Evolutionary characteristics of intergenic transcribed regions indicate rare novel genes and widespread noisy transcription in the Poaceae

Abstract Extensive transcriptional activity occurring in intergenic regions of genomes has raised the question whether intergenic transcription represents the activity of novel genes or noisy expression. To address this, we evaluated cross-species and post-duplication sequence and expression conserv...

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Autores principales:	John P. Lloyd, Megan J. Bowman, Christina B. Azodi, Rosalie P. Sowers, Gaurav D. Moghe, Kevin L. Childs, Shin-Han Shiu
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2019
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/65250de186414f50a6c8138c34bea35e
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spelling	oai:doaj.org-article:65250de186414f50a6c8138c34bea35e2021-12-02T15:08:45ZEvolutionary characteristics of intergenic transcribed regions indicate rare novel genes and widespread noisy transcription in the Poaceae10.1038/s41598-019-47797-y2045-2322https://doaj.org/article/65250de186414f50a6c8138c34bea35e2019-08-01T00:00:00Zhttps://doi.org/10.1038/s41598-019-47797-yhttps://doaj.org/toc/2045-2322Abstract Extensive transcriptional activity occurring in intergenic regions of genomes has raised the question whether intergenic transcription represents the activity of novel genes or noisy expression. To address this, we evaluated cross-species and post-duplication sequence and expression conservation of intergenic transcribed regions (ITRs) in four Poaceae species. Among 43,301 ITRs across the four species, 34,460 (80%) are species-specific. ITRs found across species tend to be more divergent in expression and have more recent duplicates compared to annotated genes. To assess if ITRs are functional (under selection), machine learning models were established in Oryza sativa (rice) that could accurately distinguish between phenotype genes and pseudogenes (area under curve-receiver operating characteristic = 0.94). Based on the models, 584 (8%) and 4391 (61%) rice ITRs are classified as likely functional and nonfunctional with high confidence, respectively. ITRs with conserved expression and ancient retained duplicates, features that were not part of the model, are frequently classified as likely-functional, suggesting these characteristics could serve as pragmatic rules of thumb for identifying candidate sequences likely to be under selection. This study also provides a framework to identify novel genes using comparative transcriptomic data to improve genome annotation that is fundamental for connecting genotype to phenotype in crop and model systems.John P. LloydMegan J. BowmanChristina B. AzodiRosalie P. SowersGaurav D. MogheKevin L. ChildsShin-Han ShiuNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 9, Iss 1, Pp 1-14 (2019)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q John P. Lloyd Megan J. Bowman Christina B. Azodi Rosalie P. Sowers Gaurav D. Moghe Kevin L. Childs Shin-Han Shiu Evolutionary characteristics of intergenic transcribed regions indicate rare novel genes and widespread noisy transcription in the Poaceae
description	Abstract Extensive transcriptional activity occurring in intergenic regions of genomes has raised the question whether intergenic transcription represents the activity of novel genes or noisy expression. To address this, we evaluated cross-species and post-duplication sequence and expression conservation of intergenic transcribed regions (ITRs) in four Poaceae species. Among 43,301 ITRs across the four species, 34,460 (80%) are species-specific. ITRs found across species tend to be more divergent in expression and have more recent duplicates compared to annotated genes. To assess if ITRs are functional (under selection), machine learning models were established in Oryza sativa (rice) that could accurately distinguish between phenotype genes and pseudogenes (area under curve-receiver operating characteristic = 0.94). Based on the models, 584 (8%) and 4391 (61%) rice ITRs are classified as likely functional and nonfunctional with high confidence, respectively. ITRs with conserved expression and ancient retained duplicates, features that were not part of the model, are frequently classified as likely-functional, suggesting these characteristics could serve as pragmatic rules of thumb for identifying candidate sequences likely to be under selection. This study also provides a framework to identify novel genes using comparative transcriptomic data to improve genome annotation that is fundamental for connecting genotype to phenotype in crop and model systems.
format	article
author	John P. Lloyd Megan J. Bowman Christina B. Azodi Rosalie P. Sowers Gaurav D. Moghe Kevin L. Childs Shin-Han Shiu
author_facet	John P. Lloyd Megan J. Bowman Christina B. Azodi Rosalie P. Sowers Gaurav D. Moghe Kevin L. Childs Shin-Han Shiu
author_sort	John P. Lloyd
title	Evolutionary characteristics of intergenic transcribed regions indicate rare novel genes and widespread noisy transcription in the Poaceae
title_short	Evolutionary characteristics of intergenic transcribed regions indicate rare novel genes and widespread noisy transcription in the Poaceae
title_full	Evolutionary characteristics of intergenic transcribed regions indicate rare novel genes and widespread noisy transcription in the Poaceae
title_fullStr	Evolutionary characteristics of intergenic transcribed regions indicate rare novel genes and widespread noisy transcription in the Poaceae
title_full_unstemmed	Evolutionary characteristics of intergenic transcribed regions indicate rare novel genes and widespread noisy transcription in the Poaceae
title_sort	evolutionary characteristics of intergenic transcribed regions indicate rare novel genes and widespread noisy transcription in the poaceae
publisher	Nature Portfolio
publishDate	2019
url	https://doaj.org/article/65250de186414f50a6c8138c34bea35e
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_version_	1718388002243215360

Evolutionary characteristics of intergenic transcribed regions indicate rare novel genes and widespread noisy transcription in the Poaceae

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