Evidence-based green algal genomics reveals marine diversity and ancestral characteristics of land plants
© 2016 van Baren et al. 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 mar...
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ftcdlib:qt4n11p2r6 2023-05-15T15:15:33+02:00 Evidence-based green algal genomics reveals marine diversity and ancestral characteristics of land plants van Baren, MJ Bachy, C Reistetter, EN Purvine, SO Grimwood, J Sudek, S Yu, H Poirier, C Deerinck, TJ Kuo, A Grigoriev, IV Wong, CH Smith, RD Callister, SJ Wei, CL Schmutz, J Worden, AZ 2016-01-01 application/pdf http://www.escholarship.org/uc/item/4n11p2r6 english eng eScholarship, University of California qt4n11p2r6 http://www.escholarship.org/uc/item/4n11p2r6 public van Baren, MJ; Bachy, C; Reistetter, EN; Purvine, SO; Grimwood, J; Sudek, S; et al.(2016). Evidence-based green algal genomics reveals marine diversity and ancestral characteristics of land plants. BMC Genomics, 17(1). doi:10.1186/s12864-016-2585-6. Lawrence Berkeley National Laboratory: Retrieved from: http://www.escholarship.org/uc/item/4n11p2r6 article 2016 ftcdlib https://doi.org/10.1186/s12864-016-2585-6 2018-07-13T22:56:03Z © 2016 van Baren et al. 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. PG biosynthesis genes from the cyanobacterial endosymbiont that became the plastid, have been selectively retained in multiple plants and algae, implying a biological function. Our studies provide robust genomic resources for emerging model algae, advancing knowledge of marine phytoplankton and plant evolution. Article in Journal/Newspaper Arctic Phytoplankton University of California: eScholarship Arctic BMC Genomics 17 1 |
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Open Polar |
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University of California: eScholarship |
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© 2016 van Baren et al. 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. PG biosynthesis genes from the cyanobacterial endosymbiont that became the plastid, have been selectively retained in multiple plants and algae, implying a biological function. Our studies provide robust genomic resources for emerging model algae, advancing knowledge of marine phytoplankton and plant evolution. |
format |
Article in Journal/Newspaper |
author |
van Baren, MJ Bachy, C Reistetter, EN Purvine, SO Grimwood, J Sudek, S Yu, H Poirier, C Deerinck, TJ Kuo, A Grigoriev, IV Wong, CH Smith, RD Callister, SJ Wei, CL Schmutz, J Worden, AZ |
spellingShingle |
van Baren, MJ Bachy, C Reistetter, EN Purvine, SO Grimwood, J Sudek, S Yu, H Poirier, C Deerinck, TJ Kuo, A Grigoriev, IV Wong, CH Smith, RD Callister, SJ Wei, CL Schmutz, J Worden, AZ Evidence-based green algal genomics reveals marine diversity and ancestral characteristics of land plants |
author_facet |
van Baren, MJ Bachy, C Reistetter, EN Purvine, SO Grimwood, J Sudek, S Yu, H Poirier, C Deerinck, TJ Kuo, A Grigoriev, IV Wong, CH Smith, RD Callister, SJ Wei, CL Schmutz, J Worden, AZ |
author_sort |
van Baren, MJ |
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 |
eScholarship, University of California |
publishDate |
2016 |
url |
http://www.escholarship.org/uc/item/4n11p2r6 |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic Phytoplankton |
genre_facet |
Arctic Phytoplankton |
op_source |
van Baren, MJ; Bachy, C; Reistetter, EN; Purvine, SO; Grimwood, J; Sudek, S; et al.(2016). Evidence-based green algal genomics reveals marine diversity and ancestral characteristics of land plants. BMC Genomics, 17(1). doi:10.1186/s12864-016-2585-6. Lawrence Berkeley National Laboratory: Retrieved from: http://www.escholarship.org/uc/item/4n11p2r6 |
op_relation |
qt4n11p2r6 http://www.escholarship.org/uc/item/4n11p2r6 |
op_rights |
public |
op_doi |
https://doi.org/10.1186/s12864-016-2585-6 |
container_title |
BMC Genomics |
container_volume |
17 |
container_issue |
1 |
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1766345919845892096 |