Bioengineering Department, Faculty of Engineering, Ege University, Izmir, Turkey.
Department of Field Crops, Faculty of Agriculture, Akdeniz University, Antalya, Turkey.
Sci Rep. 2022 Sep 5;12(1):15068. doi: 10.1038/s41598-022-17877-7.
Lens is a member of the Papilionoideae subfamily of Fabaceae and is generally used as a source of vegetable protein as part of human diets in many regions worldwide. Chloroplast (cp) genomes are highly active genetic components of plants and can be utilized as molecular markers for various purposes. As one of the wild lentil species, the Lens ervoides cp genome has been sequenced for the first time in this study using next-generation sequencing. The de novo assembly of the cp genome resulted in a single 122,722 bp sequence as two separate coexisting structural haplotypes with similar lengths. Results indicated that the cp genome of L. ervoides belongs to the inverted repeat lacking clade. Several noteworthy divergences within the coding regions were observed in ndhB, ndhF, rbcL, rpoC2, and ycf2 genes. Analysis of relative synonymous codon usage showed that certain genes, psbN, psaI, psbI, psbE, psbK, petD, and ndhC, preferred using biased codons more often and therefore might have elevated expression and translation efficiencies. Overall, this study exhibited the divergence level between the wild-type and cultured lentil cp genomes and pointed to certain regions that can be utilized as distinction markers for various goals.
扁豆是豆科蝶形花亚科的一员，通常作为人类饮食中蔬菜蛋白的来源，在世界许多地区被广泛食用。质体基因组是植物中高度活跃的遗传成分，可作为各种目的的分子标记。作为野生小扁豆物种之一，本研究首次利用下一代测序技术对小扁豆质体基因组进行了测序。质体基因组的从头组装产生了一个 122722bp 的单一序列，由两个长度相似的独立共存结构单倍型组成。结果表明，L. ervoides 的质体基因组属于无反向重复区的分支。在 ndhB、ndhF、rbcL、rpoC2 和 ycf2 基因的编码区观察到几个值得注意的差异。相对同义密码子使用分析表明，某些基因，如 psbN、psaI、psbI、psbE、psbK、petD 和 ndhC，更倾向于使用偏性密码子，因此可能具有更高的表达和翻译效率。总的来说，本研究展示了野生型和栽培型小扁豆质体基因组之间的差异水平，并指出了某些可作为各种目标区分标记的区域。
