新疆农业科学 ›› 2022, Vol. 59 ›› Issue (10): 2456-2465.DOI: 10.6048/j.issn.1001-4330.2022.10.014
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()
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:
DAI Qi1(), XU Ruiqiang1, LI Ning1,2, WANG Baike1, WANG Juan1, HUANG Shaoyong2, Patiguli Aisimutuola1, YU Qinghui1()
Received:
2021-11-30
Online:
2022-10-20
Published:
2022-12-21
Correspondence author:
YU Qinghui
Supported by:
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。
中图分类号:
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.
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 |
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
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 |
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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