Evidence-based green algal genomics reveals marine diversity and ancestral characteristics of land plants.
BackgroundPrasinophytes 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 unders...
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ftcdlib:oai:escholarship.org/ark:/13030/qt4n11p2r6 2023-05-15T15:18:47+02:00 Evidence-based green algal genomics reveals marine diversity and ancestral characteristics of land plants. van Baren, Marijke J Bachy, Charles Reistetter, Emily Nahas 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 267 2016-03-31 application/pdf https://escholarship.org/uc/item/4n11p2r6 unknown eScholarship, University of California qt4n11p2r6 https://escholarship.org/uc/item/4n11p2r6 public BMC genomics, vol 17, iss 1 Proteome RNA Algal Sequence Analysis Genomics Phylogeny Genome Plant Multigene Family Introns Models Genetic Chlorophyta Biological Evolution Embryophyta Transcriptome Archaeplastida evolution Evidence-based gene models GreenCut Introner Elements PPASP Peptidoglycan Proteomics RNA sequencing Viridiplantae Biotechnology Human Genome Genetics Generic Health Relevance Bioinformatics Biological Sciences Medical and Health Sciences Information and Computing Sciences article 2016 ftcdlib 2021-02-18T15:15:10Z BackgroundPrasinophytes 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.ResultsWe 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.ConclusionsExtensive 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 |
institution |
Open Polar |
collection |
University of California: eScholarship |
op_collection_id |
ftcdlib |
language |
unknown |
topic |
Proteome RNA Algal Sequence Analysis Genomics Phylogeny Genome Plant Multigene Family Introns Models Genetic Chlorophyta Biological Evolution Embryophyta Transcriptome Archaeplastida evolution Evidence-based gene models GreenCut Introner Elements PPASP Peptidoglycan Proteomics RNA sequencing Viridiplantae Biotechnology Human Genome Genetics Generic Health Relevance Bioinformatics Biological Sciences Medical and Health Sciences Information and Computing Sciences |
spellingShingle |
Proteome RNA Algal Sequence Analysis Genomics Phylogeny Genome Plant Multigene Family Introns Models Genetic Chlorophyta Biological Evolution Embryophyta Transcriptome Archaeplastida evolution Evidence-based gene models GreenCut Introner Elements PPASP Peptidoglycan Proteomics RNA sequencing Viridiplantae Biotechnology Human Genome Genetics Generic Health Relevance Bioinformatics Biological Sciences Medical and Health Sciences Information and Computing Sciences van Baren, Marijke J Bachy, Charles Reistetter, Emily Nahas 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. |
topic_facet |
Proteome RNA Algal Sequence Analysis Genomics Phylogeny Genome Plant Multigene Family Introns Models Genetic Chlorophyta Biological Evolution Embryophyta Transcriptome Archaeplastida evolution Evidence-based gene models GreenCut Introner Elements PPASP Peptidoglycan Proteomics RNA sequencing Viridiplantae Biotechnology Human Genome Genetics Generic Health Relevance Bioinformatics Biological Sciences Medical and Health Sciences Information and Computing Sciences |
description |
BackgroundPrasinophytes 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.ResultsWe 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.ConclusionsExtensive 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, Marijke J Bachy, Charles Reistetter, Emily Nahas 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_facet |
van Baren, Marijke J Bachy, Charles Reistetter, Emily Nahas 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 |
eScholarship, University of California |
publishDate |
2016 |
url |
https://escholarship.org/uc/item/4n11p2r6 |
op_coverage |
267 |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic Phytoplankton |
genre_facet |
Arctic Phytoplankton |
op_source |
BMC genomics, vol 17, iss 1 |
op_relation |
qt4n11p2r6 https://escholarship.org/uc/item/4n11p2r6 |
op_rights |
public |
_version_ |
1766348968810250240 |