油棕线粒体比较基因组学和系统发育关系分析

Comparative Genomic and Phylogenetic Analyses of Mitochondrial Genome in Oil Palm

油棕(Elaeis guineensis)是棕榈科(Arecaceae)油棕属(Elaeis)重要的产油物种,具有较高的经济价值,在全球热带和亚热带地区被广泛栽培利用。为探究油棕线粒体基因组特征及线粒体基因组系统发育关系,本研究利用三代测序数据组装了油棕线粒体基因组,大小为676774 bp。在油棕线粒体基因组中共鉴定到99个基因,包括45个不同功能类型的蛋白编码基因(protein coding genes,PCGs)、47个tRNA编码基因和7个rRNA编码基因,还鉴定到80个简单重复序列(simple sequence repeats,SSR)和952个大于或等于300 bp的散在重复序列。通过对裸子植物、被子植物、苔藓植物和藻类植物的线粒体进行比较,发现裸子植物的线粒体基因组的G+C含量最高,其次是被子植物的,苔藓植物线粒体基因组最小,藻类植物线粒体基因组的G+C含量最低;其中棕榈科植物油棕、椰子(Cocos nucifera)和海枣(Phoenix dactylifera)的线粒体基因组大小相近,G+C含量均为45%左右,且精氨酸(Arg)是棕榈科植物的线粒体使用频率最高的重叠密码子。系统发育关系和共线性分析表明,油棕和椰子相较油棕和海枣具有更近的亲缘关系。棕榈科3种植物的线粒体基因组展现了较低的结构变异率,但呈现出较高的序列多样性。本研究基于三代数据组装了油棕线粒体基因组,为棕榈科物种种质资源保护、线粒体比较基因组学、遗传多样性、系统发育及密码子偏好性提供了良好的数据支撑。

Elaeis guineensis L.is an important oil-producing tree in the family Arecaceae,genus Elaeis.It has high economic value and is widely cultivated and utilized in tropical regions worldwide.In order to explore the characteristics of E.guineensis mitochondrial genome and its phylogenetic relationship,the E.guineensis mitochondrial genome was assembled using third-generation of sequencing data,and the total base length was 676774 bp.A total of 99 genes were identified in the mitochondrial genome of E.guineensis,including 54 protein coding genes with different functional types,47 tRNA and 7 rRNA coding genes,and 80 simple sequence repeats and 952 scattered repeat sequences of 300 bp or longer were identified.By comparing the mitochondrial genomes of gymnosperms,angiosperms,mosses,and algae,it was found that gymnosperms have the highest G+C content,followed by angiosperms,while mosses have the smallest mitochondrial genomes,and algae have the lowest G+C content in their mitochondrial genomes.Among them,the mitochondrial genomes of E.guineensis,Cocos nucifera,and Phoenix dactylifera are similar in size,with G+C content around 45%,exhibiting an A+T preference.Additionally,arginine is the most frequently used overlapping codon in the mitochondrial genomes of Arecaceae.Phylogenetic relationship and collinear analysis showed that Elaeis guineensis and Cocos nucifera were more closely related than Elaeis guineensis and Phoenix dactylifera.Three palm species exhibit low rates of mitochondrial genome structural variation but high levels of sequence diversity.In this study,the mitochondrial genome of Elaeis guineensis was assembled based on third-generation of sequencing data,which provided good data support for Arecaceae germplasm resources conservation,mitochondrial comparative genomics,genetic diversity,phylogeny and codon preference.