Chloroplast genomes of Arabidopsis halleri ssp. gemmifera and Arabidopsis lyrata ssp. petraea: Structures and comparative analysis

Abstract

We investigated the complete chloroplast (cp) genomes of non-model Arabidopsis halleri ssp. gemmifera and Arabidopsis lyrata ssp. petraea using Illumina paired-end sequencing to understand their genetic organization and structure. Detailed bioinformatics analysis revealed genome sizes of both subspecies ranging between 154.4~154.5 kbp, with a large single-copy region (84,197~84,158 bp), a small single-copy region (17,738~17,813 bp) and pair of inverted repeats (IRa/IRb; 26,264~26,259 bp). Both cp genomes encode 130 genes, including 85 protein-coding genes, eight ribosomal RNA genes and 37 transfer RNA genes. Whole cp genome comparison of A. halleri ssp. gemmifera and A. lyrata ssp. petraea, along with ten other Arabidopsis species, showed an overall high degree of sequence similarity, with divergence among some intergenic spacers. The location and distribution of repeat sequences were determined, and sequence divergences of shared genes were calculated among related species. Comparative phylogenetic analysis of the entire genomic data set and 70 shared genes between both cp genomes confirmed the previous phylogeny and generated phylogenetic trees with the same topologies. The sister species of A. halleri ssp. gemmifera is A. umezawana, whereas the closest relative of A. lyrata spp. petraea is A. arenicola.

Integrated analysis of four new sequenced fern Chloroplast Genomes: Genome structure and Comparative Analysis

“…Similar result was also reported in chloroplast genome of higher plant, which demonstrated that the lower sequence divergence in IR regions was possibly owing to copy correction between IR sequences by gene conversion when compared with SSC and LSC regions [41]. Moreover, some previous reports revealed that LSC region contains most of the divergent genes, and display a trend towards more rapid evolution [29,32]. The divergent regions included rpoC2, rpoB, psbC, pasA, rbcL, ycf2, ycf1 and ndhB in this study, as reported previously [32].…”

“…The genomes of these four ferns chloroplast exhibit a typical quadripartite structure, including LSC, SSC and two IRs, as reported in other spore plants [27,28]. Additionally, the gene number and order were largely similar with other ferns, but there were still some differences among species, which should let the length variation in the IR and SSC regions take the responsibility [29]. We compared the chloroplast genomes of D. crassirhizoma, D. goeringiana and D. fragrans [26], and found a genomes loss of 4033 bp in D. fragrans, which caused a longest SSC and shorter IRs.…”

“…They demonstrated that ycf2, rpoB, clpP and ndhF encoded four, three, two and two introns, respectively. As reported in other angiosperm cp genomes [29,33], rps12 is a coding unequally divided gene with its 5' terminal exon located in the LSC region, while two copies of the 3' terminal exon and intron are in IRs.…”

Comparative Chloroplast Genomics of Four Pilea Species (Urticaceae): High Levels of Sequences Divergence Provides New Insight into Interspecific Diversity in Pilea

“…The overlapping areas are 108 bp. These results are also observed in Arabidopsis, the overlaps are about 30 bp [32]. Whether or not these overlaps affect the transcription or translation of these proteins is also an interesting subject.…”

Complete Chloroplast Genome Sequence and Phylogenetic Analysis of Quercus bawanglingensis Huang, Li et Xing, a Vulnerable Oak Tree in China

“…cpSSRs, which are typical uniparentally inherited material, have been used extensively in analyses of taxonomic status, phylogenetic relationships, the maternal structure of the community, diversity and differentiation [92][93][94]. SSR polymorphisms result from a mutational mechanism in which SSRs with a length of at least 10 bp appear as slipped-strand mispairings [95]. We found 82 SSRs in the Q. bawanglingensis cp genome that were mostly distributed in the LSC (62, 75.61%) and intergenic spaces (64, 78.04%).…”