AUTHOR=Yu Xiaolei , Wang Wenxiu , Yang Hongxia , Zhang Xiaoying , Wang Dan , Tian Xiaoxuan 

TITLE=Transcriptome and Comparative Chloroplast Genome Analysis of Vincetoxicum versicolor: Insights Into Molecular Evolution and Phylogenetic Implication

JOURNAL=Frontiers in Genetics

VOLUME=12

YEAR=2021

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2021.602528

DOI=10.3389/fgene.2021.602528

ISSN=1664-8021

ABSTRACT=<p><italic>Vincetoxicum versicolor</italic> (Bunge) Decne is the original plant species of the Chinese herbal medicine Cynanchi Atrati Radix et Rhizoma. The lack of information on the transcriptome and chloroplast genome of <italic>V. versicolor</italic> hinders its evolutionary and taxonomic studies. Here, the <italic>V. versicolor</italic> transcriptome and chloroplast genome were assembled and functionally annotated. In addition, the comparative chloroplast genome analysis was conducted between the genera <italic>Vincetoxicum</italic> and <italic>Cynanchum</italic>. A total of 49,801 transcripts were generated, and 20,943 unigenes were obtained from <italic>V. versicolor</italic>. One thousand thirty-two unigenes from <italic>V. versicolor</italic> were classified into 73 functional transcription factor families. The transcription factors bHLH and AP2/ERF were the most significantly abundant, indicating that they should be analyzed carefully in the <italic>V. versicolor</italic> ecological adaptation studies. The chloroplast genomes of <italic>Vincetoxicum</italic> and <italic>Cynanchum</italic> exhibited a typical quadripartite structure with highly conserved gene order and gene content. They shared an analogous codon bias pattern in which the codons of protein-coding genes had a preference for A/U endings. The natural selection pressure predominantly influenced the chloroplast genes. A total of 35 RNA editing sites were detected in the <italic>V. versicolor</italic> chloroplast genome by RNA sequencing (RNA-Seq) data, and one of them restored the start codon in the chloroplast <italic>ndhD</italic> of <italic>V. versicolor</italic>. Phylogenetic trees constructed with protein-coding genes supported the view that <italic>Vincetoxicum</italic> and <italic>Cynanchum</italic> were two distinct genera.</p>