Sequencing, Characterization, and Comparative Analyses of the Plastome of Caragana rosea var. rosea

Abstract

To exploit the drought-resistant Caragana species, we performed a comparative study of the plastomes from four species: Caragana rosea, C. microphylla, C. kozlowii, and C. Korshinskii. The complete plastome sequence of the C. rosea was obtained using the next generation DNA sequencing technology. The genome is a circular structure of 133,122 bases and it lacks inverted repeat. It contains 111 unique genes, including 76 protein-coding, 30 tRNA, and four rRNA genes. Repeat analyses obtained 239, 244, 258, and 246 simple sequence repeats in C. rosea, C. microphylla, C. kozlowii, and C. korshinskii, respectively. Analyses of sequence divergence found two intergenic regions: trnI-CAU-ycf2 and trnN-GUU-ycf1, exhibiting a high degree of variations. Phylogenetic analyses showed that the four Caragana species belong to a monophyletic clade. Analyses of Ka/Ks ratios revealed that five genes: rpl16, rpl20, rps11, rps7, and ycf1 and several sites having undergone strong positive selection in the Caragana branch. The results lay the foundation for the development of molecular markers and the understanding of the evolutionary process for drought-resistant characteristics.

Comparative analysis of chloroplast genomes for fiveDiclipteraspecies (Acanthaceae): molecular structure, phylogenetic relationships, and adaptive evolution

“…Polymorphic SSRs are mainly distributed in non-coding regions, which are also highly variable regions in the chloroplast genomes (Asaf et al, 2017). The presence of long sequence repeats are indicators of mutational hotspots (Borsch & Quandt, 2009;Jiang et al, 2018). The ycf1 gene was previously reported for its use in DNA barcodes due to its abundance of variable sites (Kurt et al, 2008;Gernandt et al, 2009;Dong et al, 2012;Drew & Sytsma, 2013;Dong et al, 2015).…”

“…According to previous studies, the ycf15 gene is a member of the PFAM protein family accession PF10705 (Sara et al, 2018) and was not considered to be a protein-coding gene because of its unknown function (Steane, 2005;Feng et al, 2018). The ycf15 gene acts as a pseudogene in some species because of its premature stop codons (Chen et al, 2018;Jiang et al, 2018). The ycf15 gene should be further investigated for its role in adaptive evolution and gene function.…”

Extensive survey of the ycf4 plastid gene throughout the IRLC legumes: Robust evidence of its locus and lineage specific accelerated rate of evolution, pseudogenization and gene loss in the tribe Fabeae

“…We also noticed that the ycf4 gene which was not identified in cpDNA of Medicago sativa [56] and 13 Lathyrus species [57] is, in fact, present in the plastid genome of these species. These Lathyrus species are still referred without ycf4 gene [58]. We identified the gene in the plastome of the species using ORF finder and comparison with other related species.…”

Comparative plastomes analysis reveals the first infrageneric evolutionary hotspots of Orthotrichum s.l. (Orthotrichaceae, Bryophyta)

“…They were located in the noncoding regions, mixed The nonrandom distribution of repeats is associated with their function in the plastome (Zhao et al, 2016). Most of the repeats may fold into secondary structures (Jiang et al, 2018). This phenomenon can be observed in the noncoding regions, where they regulate expression of the neighboring genes, increase the plastome plasticity, and take part in intragenic recombination (Zuker, 2003).…”