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两型豆属叶绿体基因组特征及密码子偏好性分析
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引用本文:余 潇,赵振宁,邓莉兰.两型豆属叶绿体基因组特征及密码子偏好性分析[J].西北农业学报,2024,(3):435~451
DOI:10.7606/j.issn.1004-1389.2024.03.007
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作者单位
余 潇,赵振宁,邓莉兰 (1.湖南财政经济学院 经济地理学院长沙 4102052.西南林业大学 园林园艺学院昆明 6502243西南林业大学 林学院昆明 650224) 
基金项目:云南省第二次国家重点保护野生植物资源调查项目(09930-216304);2021年度云南省大学生创新创业国家级项目(202110677046);湖南财政经济学院博士科研启动资金。
中文摘要:为明确锈毛两型豆的叶绿体基因组结构和两型豆属叶绿体基因组密码子使用偏性及影响因素,以亚热带中、南部地区具有广阔开发利用前景的豆科草种—锈毛两型豆(Amphicarpaea ferruginea)为试验材料,利用高通量测序技术对锈毛两型豆进行叶绿体基因组测序、组装和注释,对其叶绿体基因组结构、基因组成进行分析。同时利用 CodonW 1.4.2 软件和CUSP 在线程序等软件分析锈毛两型豆和两型豆的基因密码子使用偏性参数和核苷酸组成。结果显示:锈毛两型豆叶绿体基因组全长为 152 531 bp,包含83 364 bp的大单拷贝(LSC)区、17 935 bp的小单拷贝(SSC)区和25 616 bp的1对反向重复序列,为典型四分体结构,GC含量为35.44%;叶绿体基因组共编码130个基因,包括85个蛋白质编码基因、37个tRNA基因和8个rRNA基因;叶绿体基因组共检测出73个简单重复序列(SSRs),单、二、三、四、五和六核苷酸SSRs的数目分别为41、28、3、1、0和0。从锈毛两型豆和两型豆叶绿体基因组中筛选到适用于密码子使用偏好性分析的CDS基因共48条,两种植物叶绿体基因组具有相似的密码子使用模式,均倾向于使用A与U作为末尾碱基,48个基因的ENC 值均在35%以上,表明锈毛两型豆和两型豆叶绿体基因组的密码子偏性较弱;综合中性绘图分析、有效密码子数(ENC-plot)分析和奇偶偏好性(PR2-plot)分析的结果显示两型豆属叶绿体基因组密码子使用模式不仅受突变压力的影响,同时还受选择压力以及其他多种因素的影响;在锈毛两型豆和两型豆中分别确定18和20个最优密码子,其中共有最优密码子18个。基于豆科20个物种叶绿体基因组构建的系统发育树表明,豆科20个物种构成一个单系类群,锈毛两型豆与两型豆亲缘关系最近。
中文关键词:两型豆属  锈毛两型豆  叶绿体基因组特征  密码子偏好性  系统发育分析
 
Genomic Characteristics and Codon Usage Bias of Chloroplast Genome in Amphicarpaea Elliot
Abstract:In order to elucidate the chloroplast genome structure of Amphicarpaea ferruginea and analyze the codon usage bias and influencing factors of Amphicarpaea species chloroplast genome,the leguminous grass species of A. ferruginea which holds considerable potential for development and utilization prospects in the central and southern subtropical regions,was used as the test material. The chloroplast genome of A. ferruginea was sequenced,assembled and annotated using high-throughput sequencing technology,and its chloroplast genome structure and gene composition were analyzed. CodonW 1.4.2 software and CUSP online program were used to analyze the gene codon usage bias parameters and nucleotide composition of A. ferruginea and A. edgeworthii. The results showed that A. ferruginea chloroplast genome had a total length of 152 531 bp and followed a typical tetrad structure,including a large single copy region (LSC) of 83 364 bp,a small single copy region (SSC) of 17 935 bp,and a pair of inverted repeats of 25 616 bp. The GC content was 35.44%. The A. ferruginea chloroplast genome encoded 130 genes, comprising 85 protein-coding genes,37 tRNA genes and 8 rRNA genes. A total of 73 simple sequence repeats (SSRs) were detected in the A. ferruginea chloroplast genome. The numbers of mononucleotide,dinucleotide,trinucleotide,tetranucleotide,pentanucleotide,and hexanucleotide SSRs were 41,28,3,1,0 and 0,respectively. A total of 48 CDS genes suitable for codon usage bias analysis were screened from the A. ferruginea and A. edgeworthii chloroplast genomes. The codon usage patterns of the two plant chloroplast genomes were similar,both tending to use A and U as terminal bases. The ENC values of the 48 genes were all above 35%,indicating that the codon usage bias of A. ferruginea and A. edgeworthii chloroplast genomes was weak. The results of neutral plot analysis,effective number of codons ( ENC-plot ) analysis and parity preference (PR2-plot ) analysis showed that the codon usage patterns of Amphicarpaea chloroplast genome was not only affected by mutation pressure,but also by selection pressure and other factors. 18 and 20 optimal codons were identified in A. ferruginea and A. edgeworthii, respectively,among which there were 18 optimal codons. The phylogenetic tree construction based on the chloroplast genomes of 20 species of Leguminosae showed that the 20 species of Leguminosae constituted a monophyletic group,and A. ferruginea and A. edgeworthii were most closely related.
keywords:Amphicarpaea  Amphicarpaea ferruginea  Chloroplast genome characteristics  Code usage bias  Phylogenetic analysis
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