凌云牛心李叶绿体基因组特征及系统发育分析OA

[Objective]The paper aimed to study the structural characteristics and phylogenetic relationships of the chloroplast genome of Lingyun Niuxinli,and provide theoretical basis for its molecular identification,genetic diversity research,and germplasm resource protection and development.[Method]Illumina NovaSeq sequencing platform was used to sequence the chloroplast genome of Lingyun Niuxinli.Bioin-formatics software was used for sequence splicing,annotation,and analysis of its structural features,codon preferences,simple repeat se-quences(SSR),and phylogenetics.[Result]The chloroplast genome of Lingyun Niuxinli was a typical circular tetrad structure,with a total length of 157 926 bp,and two reverse repeat regions(IR)of 26 353 bp.The length of the large single copy region(LSC)and the small sin-gle copy region(SSC)were 86 189 bp and 19 031 bp,respectively.The total GC content of the chloroplast genome was 37.53％.The chloro-plast genome of Lingyun Niuxinli contained a total of 130 genes,including 85 protein coding genes,37 tRNA genes,and 8 rRNA genes.The relative usage of synonymous codons(RSCU)for the chloroplast genome protein coding genes of Lingyun Niuxinli was analyzed,and the re-sults showed that there were 32 high-frequency codons(RSCU＞1),of which the high-frequency codons ending in A or U accounted for 84.38％.A total of 73 SSR loci were detected in the chloroplast genome of Lingyun Niuxin plum,including single nucleotide repeats,dinucleoti-de repeats,tetranucleotide repeats,and pentanucleotide repeats.Among them,the A/T repeat sequence had the highest number of single nu-cleotide repeat motifs.Comparing the chloroplast genome IR boundaries of Lingyun Niuxin plum with five other plum species,it was found that its IR boundaries were relatively conserved.The phylogenetic analysis results indicated that Lingyun Niuxin plum had the closest genetic relationship with Fengtang plum,suggesting that it belonged to the Chinese plum type.[Conclusion]The chloroplast genome of Lingyun Niux-in plum is highly conserved,with codon preferences ending in A or U.Phylogenetic analysis suggests that Lingyun Niuxin plum may belong to the Chinese plum type.