Chloroplast genome sequence of Chongming lima bean (Phaseolus lunatus L.) and comparative analyses with other legume chloroplast genomes

Abstract

Background Lima bean (Phaseolus lunatus L.) is a member of subfamily Phaseolinae belonging to the family Leguminosae and an important source of plant proteins for the human diet. As we all know, lima beans have important economic value and great diversity. However, our knowledge of the chloroplast genome level of lima beans is limited. Results The chloroplast genome of lima bean was obtained by Illumina sequencing technology for the first time. The Cp genome with a length of 150,902 bp, including a pair of inverted repeats (IRA and IRB 26543 bp each), a large single-copy (LSC 80218 bp) and a small single-copy region (SSC 17598 bp). In total, 124 unique genes including 82 protein-coding genes, 34 tRNA genes, and 8 rRNA genes were identified in the P. lunatus Cp genome. A total of 61 long repeats and 290 SSRs were detected in the lima bean Cp genome. It has a typical 50 kb inversion of the Leguminosae family and an 70 kb inversion to subtribe Phaseolinae. rpl16, accD, petB, rsp16, clpP, ndhA, ndhF and ycf1 genes in coding regions was found significant variation, the intergenic regions of trnk-rbcL, rbcL-atpB, ndhJ-rps4, psbD-rpoB, atpI-atpA, atpA-accD, accD-psbJ, psbE-psbB, rsp11-rsp19, ndhF-ccsA was found in a high degree of divergence. A phylogenetic analysis showed that P. lunatus appears to be more closely related to P. vulgaris, V.unguiculata and V. radiata. Conclusions The characteristics of the lima bean Cp genome was identified for the first time, these results will provide useful insights for species identification, evolutionary studies and molecular biology research.

Comparative Analysis of Complete Chloroplast Genomes of Nine Species of Litsea (Lauraceae): Hypervariable Regions, Positive Selection, and Phylogenetic Relationships

“…This might suggest that the rpl16 gene went through a great mutation that was crucial to the evolution process of Litsea species. Although studies have reported rpl16 to be one of the highly divergent genes [ 59 ] and a positive selection site [ 60 ], as unique and significant as the present study is this is not a common in studies of other angiosperms. The other positive selection site, the ycf2 gene, was more commonly described in previous studies [ 61 , 62 ].…”

Complete Chloroplast Genome Sequence of Fagus longipetiolata Seemen (Fagaceae): Genome Structure, Adaptive Evolution, and Phylogenetic Relationships

“…However, in the three control groups, the Ka/Ks ratios of the ndhD, rpoA, and ndhF genes were greater than one, which showed that the three genes of F. longipetiolata were positively selected to adapt to the living environment. Positive selection of ndhD (Pterocarpus and Leguminosae) [50,72], rpoA (Trifolium alexandrinum and Trifolium resupinatum), and ndhF (T. alexandrinum, T. resupinatum and Cardamine genus) [73,74] genes has also been reported in previous studies. It is also reported that NADPH dehydrogenase genes (ndhD and ndhA) tend to evolve at a higher rate than other genes [75].…”

Comparative analyses of chloroplast genomes from Six Rhodiola species: variable DNA markers identification and phylogenetic relationships within the genus

“…the cp genome of R. gelida, reflecting the fact that Rhodiola chloroplast genomes exhibited a significant difference in type, length and number of repeats. Chloroplast SSR markers are efficient genetic resources to investigate population genetics and biogeography of closely related taxa due to their relatively richness, high reproducibility and polymorphism [38,39]. Wang et al used 11 ISSR primers to reveal the interspecific or intraspecific genetic differences and diversity of four Rhodiola species [9].In our study, A and T nucleotides were the most common, while tandem G or C repeats were quite rare (Fig.…”