title: Evidence-based green algal genomics reveals marine diversity and ancestral characteristics of land plants.
abstract: 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.
authors.affiliation: Monterey Bay Aquarium Research Institute, 7700 Sandholdt Rd, Moss Landing, CA, 95039, USA.
authors.forename: Marijke J
authors.initials: MJ
authors.lastname: van Baren
authors.affiliation: Monterey Bay Aquarium Research Institute, 7700 Sandholdt Rd, Moss Landing, CA, 95039, USA.
authors.forename: Charles
authors.initials: C
authors.lastname: Bachy
authors.affiliation: Monterey Bay Aquarium Research Institute, 7700 Sandholdt Rd, Moss Landing, CA, 95039, USA.
authors.forename: Emily Nahas
authors.initials: EN
authors.lastname: Reistetter
authors.affiliation: Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
authors.forename: Samuel O
authors.initials: SO
authors.lastname: Purvine
authors.affiliation: U.S. Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, CA, 94598, USA.|Hudson Alpha, 601 Genome Way, Huntsville, AL, 35806, USA.
authors.forename: Jane
authors.initials: J
authors.lastname: Grimwood
authors.affiliation: Monterey Bay Aquarium Research Institute, 7700 Sandholdt Rd, Moss Landing, CA, 95039, USA.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Sudek
authors.affiliation: Monterey Bay Aquarium Research Institute, 7700 Sandholdt Rd, Moss Landing, CA, 95039, USA.|Now at: Ronald and Maxine Linde Center for Global Environmental Science, California Institute of Technology, Pasadena, CA, 91125, USA.
authors.forename: Hang
authors.initials: H
authors.lastname: Yu
authors.affiliation: Monterey Bay Aquarium Research Institute, 7700 Sandholdt Rd, Moss Landing, CA, 95039, USA.
authors.forename: Camille
authors.initials: C
authors.lastname: Poirier
authors.affiliation: Center for Research in Biological Systems and the National Center for Microscopy and Imaging Research, University of California, La Jolla, San Diego, California, 92093, USA.
authors.forename: Thomas J
authors.initials: TJ
authors.lastname: Deerinck
authors.affiliation: U.S. Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, CA, 94598, USA.
authors.forename: Alan
authors.initials: A
authors.lastname: Kuo
authors.affiliation: U.S. Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, CA, 94598, USA.
authors.forename: Igor V
authors.initials: IV
authors.lastname: Grigoriev
authors.affiliation: U.S. Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, CA, 94598, USA.
authors.forename: Chee-Hong
authors.initials: CH
authors.lastname: Wong
authors.affiliation: Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
authors.forename: Richard D
authors.initials: RD
authors.lastname: Smith
authors.affiliation: Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
authors.forename: Stephen J
authors.initials: SJ
authors.lastname: Callister
authors.affiliation: U.S. Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, CA, 94598, USA.
authors.forename: Chia-Lin
authors.initials: CL
authors.lastname: Wei
authors.affiliation: U.S. Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, CA, 94598, USA.|Hudson Alpha, 601 Genome Way, Huntsville, AL, 35806, USA.
authors.forename: Jeremy
authors.initials: J
authors.lastname: Schmutz
authors.affiliation: Monterey Bay Aquarium Research Institute, 7700 Sandholdt Rd, Moss Landing, CA, 95039, USA. azworden@mbari.org.|Integrated Microbial Biodiversity Program, Canadian Institute for Advanced Research, Toronto, M5G 1Z8, Canada. azworden@mbari.org.
authors.forename: Alexandra Z
authors.initials: AZ
authors.lastname: Worden
mesh_terms: D005075:Biological Evolution; D000460:Chlorophyta / Q000235:genetics*; D019669:Embryophyta / Q000235:genetics; D018745:Genome, Plant; D023281:Genomics / Q000379:methods; D007438:Introns; D008957:Models, Genetic; D005810:Multigene Family; D010802:Phylogeny; D020543:Proteome / Q000235:genetics; D048030:RNA, Algal / Q000235:genetics; D017423:Sequence Analysis, RNA; D059467:Transcriptome
chemical_list: D020543:Proteome; D048030:RNA, Algal
keywords: Archaeplastida evolution; Evidence-based gene models; GreenCut; Introner Elements; PPASP; Peptidoglycan; Proteomics; RNA sequencing; Viridiplantae