Abstract
Plant plastomes play crucial roles in species evolution and phylogenetic reconstruction studies due to being maternally inherited and due to the moderate evolutionary rate of genomes. However, patterns of sequence divergence and molecular evolution of the plastid genomes in the horticulturally- and economically-important Lonicera L. species are poorly understood. In this study, we collected the complete plastomes of seven Lonicera species and determined the various repeat sequence variations and protein sequence evolution by comparative genomic analysis. A total of 498 repeats were identified in plastid genomes, which included tandem (130), dispersed (277), and palindromic (91) types of repeat variations. Simple sequence repeat (SSR) elements analysis indicated the enriched SSRs in seven genomes to be mononucleotides, followed by tetra-nucleotides, dinucleotides, tri-nucleotides, hex-nucleotides, and penta-nucleotides. We identified 18 divergence hotspot regions (rps15, rps16, rps18, rpl23, psaJ, infA, ycf1, trnN-GUU-ndhF, rpoC2-rpoC1, rbcL-psaI, trnI-CAU-ycf2, psbZ-trnG-UCC, trnK-UUU-rps16, infA-rps8, rpl14-rpl16, trnV-GAC-rrn16, trnL-UAA intron, and rps12-clpP) that could be used as the potential molecular genetic markers for the further study of population genetics and phylogenetic evolution of Lonicera species. We found that a large number of repeat sequences were distributed in the divergence hotspots of plastid genomes. Interestingly, 16 genes were determined under positive selection, which included four genes for the subunits of ribosome proteins (rps7, rpl2, rpl16, and rpl22), three genes for the subunits of photosystem proteins (psaJ, psbC, and ycf4), three NADH oxidoreductase genes (ndhB, ndhH, and ndhK), two subunits of ATP genes (atpA and atpB), and four other genes (infA, rbcL, ycf1, and ycf2). Phylogenetic analysis based on the whole plastome demonstrated that the seven Lonicera species form a highly-supported monophyletic clade. The availability of these plastid genomes provides important genetic information for further species identification and biological research on Lonicera.
Highlights
The genus Lonicera, which includes approximately 200 species, is a major component of the family Caprifoliaceae, comprising a large number of horticultural and economically important shrubs and tree species [1]
The plastid genomes of seven Lonicera species ranged from 154,513 bp (L. ferdinandi) to 155,545 bp (L. tragophylla) in length (Table 1)
Simple sequence repeat (SSR) elements analysis indicated the enriched SSRs in seven plastomes to be mononucleotides, followed by tetra-nucleotides, dinucleotides, tri-nucleotides, hex-nucleotides, and penta-nucleotides
Summary
The genus Lonicera, which includes approximately 200 species, is a major component of the family Caprifoliaceae, comprising a large number of horticultural and economically important shrubs and tree species [1] These plants are generally distributed in the temperate and subtropical regions of North America, Europe, Asia, and Africa [2], and about 100 Lonicera species are found in China. The phylogenetic analysis based on the nuclear ribosomal internal transcribed spacer (ITS) and five chloroplast DNA regions demonstrated that Lonicera species diverged into two major lineages: Chamaecerasus and Periclymenum [12]. He et al [13] first reported the whole plastid genome sequence of Lonicera japonica. The comparative characteristics of complete plastid genomes and phylogenetic evolution of Lonicera species are still poorly understood
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