Evidence-based green algal genomics reveals marine diversity and ancestral characteristics of land plants
Background: Prasinophytes are widespread marine green algae that are related to plants. Cellular abundance of the prasinophyte Micromonas has reportedly increased in the Arctic due to climate-induced changes. Thus, studies of these unicellular eukaryotes are important for marine ecology and for unde...
Published in: | BMC Genomics |
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Main Authors: | , , , , , , , , , , , , , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
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BioMed Central
2016
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Online Access: | https://authors.library.caltech.edu/65908/ https://authors.library.caltech.edu/65908/1/art%253A10.1186%252Fs12864-016-2585-6.pdf https://authors.library.caltech.edu/65908/2/12864_2016_2585_MOESM1_ESM.xlsx https://authors.library.caltech.edu/65908/3/12864_2016_2585_MOESM2_ESM.pdf https://resolver.caltech.edu/CaltechAUTHORS:20160404-152844868 |
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institution |
Open Polar |
collection |
Caltech Authors (California Institute of Technology) |
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language |
English |
description |
Background: Prasinophytes are widespread marine green algae that are related to plants. Cellular abundance of the prasinophyte Micromonas has reportedly increased in the Arctic due to climate-induced changes. Thus, studies of these unicellular eukaryotes are important for marine ecology and for understanding Viridiplantae evolution and diversification. Results: We generated evidence-based Micromonas gene models using proteomics and RNA-Seq to improve prasinophyte genomic resources. First, sequences of four chromosomes in the 22 Mb Micromonas pusilla (CCMP1545) genome were finished. Comparison with the finished 21 Mb genome of Micromonas commoda (RCC299; named herein) shows they share ≤8,141 of ~10,000 protein-encoding genes, depending on the analysis method. Unlike RCC299 and other sequenced eukaryotes, CCMP1545 has two abundant repetitive intron types and a high percent (26 %) GC splice donors. Micromonas has more genus-specific protein families (19 %) than other genome sequenced prasinophytes (11 %). Comparative analyses using predicted proteomes from other prasinophytes reveal proteins likely related to scale formation and ancestral photosynthesis. Our studies also indicate that peptidoglycan (PG) biosynthesis enzymes have been lost in multiple independent events in select prasinophytes and plants. However, CCMP1545, polar Micromonas CCMP2099 and prasinophytes from other classes retain the entire PG pathway, like moss and glaucophyte algae. Surprisingly, multiple vascular plants also have the PG pathway, except the Penicillin-Binding Protein, and share a unique bi-domain protein potentially associated with the pathway. Alongside Micromonas experiments using antibiotics that halt bacterial PG biosynthesis, the findings highlight unrecognized phylogenetic complexity in PG-pathway retention and implicate a role in chloroplast structure or division in several extant Viridiplantae lineages. Conclusions: Extensive differences in gene loss and architecture between related prasinophytes underscore their divergence. ... |
format |
Article in Journal/Newspaper |
author |
van Baren, Marijke J. Bachy, Charles Nahas Reistetter, Emily Purvine, Samuel O. Grimwood, Jane Sudek, Sebastian Yu, Hang Poirier, Camille Deerinck, Thomas J. Kuo, Alan Grigoriev, Igor V. Wong, Chee-Hong Smith, Richard D. Callister, Stephen J. Wei, Chia-Lin Schmutz, Jeremy Worden, Alexandra Z. |
