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属内叶绿体基因组比较及密码子使用偏好性分析

Comparative Chloroplast Genomics and Codon Usage Bias Analysis in Genus.

作者信息

Yang Yang, Liu Xueyang, He Lixia, Li Zhenhua, Yuan Boxuan, Fang Fengyan, Wang Mei, Li Aifang, Liu Cheng, He Minmin, Hui Shugang, Wang Wenda, Wang Xuchu

机构信息

Plant Stress Resistance Integrated Biology Laboratory, College of Life Sciences, Hainan Normal University, Haikou 571158, China.

Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-Bioengineering, College of Life Sciences, Guizhou University, Guiyang 550025, China.

出版信息

Genes (Basel). 2025 Feb 6;16(2):201. doi: 10.3390/genes16020201.

DOI:10.3390/genes16020201
PMID:40004530
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11855534/
Abstract

OBJECTIVES

This study investigates the cpDNA sequences from six species, aiming to explore their genomic characteristics, gene content, and genetic relationships. The objectives include understanding the structure of these genomes, identifying potential gene rearrangements, and providing insights into genetic improvement and conservation strategies for the genus.

METHODS

cpDNA sequences from six species were sequenced and analyzed. Genome sizes, GC content, gene encoding potential, and structural integrity were assessed. Simple sequence repeats (SSRs) and codon usage were analyzed, with a focus on optimal codons and their frequency. Phylogenetic analysis was conducted to determine the genetic relationships within the genus.

RESULTS

The cpDNAs from the six species exhibited genome sizes ranging from 161,093 bp to 161,254 bp, with GC content between 35.72% and 35.75%. Each genome contained 91 to 92 protein-coding genes, with the infA gene consistently present. No significant gene rearrangements were detected, and SSR analysis revealed mono-repeats primarily composed of A/T bases. Codon usage analysis indicated that leucine is predominantly encoded by the UUA codon, and 31 optimal codons were identified, mainly ending in A or U. Phylogenetic analysis clarified the genetic relationships among the species.

CONCLUSIONS

The study provides detailed insights into the cpDNA characteristics of species, highlighting stable genome structures, conserved genes, and specific patterns of codon usage. These findings are valuable for conservation efforts, genetic improvement strategies, and the sustainable use of germplasm.

摘要

目的

本研究调查了六个物种的叶绿体DNA（cpDNA）序列，旨在探索其基因组特征、基因含量和遗传关系。目标包括了解这些基因组的结构，识别潜在的基因重排，并为该属的遗传改良和保护策略提供见解。

方法

对六个物种的cpDNA序列进行了测序和分析。评估了基因组大小、GC含量、基因编码潜力和结构完整性。分析了简单序列重复（SSR）和密码子使用情况，重点关注最佳密码子及其频率。进行了系统发育分析以确定该属内的遗传关系。

结果

六个物种的cpDNA基因组大小在161,093 bp至161,254 bp之间，GC含量在35.72%至35.75%之间。每个基因组包含91至92个蛋白质编码基因，infA基因始终存在。未检测到明显的基因重排，SSR分析显示单重复主要由A/T碱基组成。密码子使用分析表明，亮氨酸主要由UUA密码子编码，并鉴定出31个最佳密码子，主要以A或U结尾。系统发育分析阐明了物种之间的遗传关系。

结论

该研究提供了对物种cpDNA特征的详细见解，突出了稳定的基因组结构、保守的基因和特定的密码子使用模式。这些发现对于保护工作、遗传改良策略和种质的可持续利用具有重要价值。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5008/11855534/cdeed917a643/genes-16-00201-g012.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5008/11855534/49ad63c7985d/genes-16-00201-g002.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5008/11855534/4d514589247a/genes-16-00201-g004.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5008/11855534/cc0585ea6c4b/genes-16-00201-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5008/11855534/a190930800fa/genes-16-00201-g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5008/11855534/f5981deb0682/genes-16-00201-g008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5008/11855534/17bc702c9c1e/genes-16-00201-g009.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5008/11855534/d36f5ea04303/genes-16-00201-g010.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5008/11855534/ac7b25f0620c/genes-16-00201-g011.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5008/11855534/cdeed917a643/genes-16-00201-g012.jpg

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