Dynamic Evolution of the Chloroplast Genome in the Green Algal Classes Pedinophyceae and Trebouxiophyceae.
Bottom Line: Our results highlight the high propensity of the rDNA-containing large inverted repeat (IR) to vary in size, gene content and gene order as well as the repeated losses it experienced during trebouxiophycean evolution.Most of the 20 IR-less genomes are more rearranged compared with their IR-containing homologs and tend to show an accelerated rate of sequence evolution.Our analyses also unveiled putative cases of gene acquisitions through horizontal transfer.
Affiliation: Département de Biochimie, de Microbiologie et de Bio-Informatique, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Québec, Canada email@example.com.Show MeSH
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Mentions: Considering that six of the eight previously analyzed trebouxiophycean chloroplast genomes featured no large IR (table 1), it was unclear how many times this structure was lost in the Trebouxiophyceae. Here, we found that all three pedinophyceans but less than half of the trebouxiophyceans (15 of 35) feature a large IR that partly encodes the rRNA genes (fig. 1). Mapping of the IR presence/absence on the phylogeny inferred by Lemieux et al. (2014a) reveals seven independent losses of this structure: Two losses in the Chlorellales, two in the Prasiolales, one in the Microthamniales, one in the lineage leading Leptosira, and one in the superclade containing the Trebouxiales, Lobosphaera, Watanabea, Choricystis and Elliptochloris lineages (fig. 8). Considering that the only IR-containing genome in the clade sister to the Parieotochloris lineage (the X. irregularis cpDNA) is very atypical in its gene partitioning pattern (with each SC region containing a number of genes ancestrally located in the SSC and LSC), one could speculate that the Xylochloris IR arose de novo. According to this hypothesis, the abovementioned superclade demarcated by an IR loss would also comprise the Microthamniales and Xylochloris lineages and five IR losses would be required to account for the phylogeny inferred by Lemieux et al. (2014a). This evolutionary scenario may seem unlikely because an IR loss and replacement has not been documented in any viridiplant chloroplast genome. The de novo creation of an IR, however, may also be invoked to account for the unusual 8.3-kb IR that contains no rRNA genes in the prasiolalean S. bacillaris, although the possibility that it represents the remnant of a bona fide rDNA-encoding IR cannot be excluded. To the best of our knowledge, only the plastid of the nonphotosynthetic orchid Rhizanthella gardneri has been reported to carry a reduced IR lacking any rRNA genes (Delannoy et al. 2011).Fig. 8.—
Affiliation: Département de Biochimie, de Microbiologie et de Bio-Informatique, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Québec, Canada firstname.lastname@example.org.