The Complete Chloroplast DNA Sequence of Eleutherococcus senticosus (Araliaceae); Comparative Evolutionary Analyses with Other Three Asterids

Abstract

This study reports the complete chloroplast (cp) DNA sequence of Eleutherococcus senticosus (GenBank: JN 637765), an endangered endemic species. The genome is 156,768 bp in length, and contains a pair of inverted repeat (IR) regions of 25,930 bp each, a large single copy (LSC) region of 86,755 bp and a small single copy (SSC) region of 18,153 bp. The structural organization, gene and intron contents, gene order, AT content, codon usage, and transcription units of the E. senticosus chloroplast genome are similar to that of typical land plant cp DNA. We aligned and analyzed the sequences of 86 coding genes, 19 introns and 113 intergenic spacers (IGS) in three different taxonomic hierarchies; Eleutherococcus vs. Panax, Eleutherococcus vs. Daucus, and Eleutherococcus vs. Nicotiana. The distribution of indels, the number of polymorphic sites and nucleotide diversity indicate that positional constraint is more important than functional constraint for the evolution of cp genome sequences in Asterids. For example, the intron sequences in the LSC region exhibited base substitution rates 5-11-times higher than that of the IR regions, while the intron sequences in the SSC region evolved 7-14-times faster than those in the IR region. Furthermore, the Ka/Ks ratio of the gene coding sequences supports a stronger evolutionary constraint in the IR region than in the LSC or SSC regions. Therefore, our data suggest that selective sweeps by base collection mechanisms more frequently eliminate polymorphisms in the IR region than in other regions. Chloroplast genome regions that have high levels of base substitutions also show higher incidences of indels. Thirty-five simple sequence repeat (SSR) loci were identified in the Eleutherococcus chloroplast genome. Of these, 27 are homopolymers, while six are di-polymers and two are tri-polymers. In addition to the SSR loci, we also identified 18 medium size repeat units ranging from 22 to 79 bp, 11 of which are distributed in the IGS or intron regions. These medium size repeats may contribute to developing a cp genome-specific gene introduction vector because the region may use for specific recombination sites.

Complete Plastid Genome Sequence of the Basal Asterid Ardisia polysticta Miq. and Comparative Analyses of Asterid Plastid Genomes

“…Among the most conserved regions, the two pairwise comparisons shared 17 homologous regions (Table 2). Twelve of these regions are in IRs, which is consistent with the observation that IRs are more conserved than LSC and SSC [45], [46], [59]. The other five regions are relatively short (<60 bp) and are located within polycistronic transcription units [60], [61].…”

“…Moreover, these lineages have longer branches compared to their sister groups (Figure 3; Figure S1) and they have the smallest SSC and the largest LSC among asterids (Figure 2). This is intriguing because the opposite would be expected due to higher evolutionary rate of genes in SSC than in LSC [45], [46]. More studies are needed to investigate such association of higher evolutionary rate, changes in plastome organization, and gene loss across a larger range of angiosperm lineages.…”

“…polysticta plastome with other available asterid plastomes (Table S1) with respect to GC content, genome organizations, and content of repetitive sequences. Because the intergenic regions are the most variable parts in plastomes [45], [46], we calculated the sequence divergence between A . polysticta and representative euasterids to find regions of potential phylogenetic utility for Ardisia at lower taxonomic levels.…”

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

“…To assemble the chloroplast genomes for the Stachys species, we first assembled the sequence for Stachys chamissonis, as this represents the species that is most closely related to the Hawaiian mints in phylogenies constructed from short chloroplast sequences (Lindqvist and Albert, 2002;Roy et al, 2013). We conducted five separate YASRA runs, using recently available chloroplast genome sequences as references: S. haliakalae, Olea europaea, Sesamum indicum (NC_016433) (Yi et al, 2012), Origanum vulgare (JX880022) (Lukas and Novak, 2013), and Salvia miltiorrhiza (NC_020431) (Qian et al, 2013). The contigs from the runs with each reference were aligned and an interim consensus sequence called.…”

The Complete Chloroplast Genome Sequence of Cephalotaxus oliveri (Cephalotaxaceae): Evolutionary Comparison of Cephalotaxus Chloroplast DNAs and Insights into the Loss of Inverted Repeat Copies in Gymnosperms

“…However, the evolutionary mechanism underlying the dynamic changes of IRs remains to be elucidated. In particular, Yi et al (2012) stress that the IR is under stronger evolutionary constraint than the large single copy (LSC) or small single copy (SSC) as shown by the distribution of repeated elements and indels and the base substitution patterns.…”