP, Brazil.
    Bardella, Vanessa B.
    UNESP Univ Estadual Paulista, Dept Biol, IB, BR-01049010 Rio Claro, SP, Brazil.
    Ferretti, Ana B. S. M.
    UNESP Univ Estadual Paulista, Dept Biol, IB, BR-01049010 Rio Claro, SP, Brazil.
    Palacios Gimenez, Octavio Manuel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. UNESP Univ Estadual Paulista, Dept Biol, IB, BR-01049010 Rio Claro, SP, Brazil.
    Melo, Adriana de S.
    UPE Univ Pernambuco, Inst Ciencias Biol, Lab Biodiversidade & Genet Insetos, BR-50100130 Recife, PE, Brazil.
    Moura, Rita C.
    UPE Univ Pernambuco, Inst Ciencias Biol, Lab Biodiversidade & Genet Insetos, BR-50100130 Recife, PE, Brazil.
    Loreto, Vilma
    UFPE Univ Fed Pernambuco, Dept Genet, CB, BR-50670901 Recife, PE, Brazil.
    Song, Hojun
    Texas A&M Univ, Dept Entomol, 2475 TAMU, College Stn, TX 77843 USA.
    Cabral-de-Mello, Diogo C.
    UNESP Univ Estadual Paulista, Dept Biol, IB, BR-01049010 Rio Claro, SP, Brazil.
    Satellite DNAs Unveil Clues about the Ancestry and Composition of B Chromosomes in Three Grasshopper Species2018In: Genes, ISSN 2073-4425, E-ISSN 2073-4425, Vol. 9, no 11, article id 523Article in journal (Refereed)
    Abstract [en]

    Supernumerary (B) chromosomes are dispensable genomic elements occurring frequently among grasshoppers. Most B chromosomes are enriched with repetitive DNAs, including satellite DNAs (satDNAs) that could be implicated in their evolution. Although studied in some species, the specific ancestry of B chromosomes is difficult to ascertain and it was determined in only a few examples. Here we used bioinformatics and cytogenetics to characterize the composition and putative ancestry of B chromosomes in three grasshopper species, Rhammatocerus brasiliensis, Schistocerca rubiginosa, and Xyleus discoideus angulatus. Using the RepeatExplorer pipeline we searched for the most abundant satDNAs in Illumina sequenced reads, and then we generated probes used in fluorescent in situ hybridization (FISH) to determine chromosomal position. We used this information to infer ancestry and the events that likely occurred at the origin of B chromosomes. We found twelve, nine, and eighteen satDNA families in the genomes of R. brasiliensis, S. rubiginosa, and X. d. angulatus, respectively. Some satDNAs revealed clustered organization on A and B chromosomes varying in number of sites and position along chromosomes. We did not find specific satDNA occurring in the B chromosome. The satDNAs shared among A and B chromosomes support the idea of putative intraspecific ancestry from small autosomes in the three species, i.e., pair S11 in R. brasiliensis, pair S9 in S. rubiginosa, and pair S10 in X. d. angulatus. The possibility of involvement of other chromosomal pairs in B chromosome origin is also hypothesized. Finally, we discussed particular aspects in composition, origin, and evolution of the B chromosome for each species.

  • 18.
    Morris, Jake
    et al.
    UCL, Dept Genet Evolut & Environm, London WC1E 6BT, England.
    Darolti, Iulia
    UCL, Dept Genet Evolut & Environm, London WC1E 6BT, England.
    Bloch, Natasha I.
    UCL, Dept Genet Evolut & Environm, London WC1E 6BT, England.
    Wright, Alison E.
    Univ Sheffield, Dept Anim & Plant Sci, Sheffield S10 2TN, S Yorkshire, England.
    Mank, Judith E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. UCL, Dept Genet Evolut & Environm, London WC1E 6BT, England.
    Shared and Species-Specific Patterns of Nascent Y Chromosome Evolution in Two Guppy Species2018In: Genes, ISSN 2073-4425, E-ISSN 2073-4425, Vol. 9, no 5, article id 238Article in journal (Refereed)
    Abstract [en]

