潘那利番茄GRF基因家族全基因组鉴定分析

doi:10.6048/j.issn.1001-4330.2022.10.014

新疆农业科学 ›› 2022, Vol. 59 ›› Issue (10): 2456-2465.DOI: 10.6048/j.issn.1001-4330.2022.10.014

• 园艺特产·林业·农产品加工工程 • 上一篇下一篇

潘那利番茄GRF基因家族全基因组鉴定分析

戴麒¹(), 徐瑞强¹, 李宁¹^,², 王柏柯¹, 王娟¹, 黄少勇², 帕提古丽·艾斯木托拉¹, 余庆辉¹()

1.新疆农业科学院园艺作物研究所,乌鲁木齐 830091
2.新疆农业大学林学与园艺学院,乌鲁木齐 830042

收稿日期:2021-11-30 出版日期:2022-10-20 发布日期:2022-12-21
通信作者: 余庆辉
作者简介:戴麒(1984-)男,辽宁人,助理研究员,研究方向为番茄遗传育种,(E-mail) daiqixj@163.com
基金资助:
国家自然科学基金(32260763);新疆农业科学院农业科技创新重点培育专项(xjkcpy-2021001);现代农业产业技术体系专项(CARS-23-G25)

Genome-Wide Characterization and Analysis of GRF Gene Family in the Solanum pennellii

DAI Qi¹(), XU Ruiqiang¹, LI Ning¹^,², WANG Baike¹, WANG Juan¹, HUANG Shaoyong², Patiguli Aisimutuola¹, YU Qinghui¹()

1. Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
2. College of Forestry & Horticulture, Xinjiang Agricultural University, Urumqi 830052, China

Received:2021-11-30 Online:2022-10-20 Published:2022-12-21
Correspondence author: YU Qinghui
Supported by:
The National Nature Science Foundation of China(32260763);Science & Technology Innovation of Xinjiang Academy of Agricultural Sciences(xjkcpy-2021001);China Agriculture Research System(CARS-23-G25)

摘要/Abstract

摘要：

【目的】分析研究潘那利番茄GRF基因家族全基因组鉴定分析。【方法】研究基于生物信息学方法对潘那利GRF基因家族成员进行全基因组鉴定和分析,并对其起源及进化进行了追溯。【结果】潘那利番茄中共鉴定了10个SpGRF成员,不均匀分布在7条染色体上,预测了SpGRFs蛋白的分子量、等电点、亲水性总均值等理化性质。SpGRFs基因可分为6个亚家族。所有SpGRF基因N端都含有1个QLQ和1个WRC结构域,C端则为多种保守基序。共线性结果显示基因组内有3对6个旁系同源基因,全部为片段复制,SpGRFs受自然选择压力下,有共同起源祖先,与拟南芥亲缘关系更近。【结论】鉴定了潘那利番茄中GRF基因家族的基本信息。

关键词: 潘那利番茄; GRF基因家族; 全基因组分析; 生物信息学

Abstract:

【Objective】 Analysis of Gene Family in the Solanum pennellii.【Methods】 In this study, the whole genome of Pannellii GRF gene family members was identified and analyzed based on bioinformatics methods, and its origin and evolution were traced.【Result】 Ten SpGRF members were identified in S.pennellii tomato, and they were unevenly distributed on seven chromosomes.The physical and chemical properties such as molecular weight, isoelectric point and total hydrophilic mean of SpGRFs protein were predicted.The phylogenetic tree showed that SpGRFs gene could be divided into six subfamilies.All SpGRF genes contained a QLQ and a WRC domain at the N-terminal and several conserved motifs at the C-terminal.The results of collinearity showed that there were three pairs of six paragenetic homologous genes in the genome, all of which were fragment replication.Under the pressure of natural selection, SpGRFs had a common ancestor, which was closer to Arabidopsis.【Conclusion】 This study successfully identifies the basic information of GRF gene family in S.pennellii, which has laid a theoretical foundation for explaining the function of GRF family and the mining of wild tomato gene resources.

Key words: Solanum pennellii; GRF gene family; genome-wide analysis; bioinformatics

中图分类号:

S641.2
S188

戴麒, 徐瑞强, 李宁, 王柏柯, 王娟, 黄少勇, 帕提古丽·艾斯木托拉, 余庆辉. 潘那利番茄GRF基因家族全基因组鉴定分析[J]. 新疆农业科学, 2022, 59(10): 2456-2465.

