Mar 29, 2020

Evolutionarily conserved non-protein-coding regions in the chicken genome harbor functionally important variation

BioRxiv : the Preprint Server for Biology
C. GrossMirte Bosse

Abstract

The availability of genomes for many species has advanced our understanding of the non-protein-coding fraction of the genome. Comparative genomics has proven to be an invaluable approach for the systematic, genome-wide identification of conserved non-protein-coding elements (CNEs). However, for many non-mammalian model species, including chicken, our capability to interpret the functional importance of variants overlapping CNEs has been limited by current genomic annotations, which rely on a single information type (e.g. conservation). We here studied CNEs in chicken using a combination of population genomics and comparative genomics. To investigate the functional importance of variants found in CNEs we develop a ch(icken) Combined Annotation-Dependent Depletion (chCADD), a variant effect prediction tool first introduced for humans and later on for mouse and pig. We show that 73 Mb of the chicken genome has been conserved across more than 280 million years of vertebrate evolution. The vast majority of the conserved elements are in non-protein-coding regions, which display SNP densities and allele frequency distributions characteristic of genomic regions constrained by purifying selection. By annotating SNPs with the chCADD scor...Continue Reading

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Mentioned in this Paper

Genome-Wide Association Study
European American
Basal Cell Carcinoma Pathway
Cross Validation
Pierre Robin Syndrome
Simulation
Analysis
Polygene
Gene Therapy
Single Nucleotide Polymorphism

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