植物学报 ›› 2017, Vol. 52 ›› Issue (6): 699-712.doi: 10.11983/CBB16244

• 研究报告 • 上一篇    下一篇

甘蓝型油菜MADS-box基因家族的鉴定与系统进化分析

高虎虎, 张云霄, 胡胜武, 郭媛*()   

  1. 西北农林科技大学农学院, 旱区作物逆境生物学国家重点实验室, 杨凌 712100
  • 收稿日期:2016-12-12 接受日期:2017-05-22 出版日期:2017-11-01 发布日期:2017-11-22
  • 通讯作者: 郭媛 E-mail:guoyuan2109@163.com
  • 基金资助:
    西北农林科技大学博士科研启动资金(No.Z109021614)、基本科研业务专项资金(No.Z109021703)和唐仲英作物育种基金(No. A212021713)

Genome-wide Survey and Phylogenetic Analysis of MADS-box Gene Family in Brassica napus

Gao Huhu, Zhang Yunxiao, Hu Shengwu, Guo Yuan*()   

  1. State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China
  • Received:2016-12-12 Accepted:2017-05-22 Online:2017-11-01 Published:2017-11-22
  • Contact: Guo Yuan E-mail:guoyuan2109@163.com

摘要:

MADS-box基因家族参与调控开花时间、花器官分化、根系生长、分生组织分化、子房和配子发育、果实膨大及衰老等植物生长发育的重要过程。基于甘蓝型油菜(Brassica napus)基因组测序数据, 利用生物信息学方法对甘蓝型油菜MADS-box基因家族进行鉴定和注释及基因结构与系统进化分析。结果显示, 在甘蓝型油菜中鉴定出307个MADS-box基因家族成员, 根据进化关系可将其分为两大类型, I型(M-type)包含α、β、γ三个亚家族, II型(MIKC-type)包括MIKCC和MIKC*两个亚家族, MIKCC可进一步分为13个小类; 甘蓝型油菜A基因组染色体上分布的MADS-box基因多于C基因组。在基因结构上, MIKC-type亚家族基因序列普遍比M-type长且含有较多的外显子; M-type亚家族蛋白序列中的motif数量为2-5个, MIKC-type亚家族蛋白序列中平均含有7个motif。拟南芥(Arabidopsis thaliana)与甘蓝型油菜MADS-box基因共线性分析结果显示, 全基因组复制事件对MADS-box基因家族尤其是MIKC亚家族的扩张起重要作用; MIKC亚家族基因在进化过程中受到的选择压力约为M-type的2倍, 这表明MIKC-type亚家族在进化过程中被选择性保留。

关键词: 甘蓝型油菜, MADS-box, 基因结构, 进化, 共线性

Abstract:

The MADS-box gene family is involved in many processes during plant growth and development, such as flowering time, floral organ differentiation, root growth, meristem differentiation, ovary and gamete development, fruit enlargement and senescence. In this study, we used rape (Brassica napus) genome sequencing data with bioinformatics methods to identify and annotate the MADS-box genes. Rape contains 307 members of MADS-box gene family. According to the evolutionary relationships, these genes can be divided into two subfamilies: I-type, also known as M-type, containing three subclades, α, β, and γ; II type, also known as MIKC-type containing two subclades, MIKCC and MIKC*. MIKCC can be further divided into 13 groups. The number of MADS-box genes is greater in the A than C subgenome chromosome of B. napus. For the gene structure, the sequence is longer for MIKC-type than M-type genes and contains more exons. The number of motifs in M-type genes is about 2-5, and MIKC-type genes contain an average of 7 motifs. Synteny analysis revealed that whole-genome duplication played a major role in the expansion of the BnaMADS gene family, especially the MIKC-type subfamily. The selection pressure of the MIKC-type subfamily was about 2 times that for the M-type, which resulted in the selective preservation of MIKC-type subfamily genes during evolution.

Key words: Brassica napus, MADS-box, gene structure, evolution, synteny

图1

甘蓝型油菜、拟南芥和水稻的MADS-box基因系统发育分析(A) M-type; (B) MIKC-type"

图2

甘蓝型油菜MADS-box基因在染色体上的分布"

图3

甘蓝型油菜MADS-box基因在染色体上分布的统计"

表1

甘蓝型油菜MADS-box基因在亚基因组上的分布"

Subgenome M-type MIKC-type Total
A 55 85 140
C 52 77 129

图4

甘蓝型油菜MADS-box基因家族的motif结构(A) MIKCC亚家族; (B) MIKC*亚家族;(C) M-type亚家族"

图5

与拟南芥共线性的MADS-box基因在甘蓝型油菜染色体上的分布"

图6

甘蓝型油菜与拟南芥MADS-box基因的共线性关系"

图7

拟南芥MADS-box基因在甘蓝型油菜中的拷贝数"

表2

甘蓝型油菜MADS-box基因亚家族的选择压力"

Subfamily Arabidopsis Brassica napus Average copy number Average Ka/Ks
thaliana
M-type 20 34 1.7 0.43
MIKC-type 29 95 3.27 0.22
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