The complete chloroplast genome sequence and phylogenetic analysis of Chuanminshen (Chuanminshenviolaceum Sheh et Shan)

Abstract

Chloroplast genome sequences are very useful for species identification and phylogenetics. Chuanminshen (Chuanminshen violaceum Sheh et Shan) is an important traditional Chinese medicinal plant, for which the phylogenetic position is still controversial. In this study, the complete chloroplast genome of Chuanminshen violaceum Sheh et Shan was determined. The total size of Chuanminshen chloroplast genome was 154,529 bp with 37.8% GC content. It has the typical quadripartite structure, a large single copy (17,800 bp) and a small single copy (84,171 bp) and a pair of inverted repeats (26,279 bp). The whole genome harbors 132 genes, which includes 85 protein coding genes, 37 tRNA genes, eight rRNA genes, and two pseudogenes. Thirty-nine SSR loci, 32 tandem repeats and 49 dispersed repeats were found. Phylogenetic analyses results with the help of MEGA showed a new insight for the Chuanminshen phylogenetic relationship with the reported chloroplast genomes in Apiales plants.

Peer Review #2 of "Phylogenetic analysis of Fritillaria cirrhosa D. Don and its closely related species based on complete chloroplast genomes (v0.1)"

“…The results for the locations and sequence lengths of the four major repeats were similar to the latest studies (Bi et al, 2018;Park et al, 2017). The research also revealed that repeat sequences were caused by illegitimate recombination and slipped-strand mispairing in the genome (Cavalier-Smith, 2002;Lu et al, 2016;Yuan et al, 2017). Furthermore, the region where the repeats existed was a potential hotspot for genomic reconfiguration (Gao et al, 2009).…”

“…Repeat sequences play an important role in genome rearrangement and variation due to the illegitimate recombination and slipped-strand mispairing in the chloroplast genome (Cavalier-Smith, 2002;Lu et al, 2016;Yuan et al, 2017). In the present repeat analysis, five types of repeats including tandem, palindrome, forward, reverse, and complement repeats were identified (Fig.…”

Comparison of eight complete chloroplast genomes of the endangered Aquilaria tree species (Thymelaeaceae) and their phylogenetic relationships

“…Frequent variation in repeat regions in most angiosperm plants occurs due to slipped-strand mispairing and illegitimate recombination. Frequent variation in repeat regions also plays an important role in variation and sequence rearrangement in cp genomes 20 , 62 . In addition, the quantity of the identified repeats is sensitive to the Hamming distance used.…”

Phylogenetic analysis of Fritillaria cirrhosa D. Don and its closely related species based on complete chloroplast genomes

“…Repeat sequences play an important role in genome rearrangement and variation due to the illegitimate recombination and slipped-strand mispairing in the chloroplast genome (Cavalier-Smith, 2002; Lu, Li & Qiu, 2016; Yuan et al, 2017). In the present repeat analysis, five types of repeats including tandem, palindrome, forward, reverse, and complement repeats were identified (Fig.…”

“…The results for the locations and sequence lengths of the four major repeats were similar to the latest studies (Bi et al, 2018; Park et al, 2017). The research also revealed that repeat sequences were caused by illegitimate recombination and slipped-strand mispairing in the genome (Cavalier-Smith, 2002; Lu, Li & Qiu, 2016; Yuan et al, 2017). Furthermore, the region where the repeats existed was a potential hotspot for genomic reconfiguration (Gao et al, 2009).…”