An inferred fitness consequence map of the rice genome

Joly-Lopez, Z., Platts, A. E., Gulko, B., Choi, J. Y., Groen, S. C., Zhong, X., Siepel, A., Purugganan, M. D. (February 2020) An inferred fitness consequence map of the rice genome. Nat Plants, 6 (2). pp. 119-130. ISSN 2055-0278 (Public Dataset)

Abstract

The extent to which sequence variation impacts plant fitness is poorly understood. High-resolution maps detailing the constraint acting on the genome, especially in regulatory sites, would be beneficial as functional annotation of noncoding sequences remains sparse. Here, we present a fitness consequence (fitCons) map for rice (Oryza sativa). We inferred fitCons scores (rho) for 246 inferred genome classes derived from nine functional genomic and epigenomic datasets, including chromatin accessibility, messenger RNA/small RNA transcription, DNA methylation, histone modifications and engaged RNA polymerase activity. These were integrated with genome-wide polymorphism and divergence data from 1,477 rice accessions and 11 reference genome sequences in the Oryzeae. We found rho to be multimodal, with ~9% of the rice genome falling into classes where more than half of the bases would probably have a fitness consequence if mutated. Around 2% of the rice genome showed evidence of weak negative selection, frequently at candidate regulatory sites, including a novel set of 1,000 potentially active enhancer elements. This fitCons map provides perspective on the evolutionary forces associated with genome diversity, aids in genome annotation and can guide crop breeding programs.

Item Type:	Paper
Subjects:	bioinformatics > genomics and proteomics > genetics & nucleic acid processing > epigenetics bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > epigenetics evolution bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes organism description > plant > rice
CSHL Authors:	Siepel, Adam Gulko, Brad Joly-Lopez, Zoe Platts, Adrian E Choi, Jae Young Groen, Simon C
Communities:	CSHL labs > Siepel lab
Depositing User:	Adrian Gomez
Date:	10 February 2020
Date Deposited:	12 Feb 2020 19:13
Last Modified:	14 Dec 2020 16:16
PMCID:	PMC7446671
Related URLs:	Publisher
Dataset ID:	SRA: PRJNA586887 Additonal info / code: http://purugganan-genomebrowser.bio.nyu.edu/insightJuly2018/greenInsight.html
URI:	https://repository.cshl.edu/id/eprint/38977

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