    Sex chromosomes form once recombination is halted around the sex-determining locus between a homologous pair of chromosomes, resulting in a male-limited Y chromosome. We recently characterized the nascent sex chromosome system in the Trinidadian guppy (Poecilia reticulata). The guppy Y is one of the youngest animal sex chromosomes yet identified, and therefore offers a unique window into the early evolutionary forces shaping sex chromosome formation, particularly the rate of accumulation of repetitive elements and Y-specific sequence. We used comparisons between male and female genomes in P. reticulata and its sister species, Endler's guppy (P. wingei), which share an ancestral sex chromosome, to identify male-specific sequences and to characterize the degree of differentiation between the X and Y chromosomes. We identified male-specific sequence shared between P. reticulata and P. wingei consistent with a small ancestral non-recombining region. Our assembly of this Y-specific sequence shows substantial homology to the X chromosome, and appears to be significantly enriched for genes implicated in pigmentation. We also found two plausible candidates that may be involved in sex determination. Furthermore, we found that the P. wingei Y chromosome exhibits a greater signature of repetitive element accumulation than the P. reticulata Y chromosome. This suggests that Y chromosome divergence does not necessarily correlate with the time since recombination suppression. Overall, our results reveal the early stages of Y chromosome divergence in the guppy.

  • 19.
    Pettersson, Mats E.
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Jern, Patric
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Whole-Genome Analysis of Domestic Chicken Selection Lines Suggests Segregating Variation in ERV Makeups2019In: Genes, ISSN 2073-4425, E-ISSN 2073-4425, Vol. 10, no 2, article id 162Article in journal (Refereed)
    Abstract [en]

    Retroviruses have invaded vertebrate hosts for millions of years and left an extensive endogenous retrovirus (ERV) record in the host genomes, which provides a remarkable source for an evolutionary perspective on retrovirus-host associations. Here we identified ERV variation across whole-genomes from two chicken lines, derived from a common founder population subjected to 50 years of bi-directional selection on body weight, and a distantly related domestic chicken line as a comparison outgroup. Candidate ERV loci, where at least one of the chicken lines indicated distinct differences, were analyzed for adjacent host genomic landscapes, selective sweeps, and compared by sequence associations to reference assembly ERVs in phylogenetic analyses. Current data does not support selection acting on specific ERV loci in the domestic chicken lines, as determined by presence inside selective sweeps or composition of adjacent host genes. The varying ERV records among the domestic chicken lines associated broadly across the assembly ERV phylogeny, indicating that the observed insertion differences result from pre-existing and segregating ERV loci in the host populations. Thus, data suggest that the observed differences between the host lineages are best explained by substantial standing ERV variation within host populations, and indicates that even truncated, presumably old, ERVs have not yet become fixed in the host population.

  • 20.
    Ramnarine, Timothy J. S.
    et al.
    Ludwig Maximilians Univ Munchen, Fac Biol, Div Evolutionary Biol, Grosshaderner Str 2, D-82152 Planegg Martinsried, Germany.
    Glaser-Schmitt, Amanda
    Ludwig Maximilians Univ Munchen, Fac Biol, Div Evolutionary Biol, Grosshaderner Str 2, D-82152 Planegg Martinsried, Germany.
    Catalan, Ana
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Ludwig Maximilians Univ Munchen, Fac Biol, Div Evolutionary Biol, Grosshaderner Str 2, D-82152 Planegg Martinsried, Germany.
    Parsch, John
    Ludwig Maximilians Univ Munchen, Fac Biol, Div Evolutionary Biol, Grosshaderner Str 2, D-82152 Planegg Martinsried, Germany.
    Population Genetic and Functional Analysis of a cis-Regulatory Polymorphism in the Drosophila melanogaster Metallothionein A gene2019In: Genes, ISSN 2073-4425, E-ISSN 2073-4425, Vol. 10, no 2, article id 147Article in journal (Refereed)
    Abstract [en]

