Prevalent Exon-Intron Structural Changes in the APETALA1/FRUITFULL, SEPALLATA, AGAMOUS-LIKE6, and FLOWERING LOCUS C MADS-Box Gene Subfamilies Provide New Insights into Their Evolution

doi:10.3389/fpls.2016.00598

CORC > 植物研究所 > 中国科学院植物研究所 > 系统与进化植物学国家重点实验室

	Prevalent Exon-Intron Structural Changes in the APETALA1/FRUITFULL, SEPALLATA, AGAMOUS-LIKE6, and FLOWERING LOCUS C MADS-Box Gene Subfamilies Provide New Insights into Their Evolution
	Yu, Xianxian 1; Duan, Xiaoshan 1; Zhang, Rui ; Fu, Xuehao 1; Ye, Lingling 1; Kong, Hongzhi ; Xu, Guixia ; Shan, Hongyan
刊名	FRONTIERS IN PLANT SCIENCE
	2016
卷号	7
关键词	APETALA1/FRUITFULL SEPALLATA AGAMOUS-LIKE6 FLOWERING LOCUS C exon-intron structural change
ISSN号	1664-462X
DOI	10.3389/fpls.2016.00598
文献子类	Article
英文摘要	AP1/FUL, SEP, AGL6, and FLC subfamily genes play important roles in flower development. The phylogenetic relationships among them, however, have been controversial, which impedes our understanding of the origin and functional divergence of these genes. One possible reason for the controversy may be the problems caused by changes in the exon-intron structure of genes, which, according to recent studies, may generate non-homologous sites and hamper the homology-based sequence alignment. In this study, we first performed exon-by-exon alignments of these and three outgroup subfamilies (SOC1, AG, and STK). Phylogenetic trees reconstructed based on these matrices show improved resolution and better congruence with species phylogeny. In the context of these phylogenies, we traced evolutionary changes of exon-intron structures in each subfamily. We found that structural changes have occurred frequently following gene duplication and speciation events. Notably, exons 7 and 8 (if present) suffered more structural changes than others. With the knowledge of exon-intron structural changes, we generated more reasonable alignments containing all the focal subfamilies. The resulting trees showed that the SEP subfamily is sister to the monophyletic group formed by AP1/FUL and FLC subfamily genes and that the AGL6 subfamily forms a sister group to the three abovementioned subfamilies. Based on this topology, we inferred the evolutionary history of exon-intron structural changes among different subfamilies. Particularly, we found that the eighth exon originated before the divergence of AP1/FUL, FLC, SEP, and AGL6 subfamilies and degenerated in the ancestral FLC-like gene. These results provide new insights into the origin and evolution of the AP1/FUL, FLC, SEP, and AGL6 subfamilies.
学科主题	Plant Sciences
出版地	LAUSANNE
WOS关键词	MULTIPLE SEQUENCE ALIGNMENT ; FLORAL ORGAN IDENTITY ; FUNCTIONAL DIVERGENCE ; TRANSCRIPTION FACTORS ; BASAL ANGIOSPERMS ; HOMEOTIC PROTEINS ; FRUIT-DEVELOPMENT ; ARABIDOPSIS ; FAMILY ; DIVERSIFICATION
WOS研究方向	Science Citation Index Expanded (SCI-EXPANDED)
语种	英语
出版者	FRONTIERS MEDIA SA
WOS记录号	WOS:000375246000001
资助机构	National Natural Science Foundation of ChinaNational Natural Science Foundation of China (NSFC) [31125005, 31422006, 31570225] ; CAS Youth Innovation Promotion Association
内容类型	期刊论文
源URL	[http://ir.ibcas.ac.cn/handle/2S10CLM1/24352]
专题	系统与进化植物学国家重点实验室
作者单位	1.Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, Beijing, Peoples R China 2.Univ Chinese Acad Sci, Beijing, Peoples R China
推荐引用方式 GB/T 7714	Yu, Xianxian,Duan, Xiaoshan,Zhang, Rui,et al. Prevalent Exon-Intron Structural Changes in the APETALA1/FRUITFULL, SEPALLATA, AGAMOUS-LIKE6, and FLOWERING LOCUS C MADS-Box Gene Subfamilies Provide New Insights into Their Evolution[J]. FRONTIERS IN PLANT SCIENCE,2016,7.
APA	Yu, Xianxian.,Duan, Xiaoshan.,Zhang, Rui.,Fu, Xuehao.,Ye, Lingling.,...&Shan, Hongyan.(2016).Prevalent Exon-Intron Structural Changes in the APETALA1/FRUITFULL, SEPALLATA, AGAMOUS-LIKE6, and FLOWERING LOCUS C MADS-Box Gene Subfamilies Provide New Insights into Their Evolution.FRONTIERS IN PLANT SCIENCE,7.
MLA	Yu, Xianxian,et al."Prevalent Exon-Intron Structural Changes in the APETALA1/FRUITFULL, SEPALLATA, AGAMOUS-LIKE6, and FLOWERING LOCUS C MADS-Box Gene Subfamilies Provide New Insights into Their Evolution".FRONTIERS IN PLANT SCIENCE 7(2016).