Genome annotation with long RNA reads reveals new patterns of gene expression and improves single-cell analyses in an ant brain.
3′ UTR annotation
Alternative splicing
Ants
Genome annotation
Harpegnathos saltator
Iso-Seq
Long-read RNA-seq
Single-cell sequencing
Journal
BMC biology
ISSN: 1741-7007
Titre abrégé: BMC Biol
Pays: England
ID NLM: 101190720
Informations de publication
Date de publication:
27 11 2021
27 11 2021
Historique:
received:
03
06
2021
accepted:
10
11
2021
entrez:
28
11
2021
pubmed:
29
11
2021
medline:
17
3
2022
Statut:
epublish
Résumé
Functional genomic analyses rely on high-quality genome assemblies and annotations. Highly contiguous genome assemblies have become available for a variety of species, but accurate and complete annotation of gene models, inclusive of alternative splice isoforms and transcription start and termination sites, remains difficult with traditional approaches. Here, we utilized full-length isoform sequencing (Iso-Seq), a long-read RNA sequencing technology, to obtain a comprehensive annotation of the transcriptome of the ant Harpegnathos saltator. The improved genome annotations include additional splice isoforms and extended 3' untranslated regions for more than 4000 genes. Reanalysis of RNA-seq experiments using these annotations revealed several genes with caste-specific differential expression and tissue- or caste-specific splicing patterns that were missed in previous analyses. The extended 3' untranslated regions afforded great improvements in the analysis of existing single-cell RNA-seq data, resulting in the recovery of the transcriptomes of 18% more cells. The deeper single-cell transcriptomes obtained with these new annotations allowed us to identify additional markers for several cell types in the ant brain, as well as genes differentially expressed across castes in specific cell types. Our results demonstrate that Iso-Seq is an efficient and effective approach to improve genome annotations and maximize the amount of information that can be obtained from existing and future genomic datasets in Harpegnathos and other organisms.
Sections du résumé
BACKGROUND
Functional genomic analyses rely on high-quality genome assemblies and annotations. Highly contiguous genome assemblies have become available for a variety of species, but accurate and complete annotation of gene models, inclusive of alternative splice isoforms and transcription start and termination sites, remains difficult with traditional approaches.
RESULTS
Here, we utilized full-length isoform sequencing (Iso-Seq), a long-read RNA sequencing technology, to obtain a comprehensive annotation of the transcriptome of the ant Harpegnathos saltator. The improved genome annotations include additional splice isoforms and extended 3' untranslated regions for more than 4000 genes. Reanalysis of RNA-seq experiments using these annotations revealed several genes with caste-specific differential expression and tissue- or caste-specific splicing patterns that were missed in previous analyses. The extended 3' untranslated regions afforded great improvements in the analysis of existing single-cell RNA-seq data, resulting in the recovery of the transcriptomes of 18% more cells. The deeper single-cell transcriptomes obtained with these new annotations allowed us to identify additional markers for several cell types in the ant brain, as well as genes differentially expressed across castes in specific cell types.
CONCLUSIONS
Our results demonstrate that Iso-Seq is an efficient and effective approach to improve genome annotations and maximize the amount of information that can be obtained from existing and future genomic datasets in Harpegnathos and other organisms.
Identifiants
pubmed: 34838024
doi: 10.1186/s12915-021-01188-w
pii: 10.1186/s12915-021-01188-w
pmc: PMC8626913
doi:
Substances chimiques
3' Untranslated Regions
0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
254Subventions
Organisme : NIMH NIH HHS
ID : DP2MH107055
Pays : United States
Organisme : NIA NIH HHS
ID : R01 AG071818
Pays : United States
Organisme : NIMH NIH HHS
ID : R21 MH123841
Pays : United States
Organisme : NIA NIH HHS
ID : R01AG071818
Pays : United States
Organisme : NIA NIH HHS
ID : R01 AG058762
Pays : United States
Informations de copyright
© 2021. The Author(s).
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