    Although gene expression can vary extensively within and among populations, the genetic basis of this variation and the evolutionary forces that maintain it are largely unknown. In Drosophila melanogaster, a 49-bp insertion/deletion (indel) polymorphism in the Metallothionein A (MtnA) gene is associated with variation in MtnA expression and oxidative stress tolerance. To better understand the functional and evolutionary significance of this polymorphism, we investigated it in several worldwide populations. In a German population, the deletion was present at a high and stable frequency over multiple seasons and years, and was associated with increased MtnA expression. There was, however, no evidence that the polymorphism was maintained by overdominant, seasonally fluctuating, or sexually antagonistic selection. The deletion was rare in a population from the species' ancestral range in sub-Saharan Africa and is likely the result of non-African admixture, suggesting that it spread to high frequency following the species' out-of-Africa expansion. Using data from a North American population, we found that the deletion was associated with MtnA expression and tolerance to oxidative stress induced by menadione sodium bisulfite. Our results are consistent with the deletion being selectively favored in temperate populations due to the increased MtnA expression and oxidative stress tolerance that it confers.

  • 21.
    Tracewska-Siemiątkowska, Anna
    et al.
    DNA Analysis Laboratory, Wrocław Research Centre EIT+, Wrocław, Poland; Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.
    Haer-Wigman, Lonneke
    Department of Human Genetics, Radboud University Medical Center, Nijmegen,The Netherlands.
    Bosch, Danielle G. M.
    Department of Human Genetics, Radboud University Medical Center, Nijmegen,The Netherlands; Bartiméus, Institute for the Visually Impaired, Zeist, The Netherlands; Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands.
    Nickerson, Deborah
    Department of Genome Sciences, University of Washington, Seattle WA, USA.
    Bamshad, Michael J.
    Department of Pediatrics, University of Washington, Seattle WA, USA.
    van de Vorst, Maartje
    Department of Human Genetics, Radboud University Medical Center, Nijmegen,The Netherlands; Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands.
    Rendtorff, Nanna Dahl
    Department of Clinical Genetics,The Kennedy Centre/Rigshospitalet/, Glostrup, Denmark.
    Möller, Claes
    Örebro University, School of Health Sciences. Audiological Research Centre, University Hospital Örebro, Örebro, Sweden; Swedish Institute of Disability Research, Örebro University, Örebro, Sweden.
    Kjellström, Ulrika
    Department of Clinical Science Lund, Ophthalmology, University of Lund, Lund, Sweden.
    Andréasson, Sten
    Department of Clinical Science Lund, Ophthalmology, University of Lund, Lund, Sweden.
    Cremers, Frans P. M.
    Department of Human Genetics, Radboud University Medical Center, Nijmegen,The Netherlands; Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen,The Netherlands.
    Tranebjærg, Lisbeth
    Department of Clinical Genetics, The Kennedy Centre/Rigshospitalet/, Glostrup, Denmark; Institute of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark.
    An Expanded Multi-Organ Disease Phenotype Associated with Mutations in YARS2017In: Genes, ISSN 2073-4425, E-ISSN 2073-4425, Vol. 8, no 12, article id E381Article in journal (Refereed)
    Abstract [en]

    Whole exome sequence analysis was performed in a Swedish mother-father-affected proband trio with a phenotype characterized by progressive retinal degeneration with congenital nystagmus, profound congenital hearing impairment, primary amenorrhea, agenesis of the corpus callosum, and liver disease. A homozygous variant c.806T > C, p.(F269S) in the tyrosyl-tRNA synthetase gene (YARS) was the only identified candidate variant consistent with autosomal recessive inheritance. Mutations in YARS have previously been associated with both autosomal dominant Charcot-Marie-Tooth syndrome and a recently reported autosomal recessive multiorgan disease. Herein, we propose that mutations in YARS underlie another clinical phenotype adding a second variant of the disease, including retinitis pigmentosa and deafness, to the spectrum of YARS-associated disorders.

