Chloroplast Genome Characteristics and Phylogenetic Relationships of Different Sorghum Germplasms

IF 1.1 4区生物学 Q3 PLANT SCIENCES Russian Journal of Plant Physiology Pub Date : 2024-08-09 DOI:10.1134/s1021443724605196

Q. Li, B. Wang, Y. Chen, Y. Zhang, S. Yan

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Abstract

Sorghum (Sorghum bicolor) is the fifth largest cereal crop in the world and is an important food and feed crop. However, the understanding of the chloroplast genome of sorghum is limited, especially for some landrace varieties. In this study, the complete chloroplast (cp) genomes of 10 sorghum varieties from southwestern China were assembled and analysed in depth. The genome sizes ranged between 140.644 and 140.814 bp; the b3 variety had the smallest genome size, and the b6, b7 and b8 varieties had the largest. Highly conserved sequences were found among the 10 cp genomes. A total of 136 genes, including 88 protein-coding genes, 40 tRNAs and 8 rRNAs, were found in each cp genome. Comparative genomic analysis revealed that the large single-copy (LSC) region had more SNPs and indels than the inverted repeat (IR) and small single-copy (SSC) regions. Furthermore, some genes, including matK, matK-trnk, psbM-petN, rps12-rpl20, and ccsA, exhibited greater sequence variation than others. Furthermore, phylogenetic analysis revealed that b3 had a distant genetic relationship with the other 9 varieties. Our findings provide valuable information for a deeper understanding of the genetic structure of sorghum germplasm resources globally and provide an important foundation for subsequent genetic improvement of sorghum.

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不同高粱种质的叶绿体基因组特征和系统发育关系

摘要高粱（Sorghum bicolor）是世界第五大谷类作物，也是重要的粮食和饲料作物。然而，人们对高粱叶绿体基因组的了解十分有限，尤其是对一些陆生品种的了解。本研究对中国西南地区 10 个高粱品种的完整叶绿体（cp）基因组进行了组装和深入分析。基因组大小介于 140.644 和 140.814 bp 之间，其中 b3 基因组最小，b6、b7 和 b8 基因组最大。在 10 个 cp 基因组中发现了高度保守的序列。每个 cp 基因组中共有 136 个基因，包括 88 个蛋白质编码基因、40 个 tRNA 和 8 个 rRNA。基因组比较分析表明，大单拷贝（LSC）区比倒位重复（IR）区和小单拷贝（SSC）区有更多的SNP和嵌合体。此外，一些基因（包括 matK、matK-trnk、psbM-petN、rps12-rpl20 和 ccsA）的序列变异比其他基因更大。此外，系统进化分析表明，b3 与其他 9 个品种的遗传关系较远。我们的研究结果为深入了解全球高粱种质资源的遗传结构提供了宝贵的信息，为后续的高粱遗传改良奠定了重要的基础。

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来源期刊

Russian Journal of Plant Physiology 生物-植物科学

CiteScore

4.00

自引率

14.30%

发文量

107

审稿时长

6 months

期刊介绍： Russian Journal of Plant Physiology is a leading journal in phytophysiology. It embraces the full spectrum of plant physiology and brings together the related aspects of biophysics, biochemistry, cytology, anatomy, genetics, etc. The journal publishes experimental and theoretical articles, reviews, short communications, and descriptions of new methods. Some issues cover special problems of plant physiology, thus presenting collections of articles and providing information in rapidly growing fields. The editorial board is highly interested in publishing research from all countries and accepts manuscripts in English.