Bayesian phylogeny analysis of vertebrate serpins illustrates evolutionary conservation of the intron and indels based six groups classification system from lampreys for ~500 MY
- Published
- Accepted
- Subject Areas
- Aquaculture, Fisheries and Fish Science, Biochemistry, Evolutionary Studies, Genetics, Genomics
- Keywords
- vertebrates, Serpins, Bayesian phylogeny, gene structure, gene duplication, intron-exon
- Copyright
- © 2015 Kumar
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ PrePrints) and either DOI or URL of the article must be cited.
- Cite this article
- 2015. Bayesian phylogeny analysis of vertebrate serpins illustrates evolutionary conservation of the intron and indels based six groups classification system from lampreys for ~500 MY. PeerJ PrePrints 3:e1126v1 https://doi.org/10.7287/peerj.preprints.1126v1
Abstract
The serpin superfamily is characterized by proteins that fold into a conserved tertiary structure and exploits a sophisticated and irreversible suicide-mechanism of inhibition. Vertebrate serpins can be conveniently classified into six groups (V1-V6), based on three independent biological features - genomic organization, diagnostic amino acid sites and rare indels. However, this classification system was based on the limited number of mammalian genomes available. In this study, several non-mammalian genomes are used to validate this classification system, using the powerful Bayesian phylogenetic method. This method supports the intron and indel based vertebrate classification and proves that serpins have been maintained from lampreys to humans for about 500 MY. Lampreys have less than 10 serpins, which expanded into 36 serpins in humans. The two expanding groups V1 and V2 have SERPINB1/SERPINB6 and SERPINA8/SERPIND1 as the ancestral serpins, respectively. Large clusters of serpins are formed by local duplications of these serpins in tetrapod genomes. Interestingly, the ancestral HCII/SERPIND1 locus (nested within PIK4CA) possesses group V4 serpin (A2APL1, homolog of α2-AP/SERPINF2 ) of lampreys; hence, pointing to the fact that group V4 might have originated from group V2. Additionally in this study, the phylogenetic history and genomic characteristics of vertebrate serpins were revisited.
Author Comment
This version has been acccepted for publication at PeerJ.
Supplemental Information
Maximum Likelihood fits of 50 different amino acid substitution models of alignment of serpins using MEGA 5.
The lowest BIC scores (Bayesian Information Criterion) are considered for the best fit of the substitution pattern.