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Hemiptera phylogenomic resources: Tree-based orthology prediction and conserved exon identification.
- Source :
-
Molecular ecology resources [Mol Ecol Resour] 2020 Sep; Vol. 20 (5), pp. 1346-1360. Date of Electronic Publication: 2020 Jul 13. - Publication Year :
- 2020
-
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.<br /> (© 2020 John Wiley & Sons Ltd.)
- Subjects :
- Animals
Genome
Genomics
Exons
Hemiptera classification
Hemiptera genetics
Phylogeny
Subjects
Details
- Language :
- English
- ISSN :
- 1755-0998
- Volume :
- 20
- Issue :
- 5
- Database :
- MEDLINE
- Journal :
- Molecular ecology resources
- Publication Type :
- Academic Journal
- Accession number :
- 32358926
- Full Text :
- https://doi.org/10.1111/1755-0998.13180