Evidence-based green algal genomics reveals marine diversity and ancestral characteristics of land plants

Journal Article · Thu Mar 31 00:00:00 EDT 2016 · BMC Genomics

DOI:https://doi.org/10.1186/s12864-016-2585-6· OSTI ID:1618541

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.

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

• Research Organization: Pacific Northwest National Laboratory (PNNL), Richland, WA (United States). Environmental Molecular Sciences Laboratory (EMSL); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
• Sponsoring Organization: USDOE Office of Science (SC), Biological and Environmental Research (BER)
• Grant/Contract Number: SC0004765; AC05-76RL01830; AC02-05CH11231
• OSTI ID: 1618541
• Alternate ID(s): OSTI ID: 1337274; OSTI ID: 1615262
• Report Number(s): PNNL-SA-114561; 267; PII: 2585
• Journal Information: BMC Genomics, Journal Name: BMC Genomics Vol. 17 Journal Issue: 1; ISSN 1471-2164
• Publisher: Springer
• Country of Publication: United Kingdom
• Language: English

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
Environmental Molecular Sciences Laboratory
GreenCut
Archaeplastida evolution
Viridiplantae
Introner Elements
RNA sequencing
Proteomics
Evidence-based gene models
Peptidoglycan
PPASP