Evolutionary Mechanisms of Long-Term Genome Diversification Associated With Niche Partitioning in Marine Picocyanobacteria

Abstract

Doré et al. Genome Diversification in Marine Picocyanobacteria variants specific to cold thermotypes, notably involved in carotenoid biosynthesis and the oxidative stress response, revealing that long-term adaptation to thermal niches relies on amino acid substitutions rather than on gene content variation. Altogether, this study not only deciphers the respective roles of gene gains/losses and sequence variation but also uncovers numerous gene candidates likely involved in niche partitioning of two key members of the marine phytoplankton.

Cyanorak v2.1: a scalable information system dedicated to the visualization and expert curation of marine and brackish picocyanobacteria genomes

“…( 22–30 )). In order to preserve at best these preexisting CLOG numbers after the addition of 83 new genomes either retrieved from Genbank or newly sequenced at our initiative (Figure 1 ; ( 9 )), all CDS from the 97 genomes were first clustered using all-against-all BLASTP+ comparison ( 31 ) and the OrthoMCL clustering algorithm ( 32 ) with an e-value threshold of 10 −5 and new CLOGs were then mapped to previously defined Cyanorak v1 CLOGs. New CLOGs containing all sequences from a v1 CLOG plus additional sequences from new genomes as well as manually curated CLOGs were assigned the previous v1 CLOG numbers.…”

“…The 81 non-redundant, high quality genomes used by Doré et al. ( 9 ) for comparative genomics are indicated by a circle surrounding the tree and among them the 14 first genomes used in the previous version of Cyanorak (v1) are shown as empty circles.…”

“…Paralogs were moved into different CLOGs when they grouped together into different branches as the bona fide orthologs. In order to refine assessment of the core genome ( 9 ), >1750 genes missed by gene prediction software tools, either because they were too short (e.g. petM , psbM ) or partially overlapping with other genes notably in the case of long 3′-3′ overlaps (e.g.…”

“…conceived to allow addition of more genomes. The current database encompasses 95 genomes and two metagenome-assembled genomes (MAGs), including 31 newly released Synechococcus and Cyanobium genomes ( 9 ), which have been closed using a custom-designed assembly and scaffolding pipeline ( 10 ). All strains whose genomes have been included in the Cyanorak v2.1 database belong to Cyanobacteria Subsection I, Cluster 5 sensu Herdman ( 11 ), a short-rod shaped group that forms a deep monophyletic branch within this ancient phylum ( 12 ).…”

“…Marinosynechococcus (SC 5.1), Cyanobium (SC 5.2) and Ca . Juxtasynechococcus (SC 5.3) ( 9 ). SC 5.1 is the most diversified of all these lineages, with about 10 phylogenetically distinct clades based on 16S rDNA phylogeny ( 16 ) and 11 to 16 using higher resolution markers ( 17 , 18 ).…”