Skip to main content

Integrative comparative analysis of avian chromosome evolution by in-silico mapping of the gene ontology of homologous synteny blocks and evolutionary breakpoint regions

Claeys, Jules, Romanov, Michael N., Griffin, Darren K. (2023) Integrative comparative analysis of avian chromosome evolution by in-silico mapping of the gene ontology of homologous synteny blocks and evolutionary breakpoint regions. Genetica, 151 (3). pp. 167-178. ISSN 0016-6707. E-ISSN 1573-6857. (doi:10.1007/s10709-023-00185-x) (KAR id:100550)

Abstract

Avian chromosomes undergo more intra- than interchromosomal rearrangements, which either induce or are associated with genome variations among birds. Evolving from a common ancestor with a karyotype not dissimilar from modern chicken, two evolutionary elements characterize evolutionary change: homologous synteny blocks (HSBs) constitute common conserved parts at the sequence level, while evolutionary breakpoint regions (EBRs) occur between HSBs, defining the points where rearrangement occurred. Understanding the link between the structural organization and functionality of HSBs and EBRs provides insight into the mechanistic basis of chromosomal change. Previously, we identified gene ontology (GO) terms associated with both; however, here we revisit our analyses in light of newly developed bioinformatic algorithms and the chicken genome assembly galGal6. We aligned genomes available for six birds and one lizard species, identifying 630 HSBs and 19 EBRs. We demonstrate that HSBs hold vast functionality expressed by GO terms that have been largely conserved through evolution. Particularly, we found that genes within microchromosomal HSBs had specific functionalities relevant to neurons, RNA, cellular transport and embryonic development, and other associations. Our findings suggest that microchromosomes may have conserved throughout evolution due to the specificity of GO terms within their HSBs. The detected EBRs included those found in the genome of the anole lizard, meaning they were shared by all saurian descendants, with others being unique to avian lineages. Our estimate of gene richness in HSBs supported the fact that microchromosomes contain twice as many genes as macrochromosomes.

Item Type: Article
DOI/Identification number: 10.1007/s10709-023-00185-x
Additional information: For the purpose of open access, the author(s) has applied a Creative Commons Attribution (CC BY) licence to any Author Accepted Manuscript version arising.
Uncontrolled keywords: Avian genome; Chromosome evolution; Evolutionary breakpoint regions; Multispecies homologous synteny blocks; Gene ontology; Bioinformatics tools
Subjects: Q Science > QH Natural history
Q Science > QH Natural history > QH426 Genetics
Q Science > QL Zoology
Divisions: Divisions > Division of Natural Sciences > Centre for Interdisciplinary Studies of Reproduction
Divisions > Division of Natural Sciences > Biosciences
Signature Themes: Food Systems, Natural Resources and Environment
Funders: Biotechnology and Biological Sciences Research Council (https://ror.org/00cwqg982)
Depositing User: Mike Romanov
Date Deposited: 21 Mar 2023 07:58 UTC
Last Modified: 20 Nov 2023 15:27 UTC
Resource URI: https://kar.kent.ac.uk/id/eprint/100550 (The current URI for this page, for reference purposes)

University of Kent Author Information

  • Depositors only (login required):

Total unique views for this document in KAR since July 2020. For more details click on the image.