Department of Biological Sciences, College of Science, University of Jeddah, 21493, Jeddah, Saudi Arabia.
Mol Biol Rep. 2024 Jan 2;51(1):60. doi: 10.1007/s11033-023-09069-x.
The complete chloroplast genome (plastome) of the annual flowering halophyte herb Suaeda monoica Forssk. ex J. F. Gmel. family (Amaranthaceae) that grows in Jeddah, Saudi Arabia, was identified for the first time in this study. Suaeda monoica is a medicinal plant species whose taxonomic classification remains controversial. Further, studying the species is useful for current conservation and management efforts. In the current study, the full chloroplast genome S. monoica was reassembled using whole-genome next-generation sequencing and compared with the previously published chloroplast genomes of Suaeda species. The chloroplast genome size of Suaeda monoica was 151,789 bp, with a single large copy of 83,404 bp, a small single copy of 18,007 bp and two inverted repeats regions of 25,189 bp. GC content in the whole genome was 36.4%. The cp genome included 87 genes that coded for proteins, 37 genes coding for tRNA, 8 genes coding for rRNA and one non-coding pseudogene. Five chloroplast genome features were compared between S. monoica and S. japonica, S. glauca, S. salsa, S. malacosperma and S. physophora. Among Suaeda genus and equal to most angiosperms chloroplast genomes, the RSCU values were conservative. Two pseudogenes (accD and ycf1), rpl16 intron and ndhF-rpl32 intergenic spacer, were highlighted as suitable DNA barcodes for different Suaeda species. Phylogenetic analyses show Suaeda cluster into three main groups; one in which S. monoica was closer to S. salsa. The obtained result provided valuable information on the characteristics of the S. monoica chloroplast genome and the phylogenetic relationships.
本研究首次鉴定出生长在沙特阿拉伯吉达的一年生盐生草本植物独根草（Suaeda monoica Forssk. ex J. F. Gmel.）的完整叶绿体基因组（质体基因组）。独根草是一种药用植物，其分类学分类仍存在争议。此外，研究该物种对当前的保护和管理工作很有用。在本研究中，使用全基因组下一代测序重新组装了独根草的完整叶绿体基因组，并与之前发表的苏达属植物的叶绿体基因组进行了比较。独根草的叶绿体基因组大小为 151789 bp，有一个单一的大拷贝 83404 bp，一个小单拷贝 18007 bp 和两个反向重复区 25189 bp。整个基因组的 GC 含量为 36.4%。cp 基因组包含 87 个编码蛋白质的基因、37 个编码 tRNA 的基因、8 个编码 rRNA 的基因和一个非编码假基因。比较了独根草和日本滨藜、盐角草、盐地碱蓬、盐穗木和盐地肤的五个叶绿体基因组特征。在苏达属植物和大多数被子植物的叶绿体基因组中，RSCU 值是保守的。两个假基因（accD 和 ycf1）、rpl16 内含子和 ndhF-rpl32 基因间间隔区被突出为不同苏达物种的合适 DNA 条形码。系统发育分析表明，苏达属植物分为三个主要组群；其中一组独根草与盐地碱蓬更为接近。所得结果为独根草叶绿体基因组的特征和系统发育关系提供了有价值的信息。
