| 扁核木属植物叶绿体基因组特征分析 |
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| 引用本文： | 王飞,赵文植,董章宏,马路遥,李卫英,夏茂甜,王正德,辛培尧.扁核木属植物叶绿体基因组特征分析[J].热带作物学报,2022,43(9):1759-1770. |
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| 作者姓名： | 王飞 赵文植 董章宏 马路遥 李卫英 夏茂甜 王正德 辛培尧 |
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| 作者单位： | 1. 西南林业大学国家林业和草原局西南风景园林工程技术研究中心,云南昆明 6502242. 西南林业大学西南地区生物多样性保育国家林业和草原局重点实验室,云南昆明 650224 |
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| 基金项目： | 云南省科技厅科技计划重点研发项目(2018BB005) |
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| 摘 要： | 扁核木属（Prinsepia）植物在中国分布有4个种,均具有极高的食用和药用价值。为解析扁核木属植物的叶绿体基因组特征,基于现已发表的扁核木属植物叶绿体基因组,利用相关生物信息学手段进行其叶绿体基因结构、SSR、密码子偏好性和序列变异情况分析,并构建系统发育树。结果表明,2种扁核木属植物叶绿体基因组大小介于159 179~ 168 206 bp之间,平均GC含量为37.3%,从编码基因数目来看,仅相差2个tRNA,而蛋白编码基因和rRNA数目均一致,种间具有较高的保守性;在扁核木和蕤核叶绿体全基因组序列中各检测出分散重复49个,其中以正向重复和回文重复为主,占比达73%~82%,而串联重复数目分别为49个和58个,经简单重复序列SSR分析,分别在2种植物叶绿体基因组序列中分别筛选出100个和84个SSR位点,且多是以A/T碱基为主的单核苷酸重复类型;扁核木属植物叶绿体基因组密码子偏好性分析发现GC3的碱基含量显著低于GC1和GC2,说明密码子偏好以A、U结尾,ENC取值均大于48%,表明其密码子偏性较弱,中性绘图和PR2-plot分析发现自然选择是影响扁核木属植物密码子使用偏好性的主要原因,通过建立高、低基因表达库,以RSCU值为参考,确定了6个扁核木属最优密码子。经叶绿体基因组序列变异分析,根据核苷酸多态性指数Pi>0.015筛选出trnH-GUG-psbA,psbZ-trnG-UCC-trnfM-CAU-rps14和psaJ-rpl33-rps18等3个高变区,以蕤核叶绿体基因组为参考,在扁核木叶绿体基因组编码区发现存在大量的插入、缺失和SNP突变位点,并在蕤核叶绿体基因组中发现了多个该物种的特有基因。基于叶绿体基因组的trnS-trnG间隔区构建的系统发育树显示,4种扁核木属植物可分为南系（扁核木、台湾扁核木）和北系（蕤核、东北扁核木）两类。研究结果可为扁核木属植物的系统发育、分类鉴定及其资源的开发利用等相关研究提供理论基础。
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| 关 键 词： | 扁核木属 叶绿体基因组 特征分析 系统发育 |
| 收稿时间： | 2022-02-15 |
Analysis of Chloroplast Genome Characteristics of Prinsepia |
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| WANG Fei,ZHAO Wenzhi,DONG Zhanghong,MA Luyao,LI Weiying,XIA Maotian,WANG Zhengde,XIN Peiyao.Analysis of Chloroplast Genome Characteristics of Prinsepia[J].Chinese Journal of Tropical Crops,2022,43(9):1759-1770. |
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| Authors: | WANG Fei ZHAO Wenzhi DONG Zhanghong MA Luyao LI Weiying XIA Maotian WANG Zhengde XIN Peiyao |
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| Institution: | 1. Southwest Research Center for Landscape Architecture Engineering, State Forestry and Grassland Administration, Southwest Forestry University, Kunming, Yunnan 650224, China2. Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Southwest China, Southwest Forestry University, Kunming, Yunnan 650224, China |
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| Abstract: | There are four species of Prinsepia Royle in China, which have high edible and medicinal value. In order to elucidate the chloroplast genome characteristics of Prinsepia, we analyzed the chloroplast genome structure, simple sequence repeats (SSR) loci, the preference of the codon, and sequence variation using bioinformatics methods based on the published chloroplast genome sequences of Prinsepia, and constructed a phylogenetic tree in Prinsepia. The results showed that the chloroplast genome sizes of Prinsepia were ranged from 159 179 bp to 168 206 bp, and the average GC content was 37.3%. In terms of the number of coding genes, only two tRNAs were different, while the number of protein-coding genes and rRNA were all consistent, showing a high level of conservation between species. A total of 49 dispersed repeats were detected in the chloroplast genomes of P. utilis and P. uniflora, including mainly forward and palindromic repeats, accounting for 73% to 82%, while the number of tandem repeats was 49 and 58, respectively. By the simple repetitive sequence (SSR) analysis, 100 and 84 SSRs loci were detected respectively in the chloroplast genome sequence of P. utilis and P. uniflora, and most of SSRs were single nucleotide repeats with A/T base. The codon bias analysis of chloroplast genome of Prinsepia found that the base content of GC3 was significantly lower than that of GC1 and GC2, indicating that the codon preference ended with A and U, and the effective number of codon (ENC) values was all greater than 48%, indicating that the codon bias was weak. Analysis of Neutral-plot and PR2-plot showed that natural selection was the main factor affecting the codon preference of Prinsepia. By establishing high and low gene expression libraries and using RSCU values as reference, six optimal codons of Prinsepia were identified. Three highly variable regions trnH-GUG-psbA, psbZ-trnG-UCC-trnfM-CAU-rps14 and psaJ-rpl33-rps18 were screened by the chloroplast genome sequence variation analysis with nucleotide polymorphism index Pi>0.015. Taking the chloroplast genome of P. uniflora as a reference, a large number of insertions, deletions and SNP mutations were found in the coding region of chloroplast genome in P. utilis, and several unique genes of P. uniflora chloroplast genome were found. Based on the phylogenetic trees by trnS-trnG spacers in the chloroplast genomes of Prinsepia, there were two groups in the four species of Prinsepia, one was southern (P. utilis, P. scandens), and the other was northern (P. uniflora, P. sinensis). The present study would provide a theoretical basis for study of the phylogeny, taxonomic identification and resource exploitation of the genus in Prinsepia. |
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| Keywords: | Prinsepia Royle chloroplast genome characteristics analysis phylogeny |
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