spellingShingle |
van Baren, Marijke J. Bachy, Charles Nahas Reistetter, Emily Purvine, Samuel O. Grimwood, Jane Sudek, Sebastian Yu, Hang Poirier, Camille Deerinck, Thomas J. Kuo, Alan Grigoriev, Igor V. Wong, Chee-Hong Smith, Richard D. Callister, Stephen J. Wei, Chia-Lin Schmutz, Jeremy Worden, Alexandra Z. Evidence-based green algal genomics reveals marine diversity and ancestral characteristics of land plants |
author_facet |
van Baren, Marijke J. Bachy, Charles Nahas Reistetter, Emily Purvine, Samuel O. Grimwood, Jane Sudek, Sebastian Yu, Hang Poirier, Camille Deerinck, Thomas J. Kuo, Alan Grigoriev, Igor V. Wong, Chee-Hong Smith, Richard D. Callister, Stephen J. Wei, Chia-Lin Schmutz, Jeremy Worden, Alexandra Z. |
author_sort |
van Baren, Marijke J. |
title |
Evidence-based green algal genomics reveals marine diversity and ancestral characteristics of land plants |
title_short |
Evidence-based green algal genomics reveals marine diversity and ancestral characteristics of land plants |
title_full |
Evidence-based green algal genomics reveals marine diversity and ancestral characteristics of land plants |
title_fullStr |
Evidence-based green algal genomics reveals marine diversity and ancestral characteristics of land plants |
title_full_unstemmed |
Evidence-based green algal genomics reveals marine diversity and ancestral characteristics of land plants |
title_sort |
evidence-based green algal genomics reveals marine diversity and ancestral characteristics of land plants |
publisher |
BioMed Central |
publishDate |
2016 |
url |
https://authors.library.caltech.edu/65908/ https://authors.library.caltech.edu/65908/1/art%253A10.1186%252Fs12864-016-2585-6.pdf https://authors.library.caltech.edu/65908/2/12864_2016_2585_MOESM1_ESM.xlsx https://authors.library.caltech.edu/65908/3/12864_2016_2585_MOESM2_ESM.pdf https://resolver.caltech.edu/CaltechAUTHORS:20160404-152844868 |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic |
genre_facet |
Arctic |
op_relation |
https://authors.library.caltech.edu/65908/1/art%253A10.1186%252Fs12864-016-2585-6.pdf https://authors.library.caltech.edu/65908/2/12864_2016_2585_MOESM1_ESM.xlsx https://authors.library.caltech.edu/65908/3/12864_2016_2585_MOESM2_ESM.pdf van Baren, Marijke J. and Bachy, Charles and Nahas Reistetter, Emily and Purvine, Samuel O. and Grimwood, Jane and Sudek, Sebastian and Yu, Hang and Poirier, Camille and Deerinck, Thomas J. and Kuo, Alan and Grigoriev, Igor V. and Wong, Chee-Hong and Smith, Richard D. and Callister, Stephen J. and Wei, Chia-Lin and Schmutz, Jeremy and Worden, Alexandra Z. (2016) Evidence-based green algal genomics reveals marine diversity and ancestral characteristics of land plants. BMC Genomics, 17 . Art. No. 267. ISSN 1471-2164. PMCID PMC4815162. doi:10.1186/s12864-016-2585-6. https://resolver.caltech.edu/CaltechAUTHORS:20160404-152844868 <https://resolver.caltech.edu/CaltechAUTHORS:20160404-152844868> |
op_rights |
cc_by cc_public_domain |
op_rightsnorm |
CC-BY PDM |
op_doi |
https://doi.org/10.1186/s12864-016-2585-6 |
container_title |
BMC Genomics |
container_volume |
17 |
container_issue |
1 |
_version_ |
1766343537057595392 |
spelling |
