Li Feng, Liu Ying, Wang Junhui, Xin Peiyao, Zhang Jiangtao, Zhao Kun, Zhang Minggang, Yun Huiling, Ma Wenjun
State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, National Innovation Alliance of Catalpa Bungei, Beijing, China.
Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Southwest China, Southwest Forestry University, Kunming, China.
Front Genet. 2022 Mar 16;13:845619. doi: 10.3389/fgene.2022.845619. eCollection 2022.
Species within the Genus are mostly semievergreen or deciduous trees with opposite or whorled leaves. , f. and are sources of traditional precious wood in China, known as the "kings of wood". Due to a lack of phenotypic and molecular studies and insufficient sequence information, intraspecific morphological differences, common DNA barcodes and partial sequence fragments cannot clearly reveal the phylogenetic or intraspecific relationships within . Therefore, we sequenced the complete chloroplast genomes of six taxa of the genus and analyzed their basic structure and evolutionary relationships. The chloroplast genome of shows a typical tetrad structure with a total length ranging from 157,765 bp () to 158,355 bp (). The length of the large single-copy (LSC) region ranges from 84,599 bp () to 85,004 bp (), that of the small single-copy (SSC) region ranges from 12,662 bp () to 12,675 bp (), and that of the inverted repeat (IR) regions ranges from 30,252 bp () to 30,338 bp (). The GC content of the six chloroplast genomes were 38.1%. In total, 113 unique genes were detected, and there were 19 genes in IR regions. The 113 genes included 79 protein-coding genes, 30 tRNA genes and four rRNA genes. Five hypervariable regions (trnH-psbA, rps2-rpoC2, rpl22, ycf15-trnl-CAA and rps15) were identified by analyzing chloroplast nucleotide polymorphisms, which might be serve as potential DNA barcodes for the species. Comparative analysis showed that single nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs) were highly diverse in the six species. Codon usage patterns were highly similar among the taxa included in the present study. In addition to the stop codons, all codons showed a preference for ending in A or T. Phylogenetic analysis of the entire chloroplast genome showed that all taxa within the genus formed a monophyletic group, clearly reflecting the relationships within the genus. This study provides information on the chloroplast genome sequence, structural variation, codon bias and phylogeny of , which will facilitate future research efforts.
该属内的物种大多为半常绿或落叶乔木，叶对生或轮生。 、 、 是中国传统珍贵木材的来源，被誉为“木中之王”。由于缺乏表型和分子研究以及序列信息不足，种内形态差异、常用DNA条形码和部分序列片段无法清晰揭示该属内的系统发育或种内关系。因此，我们对该属六个分类群的叶绿体全基因组进行了测序，并分析了它们的基本结构和进化关系。该属的叶绿体基因组呈现典型的四分体结构，全长范围从157,765 bp（ ）到158,355 bp（ ）。大单拷贝（LSC）区域长度范围从84,599 bp（ ）到85,004 bp（ ），小单拷贝（SSC）区域长度范围从12,662 bp（ ）到12,675 bp（ ），反向重复（IR）区域长度范围从30,252 bp（ ）到30,338 bp（ ）。六个叶绿体基因组的GC含量为38.1%。总共检测到113个独特基因，IR区域有19个基因。这113个基因包括79个蛋白质编码基因、30个tRNA基因和4个rRNA基因。通过分析叶绿体核苷酸多态性鉴定出五个高变区域（trnH-psbA、rps2-rpoC2、rpl22、ycf15-trnl-CAA和rps15），这些区域可能作为该物种潜在的DNA条形码。比较分析表明，六个物种中的单核苷酸多态性（SNP）和简单序列重复（SSR）高度多样。本研究中所包含的分类群之间的密码子使用模式高度相似。除终止密码子外，所有密码子都偏好以A或T结尾。对整个叶绿体基因组的系统发育分析表明，该属内所有分类群形成一个单系类群，清楚地反映了该属内各分类群之间的关系。本研究提供了该属的叶绿体基因组序列、结构变异、密码子偏好和系统发育信息，这将有助于未来的研究工作。
