Phylogenetic Inference of Homologous/Orthologous Genes Among Distantly Related Plants
Related Experiment Video
Updated: Jul 8, 2025

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
Published on: August 14, 2018
Zilong Xu1, Wenyan Sun1, Ziqiang Zhu1
1College of Life Sciences, Nanjing Normal University, Nanjing, China.
Abstract:
The recent surge in plant genomic and transcriptomic data has laid a foundation for reconstructing evolutionary scenarios and inferring potential functions of key genes related to plants' development and stress responses. The classical scheme for identifying homologous genes is sequence similarity-based searching, under the crucial assumption that homologous sequences are more similar to each other than they are to any other non-homologous sequences. Advances in plant phylogenomics and computational algorithms have enabled us to systemically identify homologs/orthologs and reconstruct their evolutionary histories among distantly related lineages. Here, we present a comprehensive pipeline for homologous sequences identification, phylogenetic relationship inference, and potential functional profiling of genes in plants. Key features • Identification of orthologs using large-scale genomic and transcriptomic data. • This protocol is generalized for analyzing the evolution of plant genes.
More Related Videos
08:09Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics
Published on: June 17, 2012
10:40Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine
Published on: December 22, 2017
Related Concept Videos
Evolutionary Relationships through Genome Comparisons
Gene Evolution - Fast or Slow?
In contrast, regions which code...
Phylogenetic Trees
Phylogeny
Gene Families
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
Synteny and Evolution
Around 80 million years ago, the human and mice lineages diverged from the common ancestor. During the course of evolution, the ancestral...