Plastome organization and evolution of chloroplast genes in Cardamine species adapted to contrasting habitats

Abstract

BackgroundPlastid genomes, also known as plastomes, are shaped by the selective forces acting on the fundamental cellular functions they code for and thus they are expected to preserve signatures of the adaptive path undertaken by different plant species during evolution. To identify molecular signatures of positive selection associated to adaptation to contrasting ecological niches, we sequenced with Solexa technology the plastomes of two congeneric Brassicaceae species with different habitat preference, Cardamine resedifolia and Cardamine impatiens.ResultsFollowing in-depth characterization of plastome organization, repeat patterns and gene space, the comparison of the newly sequenced plastomes between each other and with 15 fully sequenced Brassicaceae plastomes publically available in GenBank uncovered dynamic variation of the IR boundaries in the Cardamine lineage. We further detected signatures of positive selection in ten of the 75 protein-coding genes of the examined plastomes, identifying a range of chloroplast functions putatively involved in adaptive processes within the family. For instance, the three residues found to be under positive selection in RUBISCO could possibly be involved in the modulation of RUBISCO aggregation/activation and enzymatic specificty in Brassicaceae. In addition, our results points to differential evolutionary rates in Cardamine plastomes.ConclusionsOverall our results support the existence of wider signatures of positive selection in the plastome of C. resedifolia, possibly as a consequence of adaptation to high altitude environments. We further provide a first characterization of the selective patterns shaping the Brassicaceae plastomes, which could help elucidate the driving forces underlying adaptation and evolution in this important plant family.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1498-0) contains supplementary material, which is available to authorized users.

Species Delimitation and Interspecific Relationships of the Genus Orychophragmus (Brassicaceae) Inferred from Whole Chloroplast Genomes

“…The gene ycf 1 was crossed at the junction of IRb/SSC and SSC/IRa, leading to incomplete duplication of the protein-coding gene within IRs (Figure 1). The overall GC contents of cpDNA ranged from 36.28 to 36.35% (Table 1), suggesting that the AT-rich contents of this genus are similar to other Brassicaceae plastid genomes sequenced so far (Hu S. L. et al, 2015). In general, the genome features of six species were found to be quite similar in gene content, gene order, introns, intergenic spacers, and AT content.…”

Insights into chloroplast genome variation across Opuntioideae (Cactaceae)

“…Several regions highlighted as hyper or moderately variable regarding the nucleotide diversity values across Opuntioideae chloroplast sequences (i.e., accD, ycf1, clpP, petD, rpl32 and ccsA) have been reported to be putatively under positive selection in some lineages, such as Brassicaceae, Bignoniaceae, Rutaceae, Orchidaceae, Geraniaceae and Poaceae (Hu et al 2015;Weng et al 2016;Dong et al 2018;Carbonell-Caballero et al 2015;Ruhlman and Jansen 2018;Thode & Lohmann 2019;Park et al 2017;Piot et al 2018). Positive selection may come into play in response to environmental changes (Piot et al 2018).…”

“…For example, the accD gene, which encodes the β -carboxyl transferase subunit of acetyl-CoA carboxylase, is an essential and required component for plant leaf development (Kode et al 200), and it is suggested to have played a pivotal role in the adaptive evolution of orchids (Dong et al 2018). The signatures of positive selection under accD gene observed in Brassicaceae and Campanulaceae have also indicated that this gene may have been repeatedly involved in the adaption to specific ecological niches during the radiation of eudicotyledonous plants (Rousseau-Gueutin et al 2013;Hu et al 2015). Considering the harsh environment that cacti display their fitness already expressed in its peculiar morphology and physiology, further studies should be carried to investigate the putative relation of chloroplast rearrangement -such as pseudogenization, loss of genes, translocation and inversion -with ecological features.…”

Interspecific plastome recombination reflects ancient reticulate evolution inPicea(Pinaceae)

“…In contrast, ycf1 is exceptionally divergent across land plants (Dong et al 2015) and shows elevated ω in some angiosperm lineages (e.g. Hu et al 2015). Surprisingly, ycf1…”