The Complete Plastome Sequences of Eleven Capsicum Genotypes: Insights into DNA Variation and Molecular Evolution

Abstract

Members of the genus Capsicum are of great economic importance, including both wild forms and cultivars of peppers and chilies. The high number of potentially informative characteristics that can be identified through next-generation sequencing technologies gave a huge boost to evolutionary and comparative genomic research in higher plants. Here, we determined the complete nucleotide sequences of the plastomes of eight Capsicum species (eleven genotypes), representing the three main taxonomic groups in the genus and estimated molecular diversity. Comparative analyses highlighted a wide spectrum of variation, ranging from point mutations to small/medium size insertions/deletions (InDels), with accD, ndhB, rpl20, ycf1, and ycf2 being the most variable genes. The global pattern of sequence variation is consistent with the phylogenetic signal. Maximum-likelihood tree estimation revealed that Capsicum chacoense is sister to the baccatum complex. Divergence and positive selection analyses unveiled that protein-coding genes were generally well conserved, but we identified 25 positive signatures distributed in six genes involved in different essential plastid functions, suggesting positive selection during evolution of Capsicum plastomes. Finally, the identified sequence variation allowed us to develop simple PCR-based markers useful in future work to discriminate species belonging to different Capsicum complexes.

Comparative analyses of chloroplast genomes from 22 Lythraceae species: inferences for phylogenetic relationships and genome evolution within Myrtales

“…The SSR loci were located in 31 coding genes ( matK , atpI , rpoC2 , rpoB , trnS-UGA , rps14 , psaB , psaA , ndhK , accD , ycf4 , cemA , petA, psaJ, psbB , rpoA , rpl22 , rps19 , rpl2 , ycf2 , rrn23 , ndhF , rpl32 , ccsA , ndhD , ndhA , ycf1 , trnI-GAU , ndhB , ycf2 ) and 57 intergenic regions of the 22 Lythraceae species. Yu et al found 20 SSRs located in 9 coding genes ( matK , rpoC1 , rpoC2 , cemA , ndhD , ndhG , ndhH , ycf2 and ycf1 ) of the Fritillaria cp genome [23]. These results indicate that SSRs with large variation in cp genomes can be applied to identify related species and used in research on phylogeny.…”

“…The genes rpl2 , rpl20 and rpl23 involved in replication, rbcL and psbJ involved in photosynthesis, ycf4 of unknown functions and other genes including ccsA evolved more quickly and had high Ka/Ks (≥1). The seven genes evolved faster among 22 Lythraceae species analyzed were also found in Capsicum and Sesamum indicum species [23, 46]. Some genes are species-specific in terms of the rates of evolution, such as clpP gene.…”

Evolutionary analysis of six chloroplast genomes from three Persea americana ecological races: Insights into sequence divergences and phylogenetic relationships

“…Our previous research on the phylogenetic relationships of the three avocado ecological races based on specific length amplified fragment sequencing [18], transcriptomes examined according to single nucleotide polymorphisms [18], and transcriptomes investigated based on differentially expressed genes [19] revealed that the Mexican and Guatemalan races are more closely related to each other than to the West Indian race. Specific characteristics of chloroplast genome sequences (e.g., uniparental inheritance, low recombination, and low nucleotide substitution rates) make these sequences relevant for resolving the interspecific or intraspecific boundary, and are particularly useful for phylogenetic studies involving diverse species, including Lonicera [20], Nymphaeaceae [21], Ziziphus [22], Capsicum [23], Rosa [24], and Cruciata [25] species. However, chloroplast genomes have not been used for elucidating the phylogenetic relationships among the three avocado ecological races.…”

Allelic Diversity of Acetyl Coenzyme A Carboxylase accD/bccp Genes Implicated in Nuclear-Cytoplasmic Conflict in the Wild and Domesticated Pea (Pisum sp.)

“…The region of the chloroplast genome around the accD gene has been found to be prone to accumulation of repeats, resulting in high interspecific variability in numerous species ( Pisum and Lathyrus [45], Capsicum [54], Glycine [43], Silene [47], Oenothera [55,56], Cupressophytes [57]) but much less variability at the intraspecific level ( Medicago truncatula [44], tea, Camellia sinensis [58], and pea, Pisum sp . [39,40]).…”