Hemiptera phylogenomic resources: Tree‐based orthology prediction and conserved exon identification

Owen, Christopher L.; Stern, David B.; Hilton, Sarah K.; Crandall, Keith A.

doi:10.1111/1755-0998.13180

Hemiptera phylogenomic resources: Tree‐based orthology prediction and conserved exon identification

Journal Article · Mon Jul 13 00:00:00 EDT 2020 · Molecular Ecology Resources

DOI:https://doi.org/10.1111/1755-0998.13180· OSTI ID:1638292

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Computational Biology Institute George Washington University Washington DC USA, Systematic Entomology Laboratory USDA‐ARS Beltsville MD USA
Computational Biology Institute George Washington University Washington DC USA, Department of Integrative Biology University of Wisconsin ‐ Madison Madison WI USA
Computational Biology Institute George Washington University Washington DC USA, Department of Genome Sciences University of Washington Washington DC USA
Computational Biology Institute George Washington University Washington DC USA

Abstract

High‐throughput sequencing of transcriptomes and targeted genomic regions are advancing our knowledge of The Tree of Life. Building phylogenies with regions of the genome requires 1‐to‐1 orthologue resources of genes and noncoding loci. One organismal group that has received little attention in this area is the Hemiptera, the fifth largest insect order represented by ~103,590 named species. Here, we present a set of 3,872 Hemiptera 1‐to‐1 orthogroups based on tree‐based orthology inference of eight Hemiptera species with publicly available genome sequences. We also estimate a set of 406 orthologous exons with similar mRNA splice sites that can be used for Sanger sequencing and develop enrichment probes for targeted genome sequencing for phylogenomic inference. We show this novel set of orthologues is informative at the protein, coding sequence and exon molecular levels and provides robust branch support in both gene tree–species tree methods and concatenated sequence phylogenies. In addition, we demonstrate the utility of these loci to resolve relationships in whiteflies, Bemisia tabaci , a large species complex with few phylogenomic resources. Last, we compare our Hemiptera phylogeny with previously published phylogenies and other orthologue databases, while providing suggestions on further improvement to this phylogenomic resource.

View Accepted Manuscript (Publisher)

Sponsoring Organization:: USDOE

OSTI ID:: 1638292

Journal Information:: Molecular Ecology Resources, Journal Name: Molecular Ecology Resources Journal Issue: 5 Vol. 20; ISSN 1755-098X

Publisher:: Wiley-BlackwellCopyright Statement

Country of Publication:: United Kingdom

Language:: English

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