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

Abstract

Background: Bathycoccus 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.

Research: Its 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.

Conclusion: The minimal genomes of the Mamiellophyceae provide a baseline for evolutionary and functional analyses of metabolic processes in green plants.

Figure 1

Morphology of the Bathycoccus prasinos RCC1105 strain. Morphological characterization of the Bathycoccus RCC1105 strain: EM picture of an exponentially growing Bathycoccus RCC1105 cell. Abbreviations: c, chloroplast; n, nucleus; s, starch granule; sc, scale covering the surface of the cell.

Figure 2

Genome organization of the Bathycoccus prasinos RCC1105 strain. (a) Pulse field electrophoresis of the genomes of Bathycoccus prasinos RCC1105 (lane 1), Micromonas pussilla (lane 2) and Ostreococcus tauri (lane 3) DNA fragment length based on the chromosomes of Saccharomyces cerevisiae (lane 4). (b) Synteny between Ostreococcus lucimarinus (blue) and Bathycoccus prasinos RCC1105 (grey) genomes.

Figure 3

Integrative and comparative view of the Bathycoccus genome showing both structural (GC content, introns, colinearity) and functional characteristics (gene expression, conservation). 'Slice' represents a single chromosome or region drawn using one gene per unit. 'Introns' and 'Gene Expression' denote the number of introns and uniquely mapped ESTs per gene, respectively. To improve legibility, an upper limit was set for the EST and intron count per gene by removing the top 2%, resulting in a threshold of 12 and 13 for intron count and gene expression, respectively. The GC content is plotted using a window size of 500 bp. The 'Annotation' track represents specific chromosomes or regions denoted by the different grey boxes; BOC and SOC refer to big and small outlier chromosome, respectively. 'Conservation' represents, for each gene, the number of Mamiellales species in which a BLAST hit can be found (E-value threshold 1e-05; range 0 to 5 species). 'Colinearity' shows for each gene if it resides in a genomic region showing colinearity with another Mamiellales species. The circle plot was drawn using the Circos circular visualization software [67].

Figure 4

Distribution of the Bathycoccus BOC1 orthologous genes in the genome of several other green alga species. (a-d) Bathycoccus BOC1 orthologous genes in the genomes of Ostreococcus tauri (a), Micromonas sp. RCC299 (b), Chlamydomonas reinhardtii (c) and Coccomyxa sp. C-169 (d), each peripheral bar representing a chromosome. The Bathycoccus BOC1 region genes (lower right corner, labeled as 'Bathy_BOC1') are connected by red lines to their orthologs (curated as best BLAST hits) on the chromosomes of other species. Where a Bathycoccus gene also represents a BOC1 Mamiellales core gene (Table 3), the link is colored blue. Green bars show the BOC1 regions in Bathycoccus, Micromonas and Ostreococcus. The Micromonas sp. RCC299 region showing partial clustering of BOC1 orthologs lacks typical BOC1 features. This region has high GC content (66%), is not enriched for a high intron content and does not group highly expressed genes (Table S4 in Additional file 1). For the sake of legibility, all small scaffolds of Chlamydomonas reinhardtii that harbored a Bathycoccus BOC1 orthologous gene were joined together into a virtual chromosome 00 (scaffolds 19, 20, 22, 23, 24, 26 and 32).

Figure 5

Potential horizontal gene transfer in Bathycoccus. (a) Taxonomic distribution of horizontal gene transfer (HGT) genes identified using BLAST and by phylogenetic analysis of each gene (excluding genes with a multi-kingdom punctuate distribution). Only taxonomic groups including multiple genes are displayed (for a complete overview, see Table S5 in Additional file 1). (b) Frequency of 428 HGT genes over the different chromosomes. The last bin reports the fraction of HGT genes in the BOC1 region (a subset of chromosome 14).

Figure 6

Sialyltransferase gene family and external scales covering Bathycoccus. (a) Structural organization of the Bathycoccus RCC1105 sialyltransferase gene family. TM, transmembrane domain. L(1), S(2), (3) and VS(4) correspond to the four metazoan consensus motifs described for this gene family [43,44]. Letters in the scheme below are the amino acid one-letter code with alternative possibilities for positions indicated between brackets. (b-d) Details of external scales covering Bathycoccus RCC1105 cells; white arrows indicate positions of external scales around the plasmic membrane while the black arrow indicates one intracellular scale inside a vesicle.