[1]陈文文,吴怀通,陈赢男*.SPL家族基因复制及功能分化分析[J].南京林业大学学报(自然科学版),2020,44(05):055-66.[doi:10.3969/j.issn.1000-2006.201912052]
 CHEN Wenwen,WU Huaitong,CHEN Yingnan*.Gene duplications and functional divergence analyses of the SPL gene family[J].Journal of Nanjing Forestry University(Natural Science Edition),2020,44(05):055-66.[doi:10.3969/j.issn.1000-2006.201912052]
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SPL家族基因复制及功能分化分析
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《南京林业大学学报(自然科学版)》[ISSN:1000-2006/CN:32-1161/S]

卷:
44
期数:
2020年05期
页码:
055-66
栏目:
研究论文
出版日期:
2020-09-23

文章信息/Info

Title:
Gene duplications and functional divergence analyses of the SPL gene family
文章编号:
1000-2006(2020)05-0055-12
作者:
陈文文吴怀通陈赢男*
(南京林业大学林木遗传与生物技术省部共建教育部重点实验室,南京林业大学林学院, 南方现代林业协同创新中心,江苏 南京 210037)
Author(s):
CHEN Wenwen WU Huaitong CHEN Yingnan*
(Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Co-Innovation Center for the Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China)
关键词:
SPL基因家族 miR156 全基因组复制 串联复制 功能分化
Keywords:
SPL gene family miR156 whole-genome duplication tandem duplication functional divergence
分类号:
S718; Q78
DOI:
10.3969/j.issn.1000-2006.201912052
文献标志码:
A
摘要:
【目的】基因复制及随后的功能分化是基因组和物种演化的重要驱动力。植物特有的转录因子家族SPL(SQUAMOSA-promoter binding protein like)广泛参与调控植物生长发育及响应逆境胁迫,为研究重复基因的起源方式和进化命运提供了良好的研究系统。本研究对葡萄(Vitis vinifera)、番木瓜(Carica papaya)、毛果杨(Populus trichocarpa)和拟南芥(Arabidopsis thaliana)4种模式植物的SPL基因家族开展基因复制及功能分化分析,为进一步研究SPL基因功能、预测种属特异性的功能基因提供系统进化角度的参考。【方法】利用SBP特征结构域,鉴定葡萄、番木瓜、毛果杨和拟南芥4种模式植物中SPL基因家族成员,并利用最大似然法构建系统进化树。基于物种内、物种间基因组共线性,分析SPL基因家族发生基因复制的方式及差异保留情况,并计算保留的SPL直系和旁系同源基因的同义、非同义替换率,分析功能分化情况。【结果】在4种模式植物中共鉴定出SPL基因73个,其中42个是miR156的靶基因。系统进化分析显示:73个SPL基因聚类为9个主要分支,miR156靶向SPL基因成簇聚集在6个主要分支; Clade I中SPL基因编码的2个锌指结构基序为C4和C2HC,而其余8个分支中SPL基因的锌指结构基序由C3H和C2HC组成。大规模基因组复制事件(片段复制或全基因组复制)是SPL基因家族发生基因重复的主要方式。根据基因组复制事件推算,15个古基因位点理论上应复制出的360个位点中,83.6%的重复位点发生丢失或演化成非SPL基因。本研究鉴定出旁系同源基因17对,直系同源基因27对,且所有旁系和直系同源基因的Ka/Ks(非同义替换率和同义替换率之比)值均小于1。【结论】在不同物种中保留下来的SPL直系同源基因受到较强的纯化选择,在功能上具有保守性; 同一物种中保留下来的SPL旁系同源基因在进化过程中维持部分功能冗余,但在组织表达偏好性和蛋白功能上已呈现出不同形式的分化
Abstract:
【Objective】Duplication and subsequent divergence of genes play important roles in driving the evolution of genomes and species. The SQUAMOSA promoter-binding-like(SPL)genes be long to a family of plant-specific transcription factors that regulate numerous fundamental aspects of plant growth and development as well as stress response. The SPL gene family provides an excellent system to analyze the evolutionary fate and consequences of duplicated genes. In this study, gene duplication and the functional divergence of the SPL gene family were analyzed in four model plants, including Vitis vinifera, Carica papaya, Populus trichocarpa and Arabidopsis thaliana. 【Method】The SPL genes of V. vinifera, C. papaya, P. trichocarpa and A. thaliana were identified by using the conserved SQUAMOSA-PROMOTER BINDING PROTEIN domain as the query, and a phylogenetic tree was constructed with the maximum likelihood method. Based on the genome collinearity within and between species, the SPL gene duplication patterns and differential retention were identified in the four plants. The Ka/Ks values were calculated for each retained SPL paralog and ortholog, and functional divergence of these genes was analyzed. 【Result】A total of 73 SPL genes were identified in the four investigated plants, and 42 of them were miR156 target genes. The phylogenetic analysis revealed that the 73 SPL genes were classified into nine major clades, with the miR156 targets being clustered in six major clades. The SPL genes in Clade I encoded two zinc finger motifs, namely C4 and C2HC, while genes in the remaining clades encoded C3H and C2HC. Large-scale duplication events(segmental or whole-genome duplication)have played important roles in SPL gene expansion. Based on whole-genome duplications in each species, there were theoretically 360 loci duplicated from 15 ancestral loci; however, 83.6% of them were lost or evolved into non-SPL genes. Among the retained SPL genes, 17 paralogous and 27 orthologous pairs were identified, and the Ka/Ks values of all paralogous and orthologous pairs were lower than 1. 【Conclusion】The SPL genes originating from the ancestor have differentially been retained and expanded in the genomes of the four model plants. Orthologous or paralogous SPL pairs are under strong purifying selection and show conserved structure and function, leading to strong functional conservation. Additionally, an emerging pattern of divergence, including expression bias, subfunctionalization, and neofunctionalization, was revealed among the paralogous SPL pairs. Our findings provide phylogenetic information for studying gene function and identifying species-specific genes

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备注/Memo

备注/Memo:
收稿日期:2019-12-27 修回日期:2020-07-08 基金项目:江苏省高校“青蓝工程”优秀青年骨干教师项目; 国家自然科学基金青年项目(031010156); 青年人才托举工程项目(YESS20160121); 江苏高校优势学科建设工程资助项目(PAPD)。 第一作者:陈文文(chenww@njfu.edu.cn)。*通信作者:陈赢男(chenyingnan@njfu.edu.cn),副教授,ORCID(0000-0002-0095-6040)。
更新日期/Last Update: 1900-01-01