Genome annotation with long RNA reads reveals new patterns of gene expression and improves single-cell analyses in an ant brain

Abstract 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...

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Autores principales:	Emily J. Shields, Masato Sorida, Lihong Sheng, Bogdan Sieriebriennikov, Long Ding, Roberto Bonasio
Formato:	article
Lenguaje:	EN
Publicado:	BMC 2021
Materias:	Iso-Seq Long-read RNA-seq Harpegnathos saltator Ants Genome annotation 3′ UTR annotation Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/8f28b9479d5045a096008e49547e796b
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spelling	oai:doaj.org-article:8f28b9479d5045a096008e49547e796b2021-11-28T12:41:19ZGenome annotation with long RNA reads reveals new patterns of gene expression and improves single-cell analyses in an ant brain10.1186/s12915-021-01188-w1741-7007https://doaj.org/article/8f28b9479d5045a096008e49547e796b2021-11-01T00:00:00Zhttps://doi.org/10.1186/s12915-021-01188-whttps://doaj.org/toc/1741-7007Abstract 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.Emily J. ShieldsMasato SoridaLihong ShengBogdan SieriebriennikovLong DingRoberto BonasioBMCarticleIso-SeqLong-read RNA-seqHarpegnathos saltatorAntsGenome annotation3′ UTR annotationBiology (General)QH301-705.5ENBMC Biology, Vol 19, Iss 1, Pp 1-19 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Iso-Seq Long-read RNA-seq Harpegnathos saltator Ants Genome annotation 3′ UTR annotation Biology (General) QH301-705.5
spellingShingle	Iso-Seq Long-read RNA-seq Harpegnathos saltator Ants Genome annotation 3′ UTR annotation Biology (General) QH301-705.5 Emily J. Shields Masato Sorida Lihong Sheng Bogdan Sieriebriennikov Long Ding Roberto Bonasio Genome annotation with long RNA reads reveals new patterns of gene expression and improves single-cell analyses in an ant brain
description	Abstract 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.
format	article
author	Emily J. Shields Masato Sorida Lihong Sheng Bogdan Sieriebriennikov Long Ding Roberto Bonasio
author_facet	Emily J. Shields Masato Sorida Lihong Sheng Bogdan Sieriebriennikov Long Ding Roberto Bonasio
author_sort	Emily J. Shields
title	Genome annotation with long RNA reads reveals new patterns of gene expression and improves single-cell analyses in an ant brain
title_short	Genome annotation with long RNA reads reveals new patterns of gene expression and improves single-cell analyses in an ant brain
title_full	Genome annotation with long RNA reads reveals new patterns of gene expression and improves single-cell analyses in an ant brain
title_fullStr	Genome annotation with long RNA reads reveals new patterns of gene expression and improves single-cell analyses in an ant brain
title_full_unstemmed	Genome annotation with long RNA reads reveals new patterns of gene expression and improves single-cell analyses in an ant brain
title_sort	genome annotation with long rna reads reveals new patterns of gene expression and improves single-cell analyses in an ant brain
publisher	BMC
publishDate	2021
url	https://doaj.org/article/8f28b9479d5045a096008e49547e796b
work_keys_str_mv	AT emilyjshields genomeannotationwithlongrnareadsrevealsnewpatternsofgeneexpressionandimprovessinglecellanalysesinanantbrain AT masatosorida genomeannotationwithlongrnareadsrevealsnewpatternsofgeneexpressionandimprovessinglecellanalysesinanantbrain AT lihongsheng genomeannotationwithlongrnareadsrevealsnewpatternsofgeneexpressionandimprovessinglecellanalysesinanantbrain AT bogdansieriebriennikov genomeannotationwithlongrnareadsrevealsnewpatternsofgeneexpressionandimprovessinglecellanalysesinanantbrain AT longding genomeannotationwithlongrnareadsrevealsnewpatternsofgeneexpressionandimprovessinglecellanalysesinanantbrain AT robertobonasio genomeannotationwithlongrnareadsrevealsnewpatternsofgeneexpressionandimprovessinglecellanalysesinanantbrain
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Genome annotation with long RNA reads reveals new patterns of gene expression and improves single-cell analyses in an ant brain

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