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Related Experiment Video

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High-throughput Physical Mapping of Chromosomes using Automated in situ Hybridization

High-throughput Physical Mapping of Chromosomes using Automated in situ Hybridization

Published on: June 28, 2012

Putting the genome in insect phylogenomics.

Kevin P Johnson¹

¹Illinois Natural History Survey, Prairie Research Institute, University of Illinois, 1816 South Oak Street, Champaign, IL 61820 USA.

Current Opinion in Insect Science

|September 24, 2019

Summary

Next-generation sequencing enables large insect phylogenomic datasets. An automated Target Restricted Assembly Method (aTRAM) assembles thousands of genes from whole genomes, offering broader research applications beyond phylogenetics.

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Area of Science:

Entomology
Genomics
Bioinformatics

Background:

Next-generation sequencing (NGS) significantly expands molecular phylogenetic data for insect systematics.
Genome reduction methods like amplicon sequencing, target capture, and transcriptome sequencing are common for phylogenomics.
These methods offer limited utility for research beyond phylogenetic analysis.

Purpose of the Study:

To present an alternative method for generating large phylogenomic datasets from insect genomes.
To highlight the advantages of using whole-genome sequencing for broader biological inquiries.

Main Methods:

Sequencing entire insect genomes at modest coverage.
Employing an automated Target Restricted Assembly Method (aTRAM) to assemble single-copy ortholog genes using blast searches.
Compiling assembled genes into large phylogenomic datasets.

Main Results:

Thousands of single-copy ortholog genes can be assembled across insect groups using aTRAM.
Generated genomic libraries contain reads from mitochondrial and symbiont genomes, in addition to the nuclear genome.
These datasets are suitable for large-scale phylogenomic analyses.

Conclusions:

Whole-genome sequencing combined with aTRAM provides a powerful approach for insect phylogenetics.
This method yields comprehensive genomic libraries that support diverse research applications beyond phylogenetics, including population genomics and evolutionary studies.