朱蕉叶绿体基因组特征与系统发育分析

朱蕉(Cordyline fruticosa)是一种常见的园艺植物,广泛分布于亚洲、大洋洲、南美洲等热带地区.为了明确朱蕉叶绿体基因组特征,了解其系统发育地位,利用Illumina测序技术对其叶绿体基因组测序后,进行中线性绘图、ENC-plot、PR2-plot和SSR位点等相关数据的挖掘和分析.结果表明:朱蕉叶绿体基...

Genomic Characteristics and Phylogenetic Analysis of Chloroplast of Cordyline fruticosa

Cordyline fruticosa is an common horticultural plant, widely distributed in tropical Asia, Oceania and South America. In order to clarify the characteristics of the chloroplast genome of C. fruticosa and understand its phylogenetic status, the chloroplast genome was sequenced by Illumina sequencing technology, and the relevant data of middle linear plot, ENC-plot, PR2-plot and SSR loci were mined and analyzed. The total length of the complete chloroplast genome was 154 488 bp, and the GC content was 38%. The length of large single copy area was 85 279 bp and the GC content was 36.1%. The small single copy area was 20 325 bp, and the GC content was 32.6%. And bidirectional repetition zones were 24 442 bp, respectively, and the GC content was 43.4%. 131 genes were annotated, including 111 unigenes genes, including 78 protein-coding genes, 4 rRNA genes and 29 tRNA genes. Phylogenetic tree was constructed using the chloroplast genomes of 19 plant species in C. fruticosa and Agavaceae family. C. fruticosa was most closely related to C. indivisa. The content of GC₃ in the chloroplast genome of C. fruticosa was 29.47%, GC₁ and GC₂ were 46.45%, 39.14%, respectively. The base content of GC₃ was lower than that of GC₁ and GC₂, indicating that codon ends preferred to end with A and U. The ENC values ranged from 35.48 to 59.44, indicating that the codon bias was weak. ENC-plot analysis showed that there were 20 ENC frequency ratios between-0.05 to 0.05, indicating that codon preference was mainly affected by natural selection pressure. PR2-plot analysis revealed T>A, G>C, indicating that the chloroplast genome of C. fruticosa was affected by many factors. Codon preference is mainly influenced by selection. Using RSCU and ENC values as references, 17 codons were determined as optimal codons in the chloroplast genome of C. fruticosa. Among the 91 SSR loci detected, there were 3 pentanucleotides and 55 single nucleotides. 76.92% of the SSR loci took A, T (A / T, AT / AT and AAAT / ATTT) as repeat units. It showed that the A and T repeat units were the main SSR sites in the chloroplast genome of C. fruticosa. The results of this study could provide a theoretical basis for the taxonomy and phyletic evolution of C. fruticosa and Cordyline.