The Fate of Arabidopsis thaliana Homeologous CNSs and Their Motifs in the Paleohexaploid Brassica rapa

doi:10.1093/gbe/evt035

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	The Fate of Arabidopsis thaliana Homeologous CNSs and Their Motifs in the Paleohexaploid Brassica rapa
	Subramaniam, Sabarinath 1; Wang, Xiaowu 2; Freeling, Michael 1; Pires, J. Chris 3
刊名	GENOME BIOLOGY AND EVOLUTION
	2013
卷号	5 期号:4 页码:646-660
关键词	conserved noncoding sequence CNS fractionation mutagenesis deletion G-box PIL5 Arabidopsis Brassica rapa
ISSN号	1759-6653
DOI	10.1093/gbe/evt035
通讯作者	Subramaniam, Sabarinath
英文摘要	Following polyploidy, duplicate genes are often deleted, and if they are not, then duplicate regulatory regions are sometimes lost. By what mechanism is this loss and what is the chance that such a loss removes function? To explore these questions, we followed individual Arabidopsis thaliana-A. thaliana conserved noncoding sequences (CNSs) into the Brassica ancestor, through a paleohexaploidy and into Brassica rapa. Thus, a single Brassicaceae CNS has six potential orthologous positions in B. rapa; a single Arabidopsis CNS has three potential homeologous positions. We reasoned that a CNS, if present on a singlet Brassica gene, would be unlikely to lose function compared with a more redundant CNS, and this is the case. Redundant CNSs go nondetectable often. Using this logic, each mechanism of CNS loss was assigned a metric of functionality. By definition, proved deletions do not function as sequence. Our results indicated that CNSs that go nondetectable by base substitution or large insertion are almost certainly still functional (redundancy does not matter much to their detectability frequency), whereas those lost by inferred deletion or indels are approximately 75% likely to be nonfunctional. Overall, an average nondetectable, once-redundant CNS more than 30 bp in length has a 72% chance of being nonfunctional, and that makes sense because 97% of them sort to a molecular mechanism with "deletion" in its description, but base substitutions do cause loss. Similarly, proved-functional G-boxes go undetectable by deletion 82% of the time. Fractionation mutagenesis is a procedure that uses polyploidy as a mutagenic agent to genetically alter RNA expression profiles, and then to construct testable hypotheses as to the function of the lost regulatory site. We show fractionation mutagenesis to be a "deletion machine" in the Brassica lineage.
学科主题	Evolutionary Biology ; Genetics & Heredity ; EVOLUTIONARY BIOLOGY ; GENETICS & HEREDITY
语种	英语
出版者	OXFORD UNIV PRESS
WOS记录号	WOS:000318557200002
内容类型	期刊论文
源URL	[http://111.203.20.206/handle/2HMLN22E/101909]
专题	蔬菜花卉研究所
作者单位	1.Univ Calif Berkeley, Dept Plant & Microbial Biol, Berkeley, CA 94720 USA 2.Chinese Acad Agr Sci, Inst Vegetables & Flowers, Beijing 100193, Peoples R China 3.Univ Missouri, Div Biol Sci, Columbia, MO 65211 USA
推荐引用方式 GB/T 7714	Subramaniam, Sabarinath,Wang, Xiaowu,Freeling, Michael,et al. The Fate of Arabidopsis thaliana Homeologous CNSs and Their Motifs in the Paleohexaploid Brassica rapa[J]. GENOME BIOLOGY AND EVOLUTION,2013,5(4):646-660.
APA	Subramaniam, Sabarinath,Wang, Xiaowu,Freeling, Michael,&Pires, J. Chris.(2013).The Fate of Arabidopsis thaliana Homeologous CNSs and Their Motifs in the Paleohexaploid Brassica rapa.GENOME BIOLOGY AND EVOLUTION,5(4),646-660.
MLA	Subramaniam, Sabarinath,et al."The Fate of Arabidopsis thaliana Homeologous CNSs and Their Motifs in the Paleohexaploid Brassica rapa".GENOME BIOLOGY AND EVOLUTION 5.4(2013):646-660.