Kim Sang-Chul, Kim Jung Sung, Kim Joo-Hwan
Department of Life Science, Gachon University, Seongnamdaero 1342, Seongnam-si, Gyeonggi-do 461-701, Korea.
Department of Life Science, Gachon University, Seongnamdaero 1342, Seongnam-si, Gyeonggi-do 461-701, Korea
AoB Plants. 2016 Apr 6;8. doi: 10.1093/aobpla/plw015. Print 2016.
Genomic events including gene loss, duplication, pseudogenization and rearrangement in plant genomes are valuable sources for exploring and understanding the process of evolution in angiosperms. The family Melanthiaceae is distributed in temperate regions of the Northern Hemisphere and divided into five tribes (Heloniadeae, Chionographideae, Xerophylleae, Melanthieae and Parideae) based on the molecular phylogenetic analyses. At present, complete chloroplast genomes of the Melanthiaceae have been reported from three species. In the previous genomic study of Liliales, atrnI-CAU gene duplication event was reported fromParis verticillata, a member of Parideae. To clarify the significant genomic events of the tribe Parideae, we analysed the complete chloroplast genome sequences of twoTrilliumspecies representing two subgenera:TrilliumandPhyllantherum InTrillium tschonoskii(subgenusTrillium), the circular double-stranded cpDNA sequence of 156 852 bp consists of two inverted repeat (IR) regions of 26 501 bp each, a large single-copy (LSC) region of 83 981 bp and a small single-copy (SSC) region of 19 869 bp. The chloroplast genome sequence ofT. maculatum(subgenusPhyllantherum) is 157 359 bp in length, consisting of two IRs (25 535 bp), one SSC (19 949 bp) and one LSC (86 340 bp), and is longer than that ofT. tschonoskii The results showed that the cpDNAs of Parideae are highly conserved across genome structure, gene order and contents. However, the chloroplast genome ofT. maculatumcontained a 3.4-kb inverted sequence betweenndhCandrbcLin the LSC region, and it was a unique feature for subgeneraPhyllantherum In addition, we found three different types of gene duplication in the intergenic spacer betweenrpl23andycf2containingtrnI-CAU, which were in agreement with the circumscription of subgenera and sections in Parideae excludingT. govanianum These genomic features provide informative molecular markers for identifying the infrageneric taxa ofTrilliumand improve our understanding of the evolution patterns of Parideae in Melanthiaceae.
植物基因组中的基因丢失、复制、假基因化和重排等基因组事件是探索和理解被子植物进化过程的宝贵资源。延龄草科分布于北半球温带地区，根据分子系统发育分析分为五个族（七筋姑族、白丝草族、旱叶百合族、延龄草族和舞鹤草族）。目前，已报道了延龄草科三个物种的完整叶绿体基因组。在之前对百合目植物的基因组研究中，报道了舞鹤草族成员轮叶王孙中atrnI-CAU基因的复制事件。为了阐明舞鹤草族的重要基因组事件，我们分析了代表两个亚属（延龄草亚属和柄叶延龄草亚属）的两种延龄草属植物的完整叶绿体基因组序列。在延龄草（延龄草亚属）中，156 852 bp的环状双链叶绿体DNA序列由两个各为26 501 bp的反向重复（IR）区域、一个83 981 bp的大单拷贝（LSC）区域和一个19 869 bp的小单拷贝（SSC）区域组成。黄斑延龄草（柄叶延龄草亚属）的叶绿体基因组序列长度为157 359 bp，由两个IR（25 535 bp）、一个SSC（19 949 bp）和一个LSC（86 340 bp）组成，比延龄草的长。结果表明，舞鹤草族的叶绿体DNA在基因组结构、基因顺序和内容上高度保守。然而，黄斑延龄草的叶绿体基因组在LSC区域的ndhC和rbcL之间包含一个3.4 kb的反向序列，这是柄叶延龄草亚属的一个独特特征。此外，我们在包含trnI-CAU的rpl23和ycf2之间的基因间隔区发现了三种不同类型的基因重复，这与舞鹤草族除高黎贡山延龄草外的亚属和组的划分一致。这些基因组特征为鉴定延龄草属的属下分类群提供了信息丰富的分子标记，并增进了我们对延龄草科舞鹤草族进化模式的理解。
