School of Life Sciences, Qinghai Normal University, 38# Wusixi Road, Xining, 810008, Qinghai Province, China.
Academy of Plateau Science and Sustainability, Qinghai Normal University, 38# Wusixi Road, Xining, 810008, Qinghai Province, China.
BMC Genom Data. 2024 Jan 29;25(1):10. doi: 10.1186/s12863-024-01197-y.
Krascheninnikovia ceratoides, a perennial halophytic semi-shrub belonging to the genus Krascheninnikovia (Amarathaceae), possesses noteworthy ecological, nutritional, and economic relevance. This species is primarily distributed across arid, semi-arid, and saline-alkaline regions of the Eurasian continent, encompassing Inner Mongolia, Xinjiang, Qinghai, Gansu, Ningxia, and Tibet.
We reported the comprehensive chloroplast (cp) genome of K. ceratoides, characterized by a circular conformation spanning 151,968 bp with a GC content of 36.60%. The cp genome encompassed a large single copy (LSC, 84,029 bp), a small single copy (SSC, 19,043 bp), and a pair of inverted repeats (IRs) regions (24,448 bp each). This genome harbored 128 genes and encompassed 150 simple sequence repeats (SSRs). Through comparative analyses involving cp genomes from other Cyclolobeae (Amarathaceae) taxa, we observed that the K. ceratoides cp genome exhibited high conservation, with minor divergence events in protein-coding genes (PCGs) accD, matK, ndhF, ndhK, ycf1, and ycf2. Phylogenetic reconstructions delineated K. ceratoides as the sister taxon to Atriplex, Chenopodium, Dysphania, and Suaeda, thus constituting a robust clade. Intriguingly, nucleotide substitution ratios (Ka/Ks) between K. ceratoides and Dysphania species for ycf1 and ycf2 genes surpassed 1.0, indicating the presence of positive selection pressure on these loci.
The findings of this study augment the genomic repository for the Amarathaceae family and furnish crucial molecular instruments for subsequent investigations into the ecological adaptation mechanisms of K. ceratoides within desert ecosystems.
滨藜属 Krascheninnikovia ceratoides 是一种多年生盐生半灌木，属于滨藜属（苋科），具有显著的生态、营养和经济意义。该物种主要分布在欧亚大陆的干旱、半干旱和盐碱地区，包括内蒙古、新疆、青海、甘肃、宁夏和西藏。
我们报道了 K. ceratoides 的综合叶绿体（cp）基因组，其特征为圆形构象，大小为 151968bp，GC 含量为 36.60%。cp 基因组包含一个大单拷贝（LSC，84029bp）、一个小单拷贝（SSC，19043bp）和一对反向重复（IRs）区域（每个 24448bp）。该基因组包含 128 个基因，包含 150 个简单重复序列（SSRs）。通过涉及其他 Cyclolobeae（苋科）类群的 cp 基因组的比较分析，我们观察到 K. ceratoides cp 基因组表现出高度的保守性，在蛋白编码基因（PCGs）accD、matK、ndhF、ndhK、ycf1 和 ycf2 中存在较小的分化事件。系统发育重建将 K. ceratoides 定位为 Atriplex、Chenopodium、Dysphania 和 Suaeda 的姐妹分类群，形成一个强大的分支。有趣的是，K. ceratoides 和 Dysphania 物种之间 ycf1 和 ycf2 基因的核苷酸替代率（Ka/Ks）超过 1.0，表明这些基因座存在正选择压力。
本研究的结果增加了苋科家族的基因组资源，并为今后在荒漠生态系统中研究 K. ceratoides 的生态适应机制提供了重要的分子工具。
