Yu Xiaolei, Wang Wenxiu, Yang Hongxia, Zhang Xiaoying, Wang Dan, Tian Xiaoxuan
State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China.
Key Laboratory of Pharmacology of Traditional Chinese Medical Formulae, Tianjin University of Traditional Chinese Medicine, Tianjin, China.
Front Genet. 2021 Mar 4;12:602528. doi: 10.3389/fgene.2021.602528. eCollection 2021.
(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 hinders its evolutionary and taxonomic studies. Here, the transcriptome and chloroplast genome were assembled and functionally annotated. In addition, the comparative chloroplast genome analysis was conducted between the genera and . A total of 49,801 transcripts were generated, and 20,943 unigenes were obtained from . One thousand thirty-two unigenes from 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 ecological adaptation studies. The chloroplast genomes of and 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 chloroplast genome by RNA sequencing (RNA-Seq) data, and one of them restored the start codon in the chloroplast of . Phylogenetic trees constructed with protein-coding genes supported the view that and were two distinct genera.
（邦奇）地骨皮是中药材地骨皮的原植物物种。缺乏关于其转录组和叶绿体基因组的信息阻碍了其进化和分类学研究。在此，对其转录组和叶绿体基因组进行了组装和功能注释。此外，还对该属与其他属进行了叶绿体基因组比较分析。共产生了49,801个转录本，从地骨皮中获得了20,943个单基因。地骨皮的1032个单基因被归类到73个功能转录因子家族中。转录因子bHLH和AP2/ERF最为丰富，表明在其生态适应性研究中应仔细分析它们。地骨皮和其他属的叶绿体基因组呈现典型的四分体结构，基因顺序和基因含量高度保守。它们共享类似的密码子偏好模式，其中蛋白质编码基因的密码子偏好以A/U结尾。自然选择压力主要影响叶绿体基因。通过RNA测序（RNA-Seq）数据在地骨皮叶绿体基因组中检测到总共35个RNA编辑位点，其中一个恢复了地骨皮叶绿体中的起始密码子。用蛋白质编码基因构建的系统发育树支持地骨皮和其他属是两个不同属的观点。
