马家柚叶绿体基因组特征及其密码子偏好性分析  

Analysis of the chloroplast genome sequence characteristics and its code usage bias of Citrus maxima(L.)Osbeck‘Majiayou’

作　　者：尹明华[1,2,3,4,5] 余璐 周佳慧 刘李娜 徐文萱 孙美龄 YIN Minghua;YU Lu;ZHOU Jiahui;LIU Lina;XUWenxuan;SUN Meiling(College of Life Sciences,Shangrao Normal University,Shangrao 334001,Jiangxi China;Shangrao Agricultural Technology Innovation Research Institute,Shangrao 334001,Jiangxi China;Majiayou Industry Research Institute of Shangrao Normal University,Shangrao 334001,Jiangxi China;Key Laboratory of Protection and Utilization of Medicinal and Edible Plant Resources in Shangrao City,Shangrao 334001,Jiangxi China;Key Laboratory of Germplasm Conservation and Utilization of Potato and Taro Crops in Shangrao City,Shangrao 334001,Jiangxi China)

机构地区：[1]上饶师范学院生命科学学院,上饶334001 [2]上饶农业技术创新研究院,上饶334001 [3]上饶师范学院马家柚产业研究院,上饶334001 [4]上饶市药食同源植物资源保护与利用重点实验室,上饶334001 [5]上饶市薯芋类作物种质保存与利用重点实验室,上饶334001

出　　处：《果树学报》2024年第5期824-846,共23页Journal of Fruit Science

基　　金：国家自然科学基金项目(31960079、31860084、32060092);江西省现代农业产业技术体系建设专项(JXARS-13-赣东站);2022年上饶市科技专项项目(饶科发[2023]5号社发类)(2022A008);江西省科技厅重点研发计划一般项目(20202BBG73010);江西省教育厅科学技术研究项目(GJJ201704、GJJ211729);上饶市科技局平台载体建设项目(2020J001)。

摘　　要：【目的】为了明确马家柚叶绿体基因组结构特征及其与同属类群的系统发育关系,阐明马家柚在柑橘属中的分类地位,对马家柚叶绿体基因组的特征及其密码子的偏好性进行分析。【方法】采用DNBSEQ-T7测序平台对马家柚进行测序,采用Noveplastys、CAP3、GeSeq和tRNAscan-SE软件对马家柚叶绿体基因组进行组装、注释;采用CGViewServer、MISA、REPuter、CodonW、Gview、IRscope、NADnaSP6.0软件对马家柚叶绿体基因组特征进行分析;采用MAFFT 7.0和FastTree 2.1.10软件对马家柚及其85个同科种和山小橘属3个外群种叶绿体基因组进行序列比对和建树。【结果】马家柚叶绿体基因组全长160186 bp,包括1个大单拷贝(LSC)区、1个小单拷贝(SSC)区和2个反向重复(IR)区,为典型闭合环状双链结构。马家柚叶绿体基因组共注释到133个功能基因,包括88个编码蛋白(CDS)基因、8个核糖体RNA(rRNA)基因和37个转运RNA(tRNA)基因。马家柚叶绿体基因组共检测到79个简单序列重复(SSR)和34个长序列重复(Longrepeat)。马家柚叶绿体基因组非编码区的变异程度高于基因编码区,LSC区的变异性>SSC区>IR区,SC/IR边界较为保守。马家柚叶绿体基因组平均ENC值为48.02,密码子偏好性较弱。马家柚叶绿体基因组密码子使用偏好性主要受自然选择的影响,受内部突变的影响小。马家柚叶绿体基因有10个最优密码子(AAU、UGU、AAA、UUU、GCU、GGA、CCA、ACU、CGU、AGU),均以A、U结尾。马家柚与西双版纳东试早柚(KY055833,来源地:云南)、日本夏橙(ON193075,来源地:韩国)、福建六月早蜜柚(MT527726,来源地:福建)、福建琯溪蜜柚(MN782007,来源地:福建)有亲缘关系。【结论】马家柚是一个柑橘属中较为独特的品种,该研究结果为进一步研究马家柚的遗传资源、物种资源鉴定和系统发育分析提供了理论依据。【Objective】Citrus maxima(L.)Osbeck‘Majiayou’was approved by the former Ministry of Agriculture as a national geographical indication agricultural product in 2010.At present,all counties and cities in Shangrao City are vigorously developing the C.maxima(L.)Osbeck‘Majiayou’industry.It is urgent to trace the origin of C.maxima(L.)Osbeck‘Majiayou’to ensure its authenticity.There have been some studies indicating that the genetic relationship between C.maxima(L.)Osbeck‘Maji ayou’and C.maxima(L.)Osbeck‘Xinmuyou’in the surrounding areas is relatively close,and it is quite likely that C.maxima(L.)Osbeck‘Majiayou’is a variant strain derived from the bidirectional(natural and artificial)selection of local pomelo.However,the above research has not yet solved the phylogenetic problem of C.maxima(L.)Osbeck‘Majiayou’.The study aimed to rectify the source of C.maxima(L.)Osbeck‘Majiayou’and explore the phylogenetic relationship with other Citrus plants through surveying the characteristics of the chloroplast genome of C.maxima(L.)Osbeck‘Majiayou’and its codon preference.【Methods】The total DNA extraction from the leaves of C.maxima(L.)Osbeck‘Majiayou’was performed using an improved CTAB method.The purity of the DNA was detected using the NanoDrop 2000 spectrophotometer method;Preliminary quantification of the DNA library using Invitrogen Qubit®2.0 fluorescence quantitative instrument method;The detection of inserted fragments in the DNA library was carried out using the Agilent 2100 biological analyzer system;The accurate quantification of the effective concentration in the DNA library was carried out using real-time fluorescence quantitative PCR method;The DNA library was sequenced using the DNBSEQ-T7 sequencer method.The assembly of the chloroplast genome was carried out using Noveplastys and CAP3 software;The annotation of the chloroplast genome was performed using GeSeq and tRNAscan-SE software;The production of the chloroplast genome map was carried out using OGDRAW software.T

关 键 词：马家柚 叶绿体基因组 序列特征 密码子偏好性 最优密码子 系统发育分析 

分 类 号：S666.3[农业科学—果树学]