小拟南芥MKK基因家族全基因组鉴定及进化和表达分析

doi:10.16288/j.yczz.19-388

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Hereditas(Beijing) ›› 2020, Vol. 42 ›› Issue (4): 403-421.doi: 10.16288/j.yczz.19-388

• Research Article • Previous Articles

Genome-wide identification, phylogenetic analysis and expression profiling of the MKK gene family in Arabidopsis pumila

Xiaocui Li¹, Kaicheng Kang¹, Xianzhong Huang^2,³(), Yongbin Fan¹, Miaomiao Song¹, Yunjie Huang¹, Jiajia Ding¹

^1. Plant Genomics Laboratory, College of Life Sciences, Shihezi University, Shihezi 832003, China
^2. College of Agriculture, Anhui Science and Technology University, Fengyang 233100, China
^3. College of Life Sciences, Shihezi University, Shihezi 832003, China

Received:2019-12-30 Revised:2020-03-15 Online:2020-04-20 Published:2020-03-27
Contact: Huang Xianzhong E-mail:xianzhongh106@163.com
Supported by:
Supported by the National Natural Science Foundation of China No(U1303302);International Science and Technology Cooperation Project of Shihezi University No(GJHZ201806)

Abstract

Abstract:

Mitogen-activated protein kinase kinase (MAPKK or MKK) is an important component of the MAPK cascade, which plays important roles in plant growth and development as well as in various stress responses. At present, the MKK gene family has been identified in a variety of plants, but there has been no systematic study in Cruciferous plant Arabidopsis pumila. To explore the evolution and function of the MKK gene family in Arabidopsis pumila, 16 ApMKK genes were identified from the Arabidopsis pumila genome by genome-wide analysis, and they were distributed on 10 chromosomes of Arabidopsis pumila. According to phylogenetic analysis and multiple sequence alignment, these putative genes were divided into five known subfamilies, i.e, Groups A, B, C, D, and E, which includes 5, 2, 4, 3, 2 members, respectively. Evolutionary and syntenic analysis showed that there are seven pairs of duplication genes in Arabidopsis pumila: ApMKK1-1/1-2, ApMKK2-1/2-2, ApMKK3-1/3-2, ApMKK4-1/4-2, ApMKK5-1/5-2, ApMKK9-1/9-2, and ApMKK10-1/10-2. Ka/Ks and Tajima analysis indicated that evolution of ApMKK1-1/1-2 was accelerated after the duplication event. Combining the distribution of cis-element in the promoter region of ApMKKs and the expression profile of ApMKKs in mature leaves, stems, flowers and fruits as well as under salt stress, we found that the expressions of paralogous genes (duplication genes) were tissue-specific and their functions were diversified. The expression patterns of some duplicated genes in tissues were different, but the expression patterns under salt stress were basically the same. These results lay the foundation for analyzing the complex mechanisms of MKK-mediated growth and development and abiotic stress signal transduction pathways in Arabidopsis pumila.

Key words: mitogen-activated protein kinase kinase, Arabidopsis pumila, gene family, tissue expression, salt stress

Xiaocui Li, Kaicheng Kang, Xianzhong Huang, Yongbin Fan, Miaomiao Song, Yunjie Huang, Jiajia Ding. Genome-wide identification, phylogenetic analysis and expression profiling of the MKK gene family in Arabidopsis pumila[J]. Hereditas(Beijing), 2020, 42(4): 403-421.

Figures/Tables 13

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基因1	基因2	CDS相似性(%)	蛋白相似性(%)
ApMKK1-1	ApMKK1-2	97.27	97.46
ApMKK2-1	ApMKK2-2	97.07	98.63
ApMKK3-1	ApMKK3-2	97.95	98.66
ApMKK4-1	ApMKK4-2	97.83	98.91
ApMKK5-1	ApMKK5-2	97.09	98.03
ApMKK9-1	ApMKK9-2	96.59	99.04
ApMKK10-1	ApMKK10-2	96.07	94.90

复制基因对	Ka	Ks	Ka/Ks	进化选择模式
ApMKK4-2/ApMKK4-1	0.0036	0.0755	0.0478	纯化选择
ApMKK5-1/ApMKK5-2	0.0075	0.0787	0.0955	纯化选择
ApMKK3-2/ApMKK3-1	0.0058	0.0735	0.0795	纯化选择
ApMKK1-2/ApMKK1-1	0.0123	0.0828	0.1485	纯化选择
ApMKK2-1/ApMKK2-2	0.0084	0.1060	0.0794	纯化选择
ApMKK10-1/ApMKK10-2	0.0228	0.0992	0.2298	纯化选择
ApMKK9-1/ApMKK9-2	0.0042	0.1434	0.0294	纯化选择

测试组	Mt	M1	M2	χ²	P
ApMKK4-1/ApMKK4-2-AtMKK4	347	1	2	0.33	0.56370
ApMKK5-1/ApMKK5-2-AtMKK5	335	3	1	1.00	0.31731
ApMKK3-1/ApMKK3-2-AtMKK3	493	5	2	1.29	0.25684
ApMKK1-1/ApMKK1-2-AtMKK1	325	7	1	4.50	0.03389
ApMKK2-1/ApMKK2-1-AtMKK2	352	3	2	0.20	0.65472
ApMKK9-1/ApMKK9-2-AtMKK9	295	2	1	0.33	0.56370
ApMKK10-1/ApMKK10-1-AtMKK10	253	9	4	1.92	0.16552

Genome-wide identification, phylogenetic analysis and expression profiling of the MKK gene family in Arabidopsis pumila

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