蒲桃属叶绿体基因组特征及密码子偏好性分析  

Chloroplast genome characteristics and codon preferences analysis in Syzygium

作　　者：杨秀瑶 张梦洁 尹拓 韩沛辰 杜朝金 张汉尧[2] YANG Xiu-yao;ZHANG Meng-jie;YIN Tuo;HAN Pei-chen;DU Chao-jin;ZHANG Han-yao(Southwest Forestry University/The Key Laboratory of Biodiversity Conservation of Southwest China,National Forestry and Grassland Ad-ministration,Kunming 650224;Southwest Forestry University/Key Laboratory of Forest Genetic Improvement and Breeding,Kunming 650224,China)

机构地区：[1]西南林业大学/西南地区生物多样性保育国家林业与草原局重点实验室,昆明650224 [2]西南林业大学/云南省高校林木遗传改良与繁育重点实验室,昆明650224

出　　处：《西南农业学报》2023年第9期1869-1880,共12页Southwest China Journal of Agricultural Sciences

基　　金：国家自然科学基金项目(32160556);云南省院士(专家)工作站项目(202305AF150020)。

摘　　要：【目的】通过对蒲桃属叶绿体基因组的特征、密码子使用模式以及系统发育分析,探讨蒲桃属系统发育关系及密码子偏好性的形成因素,促进其药用价值进一步开发利用。【方法】本研究以Illumina高通量测序技术获得的红枝蒲桃叶绿体基因组序列和从NCBI直接获取的蒲桃属5个种的叶绿体基因组为研究对象,利用Rstudio及其他软件分析蒲桃属6个物种叶绿体基因组特征、密码子使用模式和系统发育关系。【结果】蒲桃属叶绿体基因组IR区相对保守,LSC区和SSC区非编码区变异较大,编码区较为保守,但6个物种编码区的ycf1基因表现出明显的变异性;蒲桃属物种大多与桉属聚在同一大支;密码子偏好性分析表明,GC、GC_(1)、GC_(2)、GC_(3)含量均稳定在一个值附近,GC3含量最低仅达28%左右,且RSCU>1的30个高频密码子中有29个以A/U结尾;GC_(3)与GC_(12)的相关系数最大为0.141,未达到显著水平;ENC比值多分布在0.05~0.15。【结论】蒲桃属叶绿体基因组高度保守,与桉属(Eucalyptus)亲缘关系较近。第三位密码子偏好使用A/U结尾,密码子使用模式在受到突变影响的同时,主要受到自然选择的影响。CGU、AGU、AAA、GCU、GGU、GUA、GAA等蒲桃属6个物种的共同最优密码子为蒲桃属叶绿体基因组的最优密码子。【Objective】The characteristics of the Syzygium chloroplast genomes,codon usage patterns and phylogenetic analyses were carried out.The phylogenetic relationships and codon preferences of Syzygium were explored to promote the further exploitation of its medicinal val⁃ue.【Method】In the study,the chloroplast genome sequences of Syzygium rubrum obtained by Illumina high⁃throughput sequencing technolo⁃gy and the five species of Syzygium obtained directly from NCBI were subjected to analyze the chloroplast genome characteristics,codon us⁃age patterns,and phylogenetic relationships using Rstudio and other software.【Result】The IR region of the chloroplast genome of Syzygium was relatively conservative,the non⁃coding regions of LSC and SSC regions had lots of variations,and the coding region was relatively conser⁃vative,but the ycf1 gene in the coding region of six species showed obvious variability;Most species of Syzygium were clustered in the same large branch as eucalyptus;The codon preference analysis showed that the contents of GC,GC_(1),GC_(2) and GC_(3) were all stable around the same value,the lowest content of GC3 was only about 28%,and 29 of the 30 high⁃frequency codons with RSCU>1 ended in A/U;The maximum correlation coefficient between GC_(3) and GC_(12) was 0.141,which did not reach a significant level;The ENC ratio was most distribu⁃ted between 0.05 and 0.15.【Conclusion】The chloroplast genome of Syzygium was highly conserved and closely related to Eucalyptus.The third codon prefered to end with A/U,and the codon use pattern was mainly affected by natural selection as well as mutation.The common optimal codon of six species of Syzygium,such as CGU,AGU,AAA,GCU,GGU,GUA,and GAA,was the optimal codon of the chloro⁃plast genome of Syzygium.

关 键 词：蒲桃属 叶绿体基因组 密码子偏好性 系统发育分析 

分 类 号：S725[农业科学—林木遗传育种]