  • 22.
    Veldman, Sarina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Kim, Seol-Jong
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    van Andel, Tinde R.
    Naturalis Biodivers Ctr, POB 9517, NL-2300 RA Leiden, Netherlands.
    Font, Maria Bello
    Univ Oslo, Nat Hist Museum, Postboks 1172, N-0318 Oslo, Norway.
    Bone, Ruth E.
    Royal Bot Gardens, Richmond TW9 3AB, Surrey, England.
    Bytebier, Benny
    Univ KwaZulu Natal, Sch Life Sci, Bews Herbarium, Pr Bag X01, ZA-3209 Scottsville, South Africa.
    Chuba, David
    Univ Zambia, Dept Biol Sci, Box 32379, Lusaka, Zambia.
    Gravendeel, Barbara
    Naturalis Biodivers Ctr, POB 9517, NL-2300 RA Leiden, Netherlands;Leiden Univ, Inst Biol Leiden, POB 9505, NL-2300 RA Leiden, Netherlands;Univ Appl Sci Leiden, Zernikedreef 11, NL-2333 CK Leiden, Netherlands.
    Martos, Florent
    Univ KwaZulu Natal, Sch Life Sci, Bews Herbarium, Pr Bag X01, ZA-3209 Scottsville, South Africa;Sorbonne Univ, Museum Natl Hist Nat, CNRS, Inst Systemat Evolut Biodiversite ISYEB,EPHE, CP50,45 Rue Buffon, F-75005 Paris, France.
    Mpatwa, Geophat
    Copperbelt Univ, Sch Nat Resources, POB 21692, Kitwe, Zambia.
    Ngugi, Grace
    Univ KwaZulu Natal, Sch Life Sci, Bews Herbarium, Pr Bag X01, ZA-3209 Scottsville, South Africa;Natl Museums Kenya, East African Herbarium, POB 40658-00100, Nairobi, Kenya.
    Vinya, Royd
    Copperbelt Univ, Sch Nat Resources, POB 21692, Kitwe, Zambia.
    Wightman, Nicholas
    Homegarden Landscape Consultants Ltd, P Bag 30C, Lusaka, Zambia.
    Yokoya, Kazutoma
    Royal Bot Gardens, Richmond TW9 3AB, Surrey, England.
    de Boer, Hugo J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Naturalis Biodivers Ctr, POB 9517, NL-2300 RA Leiden, Netherlands.
    Trade in Zambian Edible Orchids-DNA Barcoding Reveals the Use of Unexpected Orchid Taxa for Chikanda2018In: Genes, ISSN 2073-4425, E-ISSN 2073-4425, Vol. 9, no 12, article id 595Article in journal (Refereed)
    Abstract [en]

    In Zambia, wild edible terrestrial orchids are used to produce a local delicacy called chikanda, which has become increasingly popular throughout the country. Commercialization puts orchid populations in Zambia and neighbouring countries at risk of overharvesting. Hitherto, no study has documented which orchid species are traded on local markets, as orchid tubers are difficult to identify morphologically. In this study, the core land-plant DNA barcoding markers rbcL and matK were used in combination with nrITS to determine which species were sold in Zambian markets. Eighty-two interviews were conducted to determine harvesting areas, as well as possible sustainability concerns. By using nrITS DNA barcoding, a total of 16 orchid species in six different genera could be identified. Both rbcL and matK proved suitable to identify the tubers up to the genus or family level. Disa robusta, Platycoryne crocea and Satyrium buchananii were identified most frequently and three previously undocumented species were encountered on the market. Few orchid species are currently listed on the global International Union for the Conservation of Nature (IUCN) Red List. Local orchid populations and endemic species could be at risk of overharvesting due to the intensive and indiscriminate harvesting of chikanda orchids, and we therefore encourage increased conservation assessment of terrestrial African orchids.

1 - 22 of 22
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