Kim Sang-Chul, Kang Eun Su, Kim Tae-Hee, Choi Ye-Rim, Kim Hyuk-Jin
Division of Forest Biodiversity, Korea National Arboretum, 509 Gwangneungsumogwon-ro, Soheul-eup, Pocheon-si, 11186, Gyeonggi-do, Republic of Korea.
BMC Genomics. 2025 Feb 17;26(1):157. doi: 10.1186/s12864-025-11298-2.
Orobanche is a parasitic plant distributed in the temperate zone of Northern Hemisphere, with approximately 200 species found worldwide. In the Republic of Korea, two species of Orobanche, namely O. coerulescens Stephan ex Willd. and O. filicicola Nakai ex Hyun, Y. S. Lim & H. C. Shin, are present, with O. filicicola being endemic. Genome analysis of this species has not yet been performed, and characterizing its complete organelle genome will provide valuable insights into the phylogeny and genome evolution of parasitic plants.
The chloroplast and mitochondrial genomes were analyzed, revealing distinct characteristics. The chloroplast genome is 91,529 bp long with a GC content of 33.6%, containing 33 protein-coding, 30 tRNA, and 4 rRNA genes. In contrast, the mitochondrial genome is 1,058,991 bp long with a GC content of 45.5%, featuring 31 protein-coding, 16 tRNA, and 3 rRNA genes. The mitochondrial genome has over three times more simple sequence repeats and longer long repeats than the chloroplast genome. Analysis of synonymous codon usage in protein-coding genes from nine Orobanchaceae species revealed significant differences between chloroplasts and mitochondria, with codons ending in A or T exhibiting higher coding rates. Ka/Ks ratio calculations indicated that psbI and atpB had the smallest and largest ratios in chloroplasts, respectively, while ccmFC was identified as the only gene under positive selection in mitochondria genomes. Sequence alignment identified 30 homologous fragments between the two genomes, totaling 7,247 bp. Comparison of O. filicicola's chloroplast genome with related species showed gene loss and conserved inverted repeat sequences. Numerous homologous collinear blocks were found in mitochondrial genomes of related species, but some regions lacked homology. Phylogenetic analysis indicated identical topologies for chloroplasts and mitochondria, with Orobanchaceae forming a strong monophyletic group.
Characterizing the complete organelle genome of O. filicicola enabled a comprehensive analysis of the Orobanchaceae organelle genome, providing important baseline data for its structure and evolution.
列当属是一种寄生植物，分布于北半球温带地区，全球约有200种。在韩国，有两种列当属植物，即蓝列当（Orobanche coerulescens Stephan ex Willd.）和蕨叶列当（Orobanche filicicola Nakai ex Hyun, Y. S. Lim & H. C. Shin），其中蕨叶列当是特有种。尚未对该物种进行基因组分析，对其完整细胞器基因组进行表征将为寄生植物的系统发育和基因组进化提供有价值的见解。
对叶绿体和线粒体基因组进行了分析，揭示了不同的特征。叶绿体基因组长度为91,529 bp，GC含量为33.6%，包含33个蛋白质编码基因、30个tRNA基因和4个rRNA基因。相比之下，线粒体基因组长度为1,058,991 bp，GC含量为45.5%，具有31个蛋白质编码基因、16个tRNA基因和3个rRNA基因。线粒体基因组的简单序列重复和长重复序列比叶绿体基因组多三倍以上。对9种列当科物种蛋白质编码基因的同义密码子使用情况进行分析，发现叶绿体和线粒体之间存在显著差异，以A或T结尾的密码子具有更高的编码率。Ka/Ks比值计算表明，psbI和atpB在叶绿体中的比值分别最小和最大，而ccmFC被确定为线粒体基因组中唯一受正选择的基因。序列比对在两个基因组之间鉴定出30个同源片段，总长7,247 bp。将蕨叶列当的叶绿体基因组与相关物种进行比较，发现了基因丢失和保守的反向重复序列。在相关物种的线粒体基因组中发现了许多同源共线块，但有些区域缺乏同源性。系统发育分析表明，叶绿体和线粒体的拓扑结构相同，列当科形成一个强大的单系类群。
对蕨叶列当完整细胞器基因组进行表征，能够对列当科细胞器基因组进行全面分析，为其结构和进化提供重要的基础数据。
