东乡野生稻叶绿体基因组拼接及系统进化分析(英文)

Complete chloroplast genome of Dongxiang wild rice and its application in phylogenetic analysis

为了优化叶绿体基因组DNA序列的获取和拼接方法,以东乡野生稻(Oryza rufipogon)嫩绿叶为材料,不需分离叶绿体DNA,利用高通量测序获得的全基因组短序列及叶绿体基因组高度保守的特性,与参考序列进行比对,从而组装拼接出叶绿体DNA序列,并同时利用生物信息学手段和聚合酶链反应扩增进行补洞.最终获得东乡野生稻完整叶绿体基因组序列,大小为134 537bp,大、小单拷贝区和反向互补重复区大小分别为80 585bp,12 346bp,20 803bp,共注释叶绿体基因152个.基于获取的东乡野生稻及其他稻属物种叶绿体基因组序列进行系统进化分析,研究结果支持已有的关于栽培籼粳稻起源的结论,即栽培籼粳稻分别与野生稻聚类到2个亚群中,其中粳稻与中国普通野生稻聚在1个亚群中,表明粳稻驯化起源于中国,而籼稻起源于另外一次独立驯化过程.

Complete chloroplast genome sequence is very useful for studying the evolution of species . To get chloroplast genome sequences , purification of the chloroplast or PCR amplification prior to sequencing is commonly involved in conventional approaches . Advances in DNA sequencing technology provide new opportunities to obtain chloroplast genome sequence from the whole-genome high-throughput sequencing data without purification of the chloroplast . In this study , we finished the complete chloroplast genome sequence of Dongxiang wild rice based on high-throughput sequencing data from their fresh green leaves . The chloroplast genome was 134 537 bp in size , and had a typical quadripartite structure with the large single copy （ LSC , 80 585 bp） and small single copy （ SSC , 12 346 bp） regions separated by two copies of an inverted repeat （ IR , 20 803 bp each） region . One hundred and fifty-two chloroplast genes were successfully annotated . A phylogenetic tree was constructed based on the chloroplast genomes of Dongxiang wild rice , Indica , Japonica and 10 other genera of grasses using the neighbor-joining method . The result showed that Dongxiang wild rice had a closer relationship with Bambusa oldhamii and Panicoideae . Furthermore , the SNPs of 22 rice accessions were identified using the chloroplast genome of Dongxiang wild rice as a reference sequence and a phylogenetic tree was constructed based on these SNPs . The result illustrated that Indica had a closer relationship with wild rice-I , while Japonica was closer to wild rice-III , suggesting that Indica and Japonica were domesticated independently from different wild rice populations .