Haram Durre, Yan Rushan, Ma Mingxue, Naz Irum, Ullah Raza, Shah Sayed Afzal, Ahmed Ibrar, Heidari Parviz, Tian Xiaoxuan
State Key Laboratory of Chinese Medicine Modernization, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China.
Haihe Laboratory of Modern Chinese Medicine, Tianjin, 301617, China.
BMC Genomics. 2025 Jul 28;26(1):697. doi: 10.1186/s12864-025-11839-9.
Comparative analyses of chloroplast (cp.) genomes in Asclepiadoideae (Apocynaceae) have previously revealed genome size and gene content variation, primarily linked to inverted repeats (IRs) expansion or contraction and pseudogene formations. In the current study, the cp. genome of was sequenced, assembled, and compared with those of 25 other Asclepiadoideae species. The 160,494 base pairs (bp) long genome of exhibited a typical quadripartite structure, comprising a large single-copy (LSC) region of 91,508 bp and a small single-copy (SSC) region of 19,384 bp, separated by two IRs of 24,801 bp each. Across species, genome sizes varied substantially (157,158–178,400 bp), mainly due to IR dynamics. The LSC, SSC, and IR regions ranged from 85,024 to 94,367 bp, 2,294–20,026 bp, and 24,057–42,233 bp, respectively. Each cp. genome comprised 113 unique genes, including 79 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Total annotated genes ranged from 129 to 142, including 84–96 protein-coding, 8 rRNA genes, and 37–38 tRNA genes. IR contraction and expansion produced six distinct genome types, accompanied by gene rearrangements resembling inversion events. The IRs expansion reduced the rate of mutations in the part of the genome and genes that transfer from single-copy regions to IRs. Phylogenetic analysis placed Marsdenieae and Ceropegieae as sister clades, followed by Asclepiadeae and Fockeeae. A strong correlation was observed between IR contraction/expansion and phylogenetic placement, with one exception. These findings suggest that IR variations provide valuable phylogenetic signals within the subfamily Asclepiadoideae.
The online version contains supplementary material available at 10.1186/s12864-025-11839-9.
先前对萝摩亚科（夹竹桃科）叶绿体（cp.）基因组的比较分析揭示了基因组大小和基因含量的变化，主要与反向重复序列（IRs）的扩增或收缩以及假基因的形成有关。在当前研究中，对[物种名称]的cp.基因组进行了测序、组装，并与其他25种萝摩亚科物种的基因组进行了比较。[物种名称]的160,494个碱基对（bp）长的基因组呈现出典型的四分体结构，包括一个91,508 bp的大单拷贝（LSC）区域和一个19,384 bp的小单拷贝（SSC）区域，由两个各24,801 bp的IRs隔开。在不同物种中，基因组大小差异很大（157,158 - 178,400 bp），主要是由于IRs的动态变化。LSC、SSC和IR区域的长度分别为85,024至94,367 bp、2,294至20,026 bp和24,057至42,233 bp。每个cp.基因组包含113个独特基因，包括79个蛋白质编码基因、30个tRNA基因和4个rRNA基因。注释的基因总数在129至142之间，包括84至96个蛋白质编码基因、8个rRNA基因和37至38个tRNA基因。IRs的收缩和扩增产生了六种不同的基因组类型，并伴随着类似于倒位事件的基因重排。IRs的扩增降低了从单拷贝区域转移到IRs的基因组部分和基因中的突变率。系统发育分析将牛奶菜族和吊灯花族作为姐妹分支，其次是萝摩族和马利筋族。除了一个例外，在IR收缩/扩增和系统发育位置之间观察到了很强的相关性。这些发现表明，IR变异在萝摩亚科内提供了有价值的系统发育信号。
在线版本包含可在10.1186/s12864-025-11839-9获取的补充材料。
