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Comparative genomics of Chlamydomonas

Despite its role as a reference organism in the plant sciences, the green alga Chlamydomonas reinhardtii entirely lacks genomic resources from closely related species. We present highly contiguous and well-annotated genome assemblies for three unicellular C. reinhardtii relatives: Chlamydomonas ince...

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Autores principales: Craig, Rory J, Hasan, Ahmed R, Ness, Rob W, Keightley, Peter D
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8226300/
https://www.ncbi.nlm.nih.gov/pubmed/33793842
http://dx.doi.org/10.1093/plcell/koab026
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author Craig, Rory J
Hasan, Ahmed R
Ness, Rob W
Keightley, Peter D
author_facet Craig, Rory J
Hasan, Ahmed R
Ness, Rob W
Keightley, Peter D
author_sort Craig, Rory J
collection PubMed
description Despite its role as a reference organism in the plant sciences, the green alga Chlamydomonas reinhardtii entirely lacks genomic resources from closely related species. We present highly contiguous and well-annotated genome assemblies for three unicellular C. reinhardtii relatives: Chlamydomonas incerta, Chlamydomonas schloesseri, and the more distantly related Edaphochlamys debaryana. The three Chlamydomonas genomes are highly syntenous with similar gene contents, although the 129.2 Mb C. incerta and 130.2 Mb C. schloesseri assemblies are more repeat-rich than the 111.1 Mb C. reinhardtii genome. We identify the major centromeric repeat in C. reinhardtii as a LINE transposable element homologous to Zepp (the centromeric repeat in Coccomyxa subellipsoidea) and infer that centromere locations and structure are likely conserved in C. incerta and C. schloesseri. We report extensive rearrangements, but limited gene turnover, between the minus mating type loci of these Chlamydomonas species. We produce an eight-species core-Reinhardtinia whole-genome alignment, which we use to identify several hundred false positive and missing genes in the C. reinhardtii annotation and >260,000 evolutionarily conserved elements in the C. reinhardtii genome. In summary, these resources will enable comparative genomics analyses for C. reinhardtii, significantly extending the analytical toolkit for this emerging model system.
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spelling pubmed-82263002021-06-28 Comparative genomics of Chlamydomonas Craig, Rory J Hasan, Ahmed R Ness, Rob W Keightley, Peter D Plant Cell Focus on the Biology of Plant Genomes Despite its role as a reference organism in the plant sciences, the green alga Chlamydomonas reinhardtii entirely lacks genomic resources from closely related species. We present highly contiguous and well-annotated genome assemblies for three unicellular C. reinhardtii relatives: Chlamydomonas incerta, Chlamydomonas schloesseri, and the more distantly related Edaphochlamys debaryana. The three Chlamydomonas genomes are highly syntenous with similar gene contents, although the 129.2 Mb C. incerta and 130.2 Mb C. schloesseri assemblies are more repeat-rich than the 111.1 Mb C. reinhardtii genome. We identify the major centromeric repeat in C. reinhardtii as a LINE transposable element homologous to Zepp (the centromeric repeat in Coccomyxa subellipsoidea) and infer that centromere locations and structure are likely conserved in C. incerta and C. schloesseri. We report extensive rearrangements, but limited gene turnover, between the minus mating type loci of these Chlamydomonas species. We produce an eight-species core-Reinhardtinia whole-genome alignment, which we use to identify several hundred false positive and missing genes in the C. reinhardtii annotation and >260,000 evolutionarily conserved elements in the C. reinhardtii genome. In summary, these resources will enable comparative genomics analyses for C. reinhardtii, significantly extending the analytical toolkit for this emerging model system. Oxford University Press 2021-02-02 /pmc/articles/PMC8226300/ /pubmed/33793842 http://dx.doi.org/10.1093/plcell/koab026 Text en © The Author(s) 2021. Published by Oxford University Press on behalf of American Society of Plant Biologists. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) ), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Focus on the Biology of Plant Genomes
Craig, Rory J
Hasan, Ahmed R
Ness, Rob W
Keightley, Peter D
Comparative genomics of Chlamydomonas
title Comparative genomics of Chlamydomonas
title_full Comparative genomics of Chlamydomonas
title_fullStr Comparative genomics of Chlamydomonas
title_full_unstemmed Comparative genomics of Chlamydomonas
title_short Comparative genomics of Chlamydomonas
title_sort comparative genomics of chlamydomonas
topic Focus on the Biology of Plant Genomes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8226300/
https://www.ncbi.nlm.nih.gov/pubmed/33793842
http://dx.doi.org/10.1093/plcell/koab026
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