Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin 150025, China.
Int J Mol Sci. 2024 Aug 9;25(16):8689. doi: 10.3390/ijms25168689.
A perennial leguminous forage, has outstanding tolerance to abiotic stresses. The genome of is large and has a complex genetic background, making it challenging to accurately determine genetic information. However, the chloroplast genome is widely used for researching issues related to evolution, genetic diversity, and other studies. To better understand its chloroplast characteristics and adaptive evolution, chloroplast genomes of 61 were assembled (including 16 cultivated germplasm and 45 wild germplasm). These were used to construct the pan-chloroplast genome of , and the chloroplast genomes of cultivated and wild were compared and analyzed. Phylogenetic and haplotype analyses revealed two main clades of 61 germplasm chloroplast genomes, distributed in eastern and western regions. Meanwhile, based on chloroplast variation information, 61 germplasm can be divided into three genetic groups. Unlike the phylogenetic tree constructed from the chloroplast genome, a new intermediate group has been identified, mainly consisting of samples from the eastern region of Inner Mongolia, Shanxi Province, and Hebei Province. Transcriptomic analysis showed that 29 genes were upregulated and three genes were downregulated. The analysis of these genes mainly focuses on enhancing plant resilience and adapting adversity by stabilizing the photosystem structure and promoting protein synthesis. Additionally, in the analysis of adaptive evolution, the , and genes showed higher average Ka/Ks ratios and exhibited significant nucleotide diversity, indicating that these genes are strongly positively selected. The editing efficiency of the and genes significantly increases under abiotic stress, which may positively contribute to plant adaptation to the environment. In conclusion, the construction and comparative analysis of the complete chloroplast genomes of 61 germplasm from different regions not only revealed new insights into the genetic variation and phylogenetic relationships of germplasm, but also highlighted the importance of chloroplast transcriptome analysis in elucidating the model of chloroplast responses to abiotic stress. These provide valuable information for further research on the adaptive evolution of .
一种多年生豆科牧草，对非生物胁迫具有很强的耐受性。 的基因组较大，遗传背景复杂，因此准确确定遗传信息具有一定难度。然而，叶绿体基因组广泛应用于研究进化、遗传多样性等相关问题。为了更好地了解其叶绿体特征和适应性进化，我们组装了 61 个 叶绿体基因组（包括 16 个栽培 和 45 个野生 种质资源）。这些基因组被用来构建 的泛叶绿体基因组，并对栽培种和野生种的叶绿体基因组进行了比较和分析。系统发育和单倍型分析揭示了 61 个种质资源叶绿体基因组的两个主要分支，分别分布在东部和西部地区。同时，基于叶绿体变异信息，61 个种质资源可分为三个遗传群。与基于叶绿体基因组构建的系统发育树不同，我们发现了一个新的中间群体，主要由来自内蒙古东部、山西和河北的样本组成。转录组分析显示，有 29 个基因上调，3 个基因下调。这些基因的分析主要集中在通过稳定光系统结构和促进蛋白质合成来增强植物的弹性和适应逆境。此外，在适应性进化分析中， 、 和 基因表现出更高的平均 Ka/Ks 比值和显著的核苷酸多样性，表明这些基因受到强烈的正选择。在非生物胁迫下， 和 基因的编辑效率显著提高，这可能有助于植物适应环境。综上所述，构建和比较分析来自不同地区的 61 个种质资源的完整叶绿体基因组，不仅揭示了 种质资源遗传变异和系统发育关系的新见解，还强调了叶绿体转录组分析在阐明叶绿体对非生物胁迫响应的模型方面的重要性。这些为进一步研究 的适应性进化提供了有价值的信息。
