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Data for constructing insect genome content matrices for phylogenetic analysis and functional annotation.

Jeffrey Rosenfeld¹, Jonathan Foox², Rob DeSalle²

¹Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA; Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, USA.

|February 11, 2016

Summary

This summary is machine-generated.

This study used 21 insect genomes to build phylogenetic matrices, aiding in gene annotation and evolutionary analysis. It explores how e-value cutoffs impact identifying gene orthologs and understanding gene gains and losses.

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Published on: August 31, 2018

Area of Science:

Genomics
Bioinformatics
Evolutionary Biology

Background:

Insect genomes provide a rich resource for understanding evolutionary relationships and gene function.
Phylogenetic analysis is crucial for inferring evolutionary history and identifying gene orthologs.
The accuracy of ortholog determination is sensitive to the chosen parameters, such as e-value cutoffs.

Purpose of the Study:

To construct genome content matrices from 21 insect genomes for phylogenetic analysis and functional annotation.
To investigate the impact of scaled e-value cutoffs and single linkage clustering on ortholog determination.
To identify core and unique genes across five insect groups and analyze gene gain/loss events.

Main Methods:

Genome content matrix construction using 21 fully sequenced insect genomes.
Phylogenetic analysis employing scaled e-value cutoffs and single linkage clustering.
Identification of core (CORE) and unique (UNI) genes, and analysis of gene gains and losses.

Main Results:

A list of genomes used for matrix construction is provided.
Nexus files containing data matrices and Newick trees from phylogenetic analysis are available.
An Excel file details core and unique genes, alongside figures illustrating gene gain/loss patterns relative to consistency index cutoffs.

Conclusions:

The study provides valuable genomic data matrices and phylogenetic trees for insect evolutionary research.
The findings highlight the importance of e-value cutoff selection in accurate ortholog identification.
This work contributes to a better understanding of gene dynamics, including gains and losses, in insect evolution.