Insights from the Complete Chloroplast Genome into the Evolution of Sesamum indicum L

Abstract

Sesame (Sesamum indicum L.) is one of the oldest oilseed crops. In order to investigate the evolutionary characters according to the Sesame Genome Project, apart from sequencing its nuclear genome, we sequenced the complete chloroplast genome of S. indicum cv. Yuzhi 11 (white seeded) using Illumina and 454 sequencing. Comparisons of chloroplast genomes between S. indicum and the 18 other higher plants were then analyzed. The chloroplast genome of cv. Yuzhi 11 contains 153,338 bp and a total of 114 unique genes (KC569603). The number of chloroplast genes in sesame is the same as that in Nicotiana tabacum, Vitis vinifera and Platanus occidentalis. The variation in the length of the large single-copy (LSC) regions and inverted repeats (IR) in sesame compared to 18 other higher plant species was the main contributor to size variation in the cp genome in these species. The 77 functional chloroplast genes, except for ycf1 and ycf2, were highly conserved. The deletion of the cp ycf1 gene sequence in cp genomes may be due either to its transfer to the nuclear genome, as has occurred in sesame, or direct deletion, as has occurred in Panax ginseng and Cucumis sativus. The sesame ycf2 gene is only 5,721 bp in length and has lost about 1,179 bp. Nucleotides 1–585 of ycf2 when queried in BLAST had hits in the sesame draft genome. Five repeats (R10, R12, R13, R14 and R17) were unique to the sesame chloroplast genome. We also found that IR contraction/expansion in the cp genome alters its rate of evolution. Chloroplast genes and repeats display the signature of convergent evolution in sesame and other species. These findings provide a foundation for further investigation of cp genome evolution in Sesamum and other higher plants.

Complete chloroplast genome sequence of cultivated Morus L. species

“…M. multicaulis contained 22 genes (eight tRNA, 12 PCGs, and two pseudogenes), with one intron, which is consistent with that found for M. atropurpurea, with the exception of two genes (ycf3 and clpP) that contain two introns (Table 2). Of the 22 genes, 10 are situated within the IR region (4 PCGs, 4 tRNAs, and 2 pseudogenes), 1 in the SSC region (ndhA), and 11 in the LSC region (7 PCGs and 4 tRNAs), and this study also found trnK-UUU has the largest intron that contains the protein-coding gene matK, which is similar to that found in green plants (Zhang et al, 2013).…”

“…It is believed that the locations of SSC/IR and LSC/IR junctions are markers of chloroplast genome evolution (Zhang et al, 2013). Here, we compared the positions of the IR/SC boundary in six complete cpDNA sequences.…”

“…It is believed that the locations of the SSC/IR and LSC/IR junctions are markers of chloroplast genome evolution (Zhang et al, 2013). The IR junction among the potential impact of these changes in the cp genome of Morus was compared.…”

“…The length of cpDNA ranges from 120 to 160 kb, owing to the loss and gain of introns (Delannoy et al, 2011), the expansion of the IR region Zhang et al, 2013), and major structural rearrangements (Walker et al, 2014), which contain 110 to 130 genes (Huang et al, 2013). Chloroplasts are a valuable tool for use in phylogenetic studies because of their genes, which lack recombination and conversation (Ravi et al, 2008).…”

The quest to resolve recent radiations: Plastid phylogenomics of extinct and endangered Hawaiian endemic mints (Lamiaceae)

“…The chloroplast genomes of the Hawaiian mints demonstrate the typical angiosperm quadripartite structure, and the gene content, order, and GC content were consistent with most other members of the Lamiales (Mariotti et al, 2010;Wicke et al, 2014;Zhang et al, 2013). The Hawaiian mint genome did not demonstrate any rearrangements or inversions, which have been found in Jasmin nudiflorum, Schwalbea americana, and a few other species (Welch et al, 2016) (Lee et al, 2007;Wicke et al, 2013).…”