两型豆属叶绿体基因组特征及密码子偏好性分析

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...

Genomic Characteristics and Codon Usage Bias of Chloroplast Genome in Amphicarpaea Elliot

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.