One-third of the plastid genes evolved under positive selection in PACMAD grasses

Abstract

We demonstrate that rbcL underwent strong positive selection during the C -C photosynthetic transitions in PACMAD grasses, in particular the 3' end of the gene. In contrast, selective pressures on other plastid genes vary widely and environmental drivers remain to be identified. Plastid genomes have been widely used to infer phylogenetic relationships among plants, but the selective pressures driving their evolution have not been systematically investigated. In our study, we analyse all protein-coding plastid genes from 113 species of PACMAD grasses (Poaceae) to evaluate the selective pressures driving their evolution. Our analyses confirm that the gene encoding the large subunit of RubisCO (rbcL) evolved under strong positive selection after C-C photosynthetic transitions. We highlight new codons in rbcL that underwent parallel changes, in particular those encoding the C-terminal part of the protein. C-C photosynthetic shifts did not significantly affect the evolutionary dynamics of other plastid genes. Instead, while two-third of the plastid genes evolved under purifying selection or neutrality, 25 evolved under positive selection across the PACMAD clade. This set of genes encode for proteins involved in diverse functions, including self-replication of plastids and photosynthesis. Our results suggest that plastid genes widely adapt to changing ecological conditions, but factors driving this evolution largely remain to be identified.

Plastid genomics of Nicotiana (Solanaceae): insights into molecular evolution, positive selection and the origin of the maternal genome of Aztec tobacco (Nicotiana rustica)

“…K a /K s values >1, =1, and <1 indicate positive selection, natural evolution and purifying selection, respectively (Lawrie et al, 2013), while a minimal ratio of K a /K s (<0.5) in many genes represents purifying selection working on them. Many proteins and RNA molecules encoded by the chloroplast genomes are under purifying selection since they are involved in important functions of plant metabolism, self-replication and photosynthesis and therefore play a pivotal role in plant survival (Piot et al, 2018). Departure from the main purifying selection in case of plastid genes might happen in response to certain environmental changes when advantageous genetic mutations might contribute to survival and better adaptation.…”

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).…”

Comparison among the first representative chloroplast genomes ofOrontium, Lasia, Zamioculcas, andStylochaetonof the plant family Araceae: inverted repeat dynamics are not linked to phylogenetic signaling

“…We also found three genes under positive selection in the chloroplast genome of S. bogneri, including ycf2, clpP, and rpl36, which might be due to the different types of stresses faced by these species in their respective ecological niches. These genes were also found to be under positive selection in various other species [11,16,55,66,67].…”

“…The amino acid frequency analyses revealed high encoding of leucine, whereas the rarest encoding was recorded for cysteine ( Figure S1). The RNA editing analyses revealed the presence of [62][63][64][65][66][67][68][69][70][71][72][73][74] RNA editing sites in 19-21 genes (Table S4). The RNA editing sites were found in the same genes with a few exceptions: RNA editing sites were detected in psaB genes of only Z. zamiifolia, whereas the RNA editing site was not found in rpl20 of S. bogneri and rps8 of L.…”

“…We also found three genes under positive selection in the chloroplast genome of S. bogneri, including ycf2, clpP, and rpl36, which might be due to the different types of stresses faced by these species in their respective ecological niches. These genes were also found to be under positive selection in various other species [11,16,55,66,67].This study presents a comparison of the complete chloroplast genomes of four species representing three subfamilies of Araceae including Orontioideae, Lasioideae and Zamioculcadoideae, and the independent taxon S. bogneri. IR contraction and expansion appears to be homoplasious among these taxa, precluding the use of the IR architecture in phylogenetic analyses.…”