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作物学报 ›› 2018, Vol. 44 ›› Issue (9): 1334-1346.doi: 10.3724/SP.J.1006.2018.01334

• 研究论文 • 上一篇    下一篇

甘蓝型油菜PIN家族基因的鉴定与生物信息学分析

高堃1,2(),华营鹏1,2,宋海星1,2,官春云3,张振华1,2,周婷1,2,*()   

  1. 1 湖南农业大学资源环境学院, 湖南长沙 410128
    2 南方粮油作物协同创新中心, 湖南长沙 410128
    3 国家油料作物改良中心湖南分中心, 湖南长沙 410128
  • 收稿日期:2018-01-30 接受日期:2018-06-12 出版日期:2018-09-10 网络出版日期:2018-09-12
  • 通讯作者: 周婷
  • 基金资助:
    本研究由国家重点研发计划项目(2017YFD0200103);国家自然科学基金项目(31101596);国家自然科学基金项目(31372130);湖南农业大学新进教师科研启动基金项目(30555|550100100021);湖南农业大学校青年基金项目(17QN40);国家现代农业产业技术体系建设专项资助

Identification and Bioinformatics Analysis of the PIN Family Gene in Brassica napus

Kun GAO1,2(),Ying-Peng HUA1,2,Hai-Xing SONG1,2,Chun-Yun GUAN3,Zhen-Hua ZHANG1,2,Ting ZHOU1,2,*()   

  1. 1 College of Resource and Environment, Hunan Agricultural University, Changsha 410128, Hunan, China
    2 Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Changsha 410128, Hunan, China
    3 Hunan Branch, National Oil Crops Improvement Center, Changsha 410128, Hunan, China
  • Received:2018-01-30 Accepted:2018-06-12 Published:2018-09-10 Published online:2018-09-12
  • Contact: Ting ZHOU
  • Supported by:
    This study was supported by the National Key R&D Program of China(2017YFD0200103);National Natural Science Foundation of China(31101596);National Natural Science Foundation of China(31372130);Research Starting Foundation for New Teachers of Hunan Agricultural University(30555|550100100021);Youth Foundation of Hunan Agricultural University(17QN40);China Agriculture Research System

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摘要：

PIN家族基因是一类调控植物生长素极性运输的重要载体元件, PIN基因编码生长素输出蛋白, 介导生长素在植物体的运输, 然而在基因组较复杂的甘蓝型油菜中缺乏系统研究。本研究运用生物信息学方法在甘蓝型油菜全基因组数据库筛选甘蓝型油菜PIN家族基因, 对鉴定出的29个BnPINs基因开展拷贝数变异、分子特征、跨膜结构域、保守基序、染色体定位、系统进化树构建、PIN蛋白二级结构及三级结构预测等研究, 结合高通量转录组测序进行低氮胁迫下的转录水平分析。结果表明, 甘蓝型油菜PIN家族基因拷贝数明显多于拟南芥、甘蓝和白菜所具有的PIN家族基因数量; BnPINs蛋白多属于由碱性氨基酸组成的稳定蛋白, 含有保守的N末端结构域, 二级结构与拟南芥PIN蛋白相似; 系统进化选择能力分析表明, BnPINs基因与甘蓝和白菜PIN家族基因进化关系相近。转录组测序表明, BnPIN1s、BnPIN2s、BnPIN3s基因主要在甘蓝型油菜根部表达且受长期低氮(72 h)诱导, BnPIN6s和BnPIN8s基因主要在地上部表达, 低氮会抑制BnPIN6s表达。本研究结果为进一步研究甘蓝型油菜PIN家族基因生物学功能尤其是在响应低氮胁迫中的功能奠定基础, 为已知大量数据的其他物种家族基因生物信息学研究提供参考。

关键词: 甘蓝型油菜, 生长素, PIN, 家族基因, 生物信息学

Abstract:

The PIN family is a type of important carrier elements that regulate the polar transportation of auxin. The PIN genes encode auxin efflux carriers with multiple transmembrane domains that mediate auxin transport in plants. However, there is a lack of systematic research in the genome of complexity Brassica napus. In this study, the BnPIN genes were screened from the Brassica Database using bioinformatics, and study on molecular characteristics of BnPIN proteins, such as copy number variations, transmembrane domains, conserved motifs, chromosomal locations, phylogenetic relationships, secondary and three-dimensional structures, and high-throughput transcriptome sequencing was used to analyze the transcriptional level under low nitrate stress. The results showed that most of the BnPIN proteins which is belonged to the stable protein consisting of basic amino acids. The BnPIN family proteins contained secondary structures similar to those of Arabidopsis PINs accompanied by conserved N-terminal domains. The phylogenetic analysis showed that BnPIN genes were similar to the corresponding homologs of Brassica oleracea and Brassica rapa. High-throughput transcriptome analysis showed that the BnPIN1s, BnPIN2s, and BnPIN3s genes were mainly expressed in roots of Brassica napus under long-term (72 h) low nitrate (NO3 -) stress. The BnPIN6s and BnPIN8s genes were mainly expressed in the shoot and limited NO3 - repressed the BnPIN6s expression. This study is valuable for the research that the roles of the BnPIN family in the regulation of auxin transport. Our results also provide reference for the integrated genomic and transcriptomic studies of gene family in plant species with complex genomes.

Key words: Brassica napus, auxin, PIN, gene family, bioinformatics

图1

甘蓝型油菜、拟南芥、甘蓝、白菜PIN家族基因拷贝数变异柱状图顶部数值为该物种拷贝的基因数目。"

图2

甘蓝型油菜PIN家族蛋白结构域蓝色代表跨膜结构域, 粉色代表低复杂度结构。"

图3

甘蓝型油菜PIN家族蛋白氨基酸序列比对和保守结构域分析黄色区域为高度保守的氨基酸位点。"

图4

23个甘蓝型油菜PIN基因染色体分布"

图5

甘蓝型油菜PIN家族蛋白保守基序分布左侧为蛋白系列名称, 右侧不同颜色分别对应不同的保守基序在系列上的位置。"

图6

甘蓝型油菜PIN家族基因系统进化分析不同颜色代表不同的进化分支, I、II代表PIN家族2个亚组。"

图7

甘蓝型油菜BnPIN5b蛋白二级结构分析 GOR4和PSIPRED分别是进行二级结构分析的2种不同的工具。"

图8

甘蓝型油菜BnPIN2a蛋白三级结构预测三级结构预测该晶体为转运子。"

图9

低氮胁迫下甘蓝型油菜PIN家族基因转录组分析 S: 地上部; R: 根; 0、3、72 (h)代表缺氮胁迫的时间。图中结果表示3次生物学重复的平均值。"

图10

低氮胁迫下甘蓝型油菜PIN家族基因共表达网络分析和表达量分析 A: 共表达网络分析; B: 基因表达量分析; 圆圈节点代表基因, 节点的大小代表节点之间相互作用的能力, 两个节点之间的连线代表基因之间的相互作用; S: 地上部; R: 根; 0、3、72 (h)代表缺氮胁迫的时间。图中结果表示3次生物学重复的平均值。"

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