草业科学2025，Vol.42Issue(1)：101-118,18.DOI:10.11829/j.issn.1001-0629.2023-0537
苏丹草叶绿体基因组特征及系统发育分析
Genomic characteristics and phylogenetic analysis of chloroplasts in Sorghum sudanense
摘要
Abstract
In order to determine the sequence characteristics of the chloroplast genome of Sorghum sudanense and establish its systematic position in the Sorghum genus,we sequenced the chloroplast genome of S.sudanense using the DNBSEQ-T7 sequencing platform,and analyzed its gene composition,simple-sequence repeats,long repeat sequences,and inverted repeat(IR)region boundary structure;constructed neutral,ENC,and PR2 plots;and examined its systematic evolution.The results revealed that the chloroplast genome of S.sudanense has a typical tetrad structure,with a length of 140 754 bp,comprising 86 protein-coding genes,38 tRNA genes,and eight rRNA genes,although lacks the typical ccD andycf1 genes.In addition,we detected a total of 27 simple-sequence repeats(SSRs)and 47 long repeat sequences(long repeats).The numbers of nucleotide polymorphisms in the long single-copy(LSC)and small single-copy(SSC)regions were found to be significantly higher than those in the(IR)region,with the variability in the LSC region being greater than that in the SSC and IR regions.The variation of nucleotide diversity(Pi)ranged from 0 to 0.01852,and on the basis of Pi,we selected 10 high variation regions(≥ 0.01215),all of which were located in the LSC region.Furthermore,we detected differences in GC contents at different codon positions in the chloroplast genomes of S.sudanense and 11 related species,with a preference for ending with A/U,and with an average ENC value of 47.50,indicating a weak codon bias.The main factor affecting codon usage bias in these 12 species was natural selection,with less influence from internal mutation pressure.There were a total of 15 optimal codons in Sudan grass chloroplast genes(CAA,AAA,UUU,UAU,AUU,UAA,GCA,CCA,ACU,GUA,AGA,CGA,CUU,UCC,and UCU),all ending in an A or U base.Moreover,we detected a relatively close genetic relationship between S.sudanense and S.bicolor subsp.drummondii.Our findings in this study,will provide a reference for the development of molecular markers,assessment of genetic diversity,and further research on the conservation biology and population genetics of sorghum plants.关键词
苏丹草/叶绿体基因组/简单序列重复/IR区边界结构/中性绘图分析/ENC-plot分析/PR2-plot分析Key words
Sorghum sudanense/chloroplast genome/simple-sequence repetition/boundary structure of the IR region/neutral graphic analysis/ENC-plot analysis/PR2-plot analysis引用本文复制引用
尹明华,乐芸,张嘉欣,柴桑雪,李文婷,欧阳茜,王美暄,徐子林,张钦荣,张牧彤,黄添慧,何凡凡..苏丹草叶绿体基因组特征及系统发育分析[J].草业科学,2025,42(1):101-118,18.基金项目
国家自然科学基金项目(31860084、31960079、32060092) （31860084、31960079、32060092）
江西省现代农业产业技术体系建设专项(JXARS-13-赣东站) （JXARS-13-赣东站）
