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Genes 2018, 9(9), 456; https://doi.org/10.3390/genes9090456

Functional Evolution of Avian RIG-I-Like Receptors

Department of Evolutionary Studies of Biosystems, SOKENDAI (The Graduate University for Advanced Studies), Kanagawa 240-0193, Japan
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Received: 13 August 2018 / Revised: 6 September 2018 / Accepted: 6 September 2018 / Published: 12 September 2018
(This article belongs to the Special Issue Viral Genes and the Host: Evolution in Action)
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Abstract

RIG-I-like receptors (retinoic acid-inducible gene-I-like receptors, or RLRs) are family of pattern-recognition receptors for RNA viruses, consisting of three members: retinoic acid-inducible gene I (RIG-I), melanoma differentiation-associated gene 5 (MDA5) and laboratory of genetics and physiology 2 (LGP2). To understand the role of RLRs in bird evolution, we performed molecular evolutionary analyses on the coding genes of avian RLRs using filtered predicted coding sequences from 62 bird species. Among the three RLRs, conservation score and dN/dS (ratio of nonsynonymous substitution rate over synonymous substitution rate) analyses indicate that avian MDA5 has the highest conservation level in the helicase domain but a lower level in the caspase recruitment domains (CARDs) region, which differs from mammals; LGP2, as a whole gene, has a lower conservation level than RIG-I or MDA5. We found evidence of positive selection across all bird lineages in RIG-I and MDA5 but only on the stem lineage of Galliformes in LGP2, which could be related to the loss of RIG-I in Galliformes. Analyses also suggest that selection relaxation may have occurred in LGP2 during the middle of bird evolution and the CARDs region of MDA5 contains many positively selected sites, which might explain its conservation level. Spearman’s correlation test indicates that species-to-ancestor dN/dS of RIG-I shows a negative correlation with endogenous retroviral abundance in bird genomes, suggesting the possibility of interaction between immunity and endogenous retroviruses during bird evolution. View Full-Text
Keywords: molecular evolution; natural selection; innate immunity; pattern-recognition receptor; endogenous retrovirus; birds; RIG-I-like receptors (RLRs) molecular evolution; natural selection; innate immunity; pattern-recognition receptor; endogenous retrovirus; birds; RIG-I-like receptors (RLRs)
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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Zheng, W.; Satta, Y. Functional Evolution of Avian RIG-I-Like Receptors. Genes 2018, 9, 456.

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