Comparative Chloroplast Genomics of Gossypium Species: Insights Into Repeat Sequence Variations and Phylogeny

Abstract

Cotton is one of the most economically important fiber crop plants worldwide. The genus Gossypium contains a single allotetraploid group (AD) and eight diploid genome groups (A–G and K). However, the evolution of repeat sequences in the chloroplast genomes and the phylogenetic relationships of Gossypium species are unclear. Thus, we determined the variations in the repeat sequences and the evolutionary relationships of 40 cotton chloroplast genomes, which represented the most diverse in the genus, including five newly sequenced diploid species, i.e., G. nandewarense (C1-n), G. armourianum (D2-1), G. lobatum (D7), G. trilobum (D8), and G. schwendimanii (D11), and an important semi-wild race of upland cotton, G. hirsutum race latifolium (AD1). The genome structure, gene order, and GC content of cotton species were similar to those of other higher plant plastid genomes. In total, 2860 long sequence repeats (>10 bp in length) were identified, where the F-genome species had the largest number of repeats (G. longicalyx F1: 108) and E-genome species had the lowest (G. stocksii E1: 53). Large-scale repeat sequences possibly enrich the genetic information and maintain genome stability in cotton species. We also identified 10 divergence hotspot regions, i.e., rpl33-rps18, psbZ-trnG (GCC), rps4-trnT (UGU), trnL (UAG)-rpl32, trnE (UUC)-trnT (GGU), atpE, ndhI, rps2, ycf1, and ndhF, which could be useful molecular genetic markers for future population genetics and phylogenetic studies. Site-specific selection analysis showed that some of the coding sites of 10 chloroplast genes (atpB, atpE, rps2, rps3, petB, petD, ccsA, cemA, ycf1, and rbcL) were under protein sequence evolution. Phylogenetic analysis based on the whole plastomes suggested that the Gossypium species grouped into six previously identified genetic clades. Interestingly, all 13 D-genome species clustered into a strong monophyletic clade. Unexpectedly, the cotton species with C, G, and K-genomes were admixed and nested in a large clade, which could have been due to their recent radiation, incomplete lineage sorting, and introgression hybridization among different cotton lineages. In conclusion, the results of this study provide new insights into the evolution of repeat sequences in chloroplast genomes and interspecific relationships in the genus Gossypium.

Complete chloroplast genomes of Liliaceae (s.l.) species: comparative genomic and phylogenetic analyses

“…Most SSRs consisted of mono-and di-nucleotide repeats, followed by tri-, tetra-and penta-nucleotide repeat sequences, while no hexo-nucleotide repeats were found (Table 3). The plastid genome size and divergence may result in differences in the number of repeat sequences and SSRs (Wu et al 2018). Meanwhile, high variation in mutational hotspots was revealed in our analyses.…”

“…We identified 1153 SSRs in the seventeen Liliaceae species. The plastid genome size and divergence may result in differences in the number of repeat sequences and SSRs (Wu et al 2018). Most SSRs consisted of mono-and di-nucleotide repeats, followed by tri-, tetra-and penta-nucleotide repeat sequences, while no hexo-nucleotide repeats were found (Table 3).…”

Exploring evolution characteristic between cultivated tea and its wild relatives using complete chloroplast genomes

“…These positively selected genes may have played key roles in the adaptation of cultivated tea to various environments. Generally, the deletion or insertion of amino acids and bases in the coding protein gene will affect the structure and function of this gene [38][39][40]. In our study, 16 protein coding genes have nucleotide substitutions, among which ycf1 gene has the largest number of nucleotide substitution.…”

Comparison of the complete plastomes and the phylogenetic analysis of Paulownia species

“…In many other groups, multiple chloroplast genes show a positive selection effect. One-third of the chloroplast genes in PACMAD grasses, 27 genes in the genus Iodes, 19 genes in Dipsacales species, and 10 genes in Gossypium evolved under positive selection 25,32,38,39 . Those identified selected genes may be underwent certain functional diversification during their evolutionary history.…”

“…Among the selected chloroplast genes in Paulownia, the rbcL gene encodes the large subunit of RuBisCO, which plays an important role in plant photosynthesis. Previous studies showed that rbcL is often under positive selection because of being the target of selection in relation to the changes in temperature, drought and carbon dioxide concentration 24,30,32,39 . So, the rbcL gene could be a positively selected site during the evolutionary process of Paulownia.…”