甘蔗野生种割手密叶绿体基因组特征及种内系统进化关系  

Complete Chloroplast Genome Characteristics and Intraspecific Phylogenetic Relationships of Saccharum spontaneum

作　　者：余熙恺 余泽怀 张清 张兴坦 YU Xikai;YU Zehuai;ZHANG Qing;ZHANG Xingtan(College of Agriculture,Guangxi University,Nanning,530004;Chinese Academy of Agricultural Sciences,Agricultural Genomics Institute at Shenzhen,Shenzhen,518120)

机构地区：[1]广西大学农学院,南宁530004 [2]中国农业科学院深圳农业基因组研究所,深圳518120

出　　处：《基因组学与应用生物学》2023年第12期1295-1310,共16页Genomics and Applied Biology

基　　金：国家自然科学基金项目(32222019,32201794)共同资助。

摘　　要：甘蔗野生种割手密(Saccharum spontaneum)为栽培种甘蔗提供了对多种病原菌与逆境具有抗性的优良性状。本研究基于已发表的群体重测序数据,组装并注释了来自亚洲、地中海、印度次大陆、非洲等地域的64个割手密的叶绿体基因组。组装结果显示,64个叶绿体基因组平均长度为141 185.72 bp, G+C含量平均为38.4%。长单拷贝(long single-copy, LSC)区域平均长度为83 062.8 bp,短单拷贝(short single-copy, SSC)区域平均长度为12 544 bp,反向重复a/b(inverted repeat a/b, IRa/b)区域平均长度为22 789.47 bp。64个叶绿体基因组均注释到132个基因。IR区域边界分析表明割手密的IR区域较保守,序列相似度为99.9%,边界未观察到明显的扩张与收缩。对割手密叶绿体的SSR注释发现其分为单碱基重复(P1)与多碱基重复(C)类型。相对同义密码子使用度(relative synonymous codon usage, RSCU)统计表明,割手密叶绿体基因组受到环境选择压力的影响。系统进化分析揭示了割手密叶绿体的种内系统发育关系。本研究揭示了64个甘蔗野生种割手密的叶绿体基因组信息,为进一步开展甘蔗割手密种内泛基因组、核质冲突、系统发育地理学与叶绿体密码子优化算法提供理论支撑。The wild species of sugarcane, Saccharum spontaneum, provides modern cultivars of sugarcane with excellent traits for resistance to a wide range of pathogens and adversities. In this study, 64 chloroplast genomes of S. spontaneum from Asian, Mediterranean, Indian subcontinent and African regions were assembled and annotated based on published population resequencing data. Assembly result shows that the average length of the 64 chloroplast genomes was 141 185.72 bp, with an average G+C content of 38.4%. The average length of the long single-copy(LSC) region was 83 062.8 bp, the average length of the short single-copy(SSC) region was 12 544 bp, and the average length of the inverted repeat a/b(IRa/b) region was 22 789.47 bp. The 64 chloroplast genomes were annotated to 132 genes. The IR region boundary analysis showed that the IR region of S. spontaneum was conserved with 99.9% sequence similarity and no significant expansion or contraction of the boundary was observed. SSR annotation of the chloroplasts of S. spontaneum revealed that they were classified as single base repeat(P1) and multiple base repeat(C) types. Relative synonymous codon usage(RSCU) statistics indicate that the chloroplast genome of S. spontaneum is influenced by environmental selection pressures. Phylogenetic analyses revealed intraspecific phylogenetic relationships in the chloroplasts of S. spontaneum. This study reveals chloroplast genomic information of 64 wild sugarcane species of S. spontaneum and provides theoretical support for further development of intraspeci-fic pan-genomic, nucleoplasmic conflict, phylogenetic geography and chloroplast codon optimisation algorithms in S. spontaneum.

关 键 词：甘蔗属 割手密 叶绿体基因组 系统发育分析 生物信息学 

分 类 号：S566.1[农业科学—作物学]