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Genomics of Sorocarpic Amoebae
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
2017 (English)Doctoral thesis, comprehensive summary (Other academic)
Description
Abstract [en]

Sorocarpy is the aggregation of unicellular organisms to form multicellular fruiting bodies (sorocarps). This thesis is about the two best-known groups of sorocarpic amoebae, Dictyostelids and Acrasids.

Paper I describes assembly and analysis of a multigene dataset to identify the root of the dictyostelid tree. Phylogenetic analyses of 213 genes (conserved in all sequenced dictyostelid genomes and an outgroup) place the root between Groups 1+2 and 3+4 (now: Cavenderiaceae + Acytosteliaceae and Raperosteliaceae + Dictyosteliaceae). Resolution of the dictyostelid root made it possible to proceed with a major taxonomic revision of the group.

Paper II focuses on the taxonomic revision of Dictyostelia based on molecular phylogeny and SSU ribosomal RNA sequence signatures. The two major divisions were treated at the rank of order as Acytosteliales ord. nov. and Dictyosteliales. The two major clades within each of these orders were given the rank of family. Twelve genera were recognized. This is the first revision of a major protist taxon using molecular signatures and offers guidelines for taxonomic revision of protist groups where morphology is insufficient.

Paper III presents the mitochondrial genome (mtDNA) of Acrasis kona. Over a quarter of the genome consists of novel open reading frames, while 16 genes present in the mtDNA of its relative, Naegleria gruberi, are missing. We identified many of these genes in the A. kona nuclear DNA, and used phylogenetic analyses to show that most of these genes arose by transfer from mtDNA.

Paper IV presents the nuclear genome of A. kona, the second genome sequence of a free-living excavate. The 44 Mb genome has 15,868 open reading frames of which 4,987 are novel. A surprising number of genes are most similar to homologs in distant relatives, suggesting acquisition by horizontal gene transfer (HGT). Most HGT candidates are expressed and many constitute multi-gene families and/or have acquired introns and membrane targeting sequences. Strong HGT candidates include some genes essential to development and signaling in Dictyostelia. Flagellar motility and meiosis genes are also present and conserved, suggesting cryptic flagellar and sexual stages.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2017. , 45 p.
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 1516
National Category
Natural Sciences
Identifiers
URN: urn:nbn:se:uu:diva-320432ISBN: 978-91-554-9913-6 (print)OAI: oai:DiVA.org:uu-320432DiVA: diva2:1089497
Public defence
2017-06-09, Lindhalsalen, Norbyvägen 18D, Uppsala, 09:00 (English)
Opponent
Supervisors
Available from: 2017-05-18 Created: 2017-04-20 Last updated: 2017-05-18
List of papers
1. Root of Dictyostelia based on 213 universal proteins
Open this publication in new window or tab >>Root of Dictyostelia based on 213 universal proteins
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2015 (English)In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 92, 53-62 p.Article in journal (Refereed) Published
National Category
Natural Sciences
Identifiers
urn:nbn:se:uu:diva-320243 (URN)
Available from: 2017-04-18 Created: 2017-04-18 Last updated: 2017-04-20
2. A new classification of the dictyostelids
Open this publication in new window or tab >>A new classification of the dictyostelids
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(English)Manuscript (preprint) (Other academic)
National Category
Natural Sciences
Identifiers
urn:nbn:se:uu:diva-320430 (URN)
Available from: 2017-04-20 Created: 2017-04-20 Last updated: 2017-04-20
3. Missing Genes, Multiple ORFs, and C-to-U Type RNA Editing in Acrasis kona (Heterolobosea, Excavata) Mitochondrial DNA
Open this publication in new window or tab >>Missing Genes, Multiple ORFs, and C-to-U Type RNA Editing in Acrasis kona (Heterolobosea, Excavata) Mitochondrial DNA
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2014 (English)In: Genome Biology and Evolution, ISSN 1759-6653, E-ISSN 1759-6653Article in journal (Refereed) Published
National Category
Natural Sciences
Identifiers
urn:nbn:se:uu:diva-320429 (URN)
Available from: 2017-04-20 Created: 2017-04-20 Last updated: 2017-04-20
4. Multicellularity in the Excavata, the genome sequence of Acrasis kona
Open this publication in new window or tab >>Multicellularity in the Excavata, the genome sequence of Acrasis kona
(English)Manuscript (preprint) (Other academic)
National Category
Natural Sciences
Identifiers
urn:nbn:se:uu:diva-320431 (URN)
Available from: 2017-04-20 Created: 2017-04-20 Last updated: 2017-04-20

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