Plant Molecular Biology Reporter ( IF 1.6 ) Pub Date : 2023-05-27 , DOI: 10.1007/s11105-023-01389-3 Nga Thi Thu Nguyen , Hang Thi Thuy Pho , Quan Huu Nguyen , Nhung Thi Doan , Lan Thi Ngoc Nguyen , Huong Mai Pham , Lam Tung Le , Thuong Danh Sy , Ha Hoang Chu , Lien Thi Kim Vu , Mau Hoang Chu
Adinandra bockiana E. Pritz. ex Diels is a potential plant of the Adinandra genus that contains bioactive. This study presents the results of assembly and annotation of the chloroplast (cp) genome of A. bockiana, a comparison of it with Adinandra cp genomes of several other species, and proposed candidate DNA barcoding from the cp genome. The A. bockiana cp genome was reconstructed by raw reads from total DNA, assembling reads (each read is 150 bp in length) into contigs, and then the contigs were assembled again to sequence the complete cp genome. The A. bockiana cp genome is 156,284 bp in length and consists of a large single-copy (LSC) region of 85,693 bp, a small single-copy (SSC) region of 18,411 bp, a pair of inverted repeats (IRa and IRb) of 26,090 bp each, 129 functional genes, 51 SSRs, and other 70 repeat structures. The functional genes of the A. bockiana cp genome contain 84 protein-coding genes, 37 transfer RNA genes, and eight ribosomal RNA genes. A comparative analysis of the A. bockiana cp genome with the rest of the public Adinandra genomes showed that the number of genes and their structure were highly conserved in the surveyed group. Based on complete cp genomes and matK and trnL sequences of some species of the Adinandra and other genera, molecular phylogenetic trees were established which show the genetic relationships of the species belonging to the Pentaphylacaceae family. Among the chloroplast genes of A. bockiana, the matK and trnL genes are better candidates for phylogenetic analysis.
中文翻译:
沙枣叶绿体基因组特征及其与五叶草科植物的比较分析
Adinandra bockiana E. Pritz。ex Diels 是Adinandra属的潜在植物,含有生物活性。本研究介绍了A. bockiana叶绿体 (cp) 基因组的组装和注释结果,将其与其他几个物种的Adinandra cp 基因组进行了比较,并提出了来自 cp 基因组的候选 DNA 条形码。A. bockiana cp 基因组是通过总 DNA 的原始读数重建的,将读数(每个读数的长度为 150 bp)组装成重叠群,然后再次组装重叠群以对完整的 cp 基因组进行测序。A. bockianacp 基因组长度为 156,284 bp,由一个 85,693 bp 的大单拷贝 (LSC) 区域、一个 18,411 bp 的小单拷贝 (SSC) 区域、一对各为 26,090 bp 的反向重复序列(IRa 和 IRb)组成、129个功能基因、51个SSRs和其他70个重复结构。A. bockiana cp 基因组的功能基因包含 84 个蛋白质编码基因、37 个转移 RNA 基因和 8 个核糖体 RNA 基因。A. bockiana cp 基因组与其余公共Adinandra基因组的比较分析表明,基因的数量及其结构在调查组中高度保守。基于Adinandra某些物种的完整 cp 基因组和matK和trnL序列和其他属,建立了分子系统发育树,显示了属于 Pentaphylacaceae 科的物种的遗传关系。在A. bockiana的叶绿体基因中,matK和trnL基因更适合用于系统发育分析。