Gene functionalities and genome structure in Bathycoccus prasinos reflect cellular specializations at the base of the green lineage

Abstract

BackgroundBathycoccus prasinos is an extremely small cosmopolitan marine green alga whose cells are covered with intricate spider's web patterned scales that develop within the Golgi cisternae before their transport to the cell surface. The objective of this work is to sequence and analyze its genome, and to present a comparative analysis with other known genomes of the green lineage.ResearchIts small genome of 15 Mb consists of 19 chromosomes and lacks transposons. Although 70% of all B. prasinos genes share similarities with other Viridiplantae genes, up to 428 genes were probably acquired by horizontal gene transfer, mainly from other eukaryotes. Two chromosomes, one big and one small, are atypical, an unusual synapomorphic feature within the Mamiellales. Genes on these atypical outlier chromosomes show lower GC content and a significant fraction of putative horizontal gene transfer genes. Whereas the small outlier chromosome lacks colinearity with other Mamiellales and contains many unknown genes without homologs in other species, the big outlier shows a higher intron content, increased expression levels and a unique clustering pattern of housekeeping functionalities. Four gene families are highly expanded in B. prasinos, including sialyltransferases, sialidases, ankyrin repeats and zinc ion-binding genes, and we hypothesize that these genes are associated with the process of scale biogenesis.ConclusionThe minimal genomes of the Mamiellophyceae provide a baseline for evolutionary and functional analyses of metabolic processes in green plants.

Agrigenomics for Microalgal Biofuel Production: An Overview of Various Bioinformatics Resources and Recent Studies to Link OMICS to Bioenergy and Bioeconomy

“…To date, the whole genome sequences of more than ten microalgae have been generated (Guarnieri et al, 2011;Liu and Benning, 2012;) (Table 1). These includes the Cyanidioschyzon merolae 10D (Matsuzaki et al, 2004), Phaeodactylum tricornutum CCP1055/1 , Thalassiosira pseudonana CCMP1335 (Armbrust et al, 2004), Guillardia theta CCMP2712 (Curtis et al, 2012), Chlamydomonas reinhardtii CC-503 (Merchant et al, 2007), Ostreococcus tauri OTH95 (Derelle et al, 2006), Ostreococcus lucimarinus CCE9901 (Palenik et al, 2007), two strains of Micromonas pusilla, RCC299 and CCMP1545 (Worden et al, 2009), Bathycoccus prasinos RCC1105 (Moreau et al, 2012), Volvox carteri UTEX2908 (Prochnik et al, 2010), Chlorella vulgaris NC64A (Blanc et al, 2010), Coccomyxa subellipsoidea C-169 (Blanc et al, 2012), Ectocarpus siliculosus EC32 (Cock et al, 2010), Aureococcus anophagefferens CCMP1984 (Gobler et al, 2011), Nannochloropsis gaditana (Radakovits et al, 2012), and Bigelowiella natans CCMP2755 (Curtis et al, 2012). Other algal genomes in the sequencing pipeline are Ostreococcus sp RCC809, Botryococcus braunii Berkeley strain, Dunaliella salina CCAP19/18, Galdieria sulphuraria, Chondrus crispus, Fragilariopsis cylindrus CCMP1102, Pseudo-nitzchia multiseries CLN-47, Emiliana huxleyi CCMP1516 (Radakovits et al, 2010;Tirichine and Bowler, 2011).…”

Diversity and oceanic distribution of prasinophytes clade VII, the dominant group of green algae in oceanic waters

“…The genus Micromonas can be dominant in Arctic ecosystems (Lovejoy et al, 2007;Balzano et al, 2012). Members of these three genera are easily isolated into cultures and genome sequences from representative strains are available (Derelle et al, 2006;Worden et al, 2009;Moreau et al, 2012), fostering their use as biological models for marine photosynthetic eukaryotes.…”

Algal photoreceptors: in vivo functions and potential applications

“…During evolution, these organisms also developed diverse light-sensitive proteins, so-called photoreceptors, and the corresponding signaling pathways for algal model systems with available genome and transcriptome information are Chlamydomonas reinhardtii (C. reinhardtii) , Volvox carteri (V. carteri) (Prochnik et al 2010), Phaeodactylum tricornutum (Bowler et al 2008), Ostreococcus tauri (Derelle et al 2006), Ostreococcus lucimarinus (Palenik et al 2007), Thalassiosira pseudonana (Armbrust et al 2004), Cyanidioschyzon merolae (Matsuzaki et al 2004), Nannochloropsis (Radakovits et al 2012;Vieler et al 2012), Bathycoccus prasinos (Moreau et al 2012) and Coccomyxa subellipsoidea (Blanc et al 2012). The production of additional genome and transcriptome data of the algae Haematococcus pluvialis, Gonium pectorale, Eudorina elegans and Pleodorina starii ( Fig.…”