ftcaltechauth:oai:authors.library.caltech.edu:65908 2023-05-15T15:12:55+02:00 Evidence-based green algal genomics reveals marine diversity and ancestral characteristics of land plants van Baren, Marijke J. Bachy, Charles Nahas Reistetter, Emily Purvine, Samuel O. Grimwood, Jane Sudek, Sebastian Yu, Hang Poirier, Camille Deerinck, Thomas J. Kuo, Alan Grigoriev, Igor V. Wong, Chee-Hong Smith, Richard D. Callister, Stephen J. Wei, Chia-Lin Schmutz, Jeremy Worden, Alexandra Z. 2016-03-31 application/pdf application/vnd.ms-excel https://authors.library.caltech.edu/65908/ https://authors.library.caltech.edu/65908/1/art%253A10.1186%252Fs12864-016-2585-6.pdf https://authors.library.caltech.edu/65908/2/12864_2016_2585_MOESM1_ESM.xlsx https://authors.library.caltech.edu/65908/3/12864_2016_2585_MOESM2_ESM.pdf https://resolver.caltech.edu/CaltechAUTHORS:20160404-152844868 en eng BioMed Central https://authors.library.caltech.edu/65908/1/art%253A10.1186%252Fs12864-016-2585-6.pdf https://authors.library.caltech.edu/65908/2/12864_2016_2585_MOESM1_ESM.xlsx https://authors.library.caltech.edu/65908/3/12864_2016_2585_MOESM2_ESM.pdf van Baren, Marijke J. and Bachy, Charles and Nahas Reistetter, Emily and Purvine, Samuel O. and Grimwood, Jane and Sudek, Sebastian and Yu, Hang and Poirier, Camille and Deerinck, Thomas J. and Kuo, Alan and Grigoriev, Igor V. and Wong, Chee-Hong and Smith, Richard D. and Callister, Stephen J. and Wei, Chia-Lin and Schmutz, Jeremy and Worden, Alexandra Z. (2016) Evidence-based green algal genomics reveals marine diversity and ancestral characteristics of land plants. BMC Genomics, 17 . Art. No. 267. ISSN 1471-2164. PMCID PMC4815162. doi:10.1186/s12864-016-2585-6. https://resolver.caltech.edu/CaltechAUTHORS:20160404-152844868 <https://resolver.caltech.edu/CaltechAUTHORS:20160404-152844868> cc_by cc_public_domain CC-BY PDM Article PeerReviewed 2016 ftcaltechauth https://doi.org/10.1186/s12864-016-2585-6 2022-05-12T17:50:43Z Background: Prasinophytes are widespread marine green algae that are related to plants. Cellular abundance of the prasinophyte Micromonas has reportedly increased in the Arctic due to climate-induced changes. Thus, studies of these unicellular eukaryotes are important for marine ecology and for understanding Viridiplantae evolution and diversification. Results: We generated evidence-based Micromonas gene models using proteomics and RNA-Seq to improve prasinophyte genomic resources. First, sequences of four chromosomes in the 22 Mb Micromonas pusilla (CCMP1545) genome were finished. Comparison with the finished 21 Mb genome of Micromonas commoda (RCC299; named herein) shows they share ≤8,141 of ~10,000 protein-encoding genes, depending on the analysis method. Unlike RCC299 and other sequenced eukaryotes, CCMP1545 has two abundant repetitive intron types and a high percent (26 %) GC splice donors. Micromonas has more genus-specific protein families (19 %) than other genome sequenced prasinophytes (11 %). Comparative analyses using predicted proteomes from other prasinophytes reveal proteins likely related to scale formation and ancestral photosynthesis. Our studies also indicate that peptidoglycan (PG) biosynthesis enzymes have been lost in multiple independent events in select prasinophytes and plants. However, CCMP1545, polar Micromonas CCMP2099 and prasinophytes from other classes retain the entire PG pathway, like moss and glaucophyte algae. Surprisingly, multiple vascular plants also have the PG pathway, except the Penicillin-Binding Protein, and share a unique bi-domain protein potentially associated with the pathway. Alongside Micromonas experiments using antibiotics that halt bacterial PG biosynthesis, the findings highlight unrecognized phylogenetic complexity in PG-pathway retention and implicate a role in chloroplast structure or division in several extant Viridiplantae lineages. Conclusions: Extensive differences in gene loss and architecture between related prasinophytes underscore their divergence. ... Article in Journal/Newspaper Arctic Caltech Authors (California Institute of Technology) Arctic BMC Genomics 17 1 |