DAI Qi, XU Ruiqiang, LI Ning, WANG Baike, WANG Juan, HUANG Shaoyong, Patiguli Aisimutuola, YU Qinghui. Genome-Wide Characterization and Analysis of GRF Gene Family in the Solanum pennellii[J]. Xinjiang Agricultural Sciences, 2022, 59(10): 2456-2465.

图/表 10

表1 SpGRFs基因家族理化性质

Table 1 SpGRFs gene family physicochemical properties

基因名 name	基因 id	染色体 Chromosome	氨基酸数目 Number of amino acids (aa)	分子量 MW (Da)	等电点 pI	亲水性 (GRAVY)	脂肪指数 Aliphatic index	亚细胞定位 Subcellular localization
SpGRF1	Sopen01g037310	Spenn-ch01	420	46 630.8	9.31	-0.755	61.26	N,Cy,Ch,E
SpGRF2	Sopen02g036640	Spenn-ch02	604	64 906.7	8.23	-0.504	62.4	N,Cy,Ch
SpGRF3	Sopen03g022150	Spenn-ch03	461	50 686.8	6.69	-0.582	60.74	N,Ch
SpGRF4	Sopen04g031110	Spenn-ch04	595	64 143.4	8.22	-0.649	58.27	N,Cy,PM
SpGRF5	Sopen07g021120	Spenn-ch07	339	38 958.1	9.07	-0.932	47.46	N
SpGRF6	Sopen08g001470	Spenn-ch08	356	39 157	8.73	-0.725	48.71	N
SpGRF7	Sopen08g024600	Spenn-ch08	361	39 825.8	8.13	-0.753	50.25	N
SpGRF8	Sopen08g028160	Spenn-ch08	202	23 232.7	9.31	-0.621	66.53	N
SpGRF9	Sopen08g031420	Spenn-ch08	385	42 692.3	8.48	-0.788	53.25	N
SpGRF10	Sopen10g032980	Spenn-ch10	388	42 247.5	9.27	-0.659	57.86	N

图1 SpGRFs基因家族染色体核型

Fig.1 SpGRfs gene family Karyotype mapping

图2 SpGRFs基因家族进化树

Fig.2 SpGRFs gene family cladogram

图3 多物种间GRF基因家族进化关系

Fig.3 GRF gene family evolutionary relationships among multiple species

图4 SpGRFs基因家族保守基序及结构注:A.基因结构(外显子/内含子分布);B.保守基序分布。相同颜色的方块代表相同的基序

Fig.4 SpGRFs gene family conserved motifs and structural analysis Note:A.Distribution of the conserved motifs.B.Exon/intron distribution of SpGRF genes.The same colored boxes represent the same motifs

图5 SpGRFs蛋白的基序

Fig.5 SpGRFs gene family Motifs of the protein

图6 SpGRFs基因家族部分顺式作用元件分布

Fig.6 Distribution of cis acting elements in part of the SpGRFs gene family

图7 SpGRFs基因家族种内共线性

Fig.7 SpGRFs gene family intraspecies colinearity analysis

表2 GRF旁系同源基因KaKs分析及分化时间计算

Table 2 Analysis of spgrf paralog KaKs and calculation of differentiation time

重复基因对 Duplicated Gene Pairs	同义替换率 Ks	非同义替换率Ka	Ka/Ks	复制类型 Duplicated Type	分化时间 Time(Mya^*)
SpGRF6/SpGRF7	1.077	0.979	0.909	Segmental	2.835
SpGRF2/SpGRF4	1.006	0.998	0.992	Segmental	2.648
SpGRF3/SpGRF9	0.869	1.035	1.191	Segmental	2.287

图8 SpGRFs基因家族种间共线性注:从上往下依次为水稻(蓝色)、潘那利番茄(红色)和拟南芥(绿色)的基因组,红线为共线性关系

Fig.8 SpGRFs gene families Interspecies colinearity analysis Note:Genomes of rice(blue),panari tomato(red) and Arabidopsis(green) from top to bottom,The red line connects the collinearity gene

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潘那利番茄GRF基因家族全基因组鉴定分析

Genome-Wide Characterization and Analysis of GRF Gene Family in the Solanum pennellii

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