Revealing mammalian evolutionary relationships by comparative analysis of gene clusters

Song, G, Riemer, C, Dickins, B ORCID: https://orcid.org/0000-0002-0866-6232, Kim, HL, Zhang, L, Zhang, Y, Hsu, C-H, Hardison, RC, NISC Comparative Sequencing Program, Green, ED and Miller, W, 2012. Revealing mammalian evolutionary relationships by comparative analysis of gene clusters. Genome Biology and Evolution, 4 (4), pp. 586-601. ISSN 1759-6653

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Abstract

Many software tools for comparative analysis of genomic sequence data have been released in recent decades. Despite this, it remains challenging to determine evolutionary relationships in gene clusters due to their complex histories involving duplications, deletions, inversions, and conversions. One concept describing these relationships is orthology. Orthologs derive from a common ancestor by speciation, in contrast to paralogs, which derive from duplication. Discriminating orthologs from paralogs is a necessary step in most multispecies sequence analyses, but doing so accurately is impeded by the occurrence of gene conversion events. We propose a refined method of orthology assignment based on two paradigms for interpreting its definition: by genomic context or by sequence content. X-orthology (based on context) traces orthology resulting from speciation and duplication only, while N-orthology (based on content) includes the influence of conversion events.

Item Type:	Journal article
Alternative Title:	Revealing evolutionary relationships in gene clusters [working title]
Publication Title:	Genome Biology and Evolution
Creators:	Song, G., Riemer, C., Dickins, B., Kim, H.L., Zhang, L., Zhang, Y., Hsu, C.-H., Hardison, R.C., NISC Comparative Sequencing Program, Green, E.D. and Miller, W.
Publisher:	Oxford University Press
Place of Publication:	Oxford
Date:	2012
Volume:	4
Number:	4
ISSN:	1759-6653
Identifiers:	Number Type 10.1093/gbe/evs032 DOI
Rights:	This is a pre-copy-editing, author-produced PDF of an article accepted for publication in Genome Biology and Evolution following peer review. The definitive publisher-authenticated version [citation above] is available online at: http://dx.doi.org/10.1093/gbe/evs032
Divisions:	Schools > School of Science and Technology
Record created by:	EPrints Services
Date Added:	09 Oct 2015 11:17
Last Modified:	09 Jun 2017 13:55
URI:	https://irep.ntu.ac.uk/id/eprint/25606

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