Abstract
BackgroundNumerous biological functions of long intergenic non-coding RNAs (lincRNAs) have been identified. However, the contribution of lincRNAs to the domestication process has remained elusive. Following domestication from their wild ancestors, animals display substantial changes in many phenotypic traits. Therefore, it is possible that diverse molecular drivers play important roles in this process.ResultsWe analyzed 821 transcriptomes in this study and annotated 4754 lincRNA genes in the chicken genome. Our population genomic analysis indicates that 419 lincRNAs potentially evolved during artificial selection related to the domestication of chicken, while a comparative transcriptomic analysis identified 68 lincRNAs that were differentially expressed under different conditions. We also found 47 lincRNAs linked to special phenotypes.ConclusionsOur study provides a comprehensive view of the genome-wide landscape of lincRNAs in chicken. This will promote a better understanding of the roles of lincRNAs in domestication, and the genetic mechanisms associated with the artificial selection of domestic animals.
Highlights
Numerous biological functions of long intergenic non-coding RNAs have been identified
Constructing the lincRNA gene repertoire in the chicken genome based on 821 transcriptomes In order to capture the spectrum of chicken transcriptional diversity, we curated 715 RNA-seq libraries from 48 public datasets available in the National Center for Biotechnology Information (NCBI) database
We identified 2942 novel putative lincRNAs not previously reported in two long noncoding RNAs (lncRNAs) databases, a domestic-animal long noncoding RNA database (ALDB) [40] and NONCODE (Additional file 4: Figure S1A)
Summary
Numerous biological functions of long intergenic non-coding RNAs (lincRNAs) have been identified. The contribution of lincRNAs to the domestication process has remained elusive. Following domestication from their wild ancestors, animals display substantial changes in many phenotypic traits. Domestic animals generally display many phenotypic changes in behavior, morphology, and physiology compared to their wild ancestors. There is a very high phenotypic diversity among chicken breeds than any other bird species. These phenotypic variations are valuable resources for studying the evolution of complex genetic traits. Previous studies on the genetic mechanisms underlying the evolution of complex traits have mainly focused on protein-coding genes [1,2,3,4].
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