Revising transcriptome assemblies with phylogenetic information.
Journal
PloS one
ISSN: 1932-6203
Titre abrégé: PLoS One
Pays: United States
ID NLM: 101285081
Informations de publication
Date de publication:
2021
2021
Historique:
received:
06
07
2020
accepted:
04
12
2020
entrez:
12
1
2021
pubmed:
13
1
2021
medline:
24
4
2021
Statut:
epublish
Résumé
A common transcriptome assembly error is to mistake different transcripts of the same gene as transcripts from multiple closely related genes. This error is difficult to identify during assembly, but in a phylogenetic analysis such errors can be diagnosed from gene phylogenies where they appear as clades of tips from the same species with improbably short branch lengths. treeinform is a method that uses phylogenetic information across species to refine transcriptome assemblies within species. It identifies transcripts of the same gene that were incorrectly assigned to multiple genes and reassign them as transcripts of the same gene. The treeinform method is implemented in Agalma, available at https://bitbucket.org/caseywdunn/agalma, and the general approach is relevant in a variety of other contexts.
Identifiants
pubmed: 33434218
doi: 10.1371/journal.pone.0244202
pii: PONE-D-20-20890
pmc: PMC7802918
doi:
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
e0244202Subventions
Organisme : NIGMS NIH HHS
ID : P20 GM109035
Pays : United States
Déclaration de conflit d'intérêts
The authors have declared that no competing interests exist.
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