Teshome Girma Eshetu, Mekbib Yeshitila, Hu Guangwan, Li Zhi-Zhong, Chen Jinming
CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China.
Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, China.
PeerJ. 2020 Jun 19;8:e9314. doi: 10.7717/peerj.9314. eCollection 2020.
is an important cereal crop in Ethiopia with excellent storage properties, high-quality food, and the unique ability to thrive in extreme environmental conditions. However, the application of advanced molecular tools for breeding and conservation of these species is extremely limited. Therefore, developing chloroplast genome resources and high-resolution molecular markers are valuable to population and biogeographic studies. In the current study, we assembled and compared the complete plastomes of 32 accessions. The size of the plastomes ranged from 134,349 to 134,437 bp with similar GC content (∼38.3%). Genomes annotations revealed 112 individual genes, including 77 protein-coding, 31 tRNA, and 4 rRNA genes. Comparison of plastomes revealed a low degree of intraspecific sequence variations and no structural differentiations. Furthermore, we found 34 polymorphic sites (13 cpSSRs, 12 InDels, and 9 SNPs) that can be used as valuable DNA barcodes. Among them, the majority (88%) of the polymorphic sites were identified in the noncoding genomic regions. Nonsynonymous (ka) and synonymous (ks) substitution analysis showed that all PCGs were under purifying selection (ka/ks <1). The phylogenetic analyses of the whole plastomes and polymorphic region sequences were able to distinguish the accession from the southern population, indicating its potential to be used as a super-barcode. In conclusion, the newly generated plastomes and polymorphic markers developed here could be a useful genomic resource in molecular breeding, population genetics and the biogeographical study of .
是埃塞俄比亚一种重要的谷类作物，具有优良的储存特性、高品质的食物，以及在极端环境条件下茁壮成长的独特能力。然而，用于这些物种育种和保护的先进分子工具的应用极其有限。因此，开发叶绿体基因组资源和高分辨率分子标记对于种群和生物地理学研究具有重要价值。在本研究中，我们组装并比较了32个种质的完整质体基因组。质体基因组的大小在134,349至134,437 bp之间，GC含量相似（约38.3%）。基因组注释显示有112个个体基因，包括77个蛋白质编码基因、31个tRNA基因和4个rRNA基因。质体基因组的比较显示种内序列变异程度较低，且无结构差异。此外，我们发现了34个多态性位点（13个cpSSR、12个插入缺失和9个SNP），可作为有价值的DNA条形码。其中，大多数（88%）多态性位点位于非编码基因组区域。非同义（ka）和同义（ks）替换分析表明，所有PCG都受到纯化选择（ka/ks <1）。对整个质体基因组和多态性区域序列的系统发育分析能够区分来自南方种群的种质，表明其有潜力用作超级条形码。总之，这里新生成的质体基因组和开发的多态性标记可能是分子育种、种群遗传学和生物地理学研究中有用的基因组资源。
