Comparison of orthologs across multiple species by various strategies
type: CreativeWork
description: Thanks to the improvement of genome sequencing technology, abundant multi-species genomic data now became available and comparative genomics continues to be a fast prospering filed of biological research. Through the comparison of genomes of different organisms, we can understand what, at the molecular level, distinguishes different life forms from each other. It shed light on revealing the evolution of biology. And it also helps to refine the annotations and functions of individual genomes. For example, through comparisons across mammalian genomes, we can give an estimate of the conserved set of genes across mammals and correspondingly, find the species-specific sets of genes or functions. However, comparative genomics can be feasible only if a meaningful classification of genes exists. A natural way to do so is to delineate sets of orthologous genes. However, debates exist about the appropriate way to define orthologs. It is originally defined as genes in different species which derive from speciation events. But such definition is not sufficient to derive orthologous genes due to the complexity of evolutionary events such as gene duplication and gene loss. While it is possible to correctly figure out all the evolutionary events with the true phylogenetic tree, the true phylogenetic tree itself is impractical to be inferred. Furthermore, evolutionary orthology does not necessarily have a strict correspondence to function similarity. Kruppel type zinc finger genes are important transcription factor families in eukaryotic species. Important as it is, the evolution of this zinc finger family is not completely clear yet. For example, the vertebrate roots of the KRAB-ZNF family in particular and of polydactyl ZNF genes in general, remain somewhat mysterious. In addition, due to its repeating gene structure and the fact that they often reside as clusters, these genes can be difficult to model correctly with common gene-finding tools. Furthermore, due to the repeating ge…
abstract: Thanks to the improvement of genome sequencing technology, abundant multi-species genomic data now became available and comparative genomics continues to be a fast prospering filed of biological research. Through the comparison of genomes of different organisms, we can understand what, at the molecular level, distinguishes different life forms from each other. It shed light on revealing the evolution of biology. And it also helps to refine the annotations and functions of individual genomes. For example, through comparisons across mammalian genomes, we can give an estimate of the conserved set of genes across mammals and correspondingly, find the species-specific sets of genes or functions. However, comparative genomics can be feasible only if a meaningful classification of genes exists. A natural way to do so is to delineate sets of orthologous genes. However, debates exist about the appropriate way to define orthologs. It is originally defined as genes in different species which derive from speciation events. But such definition is not sufficient to derive orthologous genes due to the complexity of evolutionary events such as gene duplication and gene loss. While it is possible to correctly figure out all the evolutionary events with the true phylogenetic tree, the true phylogenetic tree itself is impractical to be inferred. Furthermore, evolutionary orthology does not necessarily have a strict correspondence to function similarity. Kruppel type zinc finger genes are important transcription factor families in eukaryotic species. Important as it is, the evolution of this zinc finger family is not completely clear yet. For example, the vertebrate roots of the KRAB-ZNF family in particular and of polydactyl ZNF genes in general, remain somewhat mysterious. In addition, due to its repeating gene structure and the fact that they often reside as clusters, these genes can be difficult to model correctly with common gene-finding tools. Furthermore, due to the repeating ge…
author: Liu, Hui
language: en
keywords: orthology, alignment, zinc finger, honeybee, social-behavior
date published: 2014-05-30T16:44:00Z
date modified: 2026-07-22T22:25:38Z
provider: University of Illinois - Urbana-Champaign
publisher: Networked Digital Library of Theses and Dissertations
type: WebPage
source organization: University of Illinois at Urbana-Champaign

PropertyValue
property ID: Handle
value: http://hdl.handle.net/2142/49436