Enriched atlas of lncRNA and protein-coding genes for the GRCg7b chicken assembly and its functional annotation across 47 tissues

Fabien Degalez; Mathieu Charles; Sylvain Foissac; Haijuan Zhou; Dailu Guan; Lingzhao Fang; Christophe Klopp; Coralie Allain; Laetitia Lagoutte; Frédéric Lecerf; Hervé Acloque; Elisabetta Giuffra; Frédérique Pitel; Sandrine Lagarrigue

doi:10.1038/s41598-024-56705-y

Enriched atlas of lncRNA and protein-coding genes for the GRCg7b chicken assembly and its functional annotation across 47 tissues

Fabien Degalez, Mathieu Charles, Sylvain Foissac, Haijuan Zhou, Dailu Guan, Lingzhao Fang, Christophe Klopp, Coralie Allain, Laetitia Lagoutte, Frédéric Lecerf, Hervé Acloque, Elisabetta Giuffra, Frédérique Pitel, Sandrine Lagarrigue^*

^*Corresponding author for this work

Center for Quantitative Genetics and Genomics

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaper › Journal article › Research › peer-review

7 Citations (Scopus)

Abstract

Gene atlases for livestock are steadily improving thanks to new genome assemblies and new expression data improving the gene annotation. However, gene content varies across databases due to differences in RNA sequencing data and bioinformatics pipelines, especially for long non-coding RNAs (lncRNAs) which have higher tissue and developmental specificity and are harder to consistently identify compared to protein coding genes (PCGs). As done previously in 2020 for chicken assemblies galgal5 and GRCg6a, we provide a new gene atlas, lncRNA-enriched, for the latest GRCg7b chicken assembly, integrating "NCBI RefSeq", "EMBL-EBI Ensembl/GENCODE" reference annotations and other resources such as FAANG and NONCODE. As a result, the number of PCGs increases from 18,022 (RefSeq) and 17,007 (Ensembl) to 24,102, and that of lncRNAs from 5789 (RefSeq) and 11,944 (Ensembl) to 44,428. Using 1400 public RNA-seq transcriptome representing 47 tissues, we provided expression evidence for 35,257 (79%) lncRNAs and 22,468 (93%) PCGs, supporting the relevance of this atlas. Further characterization including tissue-specificity, sex-differential expression and gene configurations are provided. We also identified conserved miRNA-hosting genes with human counterparts, suggesting common function. The annotated atlas is available at gega.sigenae.org

Original language	English
Article number	6588
Journal	Scientific Reports
Volume	14
Issue	1
ISSN	2045-2322
DOIs	https://doi.org/10.1038/s41598-024-56705-y
Publication status	Published - Mar 2024

Keywords

Chicken
Co-expression
Gene atlas
Genome annotation
Long non coding RNAs
miRNA
Tissue specificity

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Cite this

Degalez, F., Charles, M., Foissac, S., Zhou, H., Guan, D., Fang, L., Klopp, C., Allain, C., Lagoutte, L., Lecerf, F., Acloque, H., Giuffra, E., Pitel, F., & Lagarrigue, S. (2024). Enriched atlas of lncRNA and protein-coding genes for the GRCg7b chicken assembly and its functional annotation across 47 tissues. Scientific Reports, 14(1), Article 6588. https://doi.org/10.1038/s41598-024-56705-y

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title = "Enriched atlas of lncRNA and protein-coding genes for the GRCg7b chicken assembly and its functional annotation across 47 tissues",

abstract = "Gene atlases for livestock are steadily improving thanks to new genome assemblies and new expression data improving the gene annotation. However, gene content varies across databases due to differences in RNA sequencing data and bioinformatics pipelines, especially for long non-coding RNAs (lncRNAs) which have higher tissue and developmental specificity and are harder to consistently identify compared to protein coding genes (PCGs). As done previously in 2020 for chicken assemblies galgal5 and GRCg6a, we provide a new gene atlas, lncRNA-enriched, for the latest GRCg7b chicken assembly, integrating {"}NCBI RefSeq{"}, {"}EMBL-EBI Ensembl/GENCODE{"} reference annotations and other resources such as FAANG and NONCODE. As a result, the number of PCGs increases from 18,022 (RefSeq) and 17,007 (Ensembl) to 24,102, and that of lncRNAs from 5789 (RefSeq) and 11,944 (Ensembl) to 44,428. Using 1400 public RNA-seq transcriptome representing 47 tissues, we provided expression evidence for 35,257 (79%) lncRNAs and 22,468 (93%) PCGs, supporting the relevance of this atlas. Further characterization including tissue-specificity, sex-differential expression and gene configurations are provided. We also identified conserved miRNA-hosting genes with human counterparts, suggesting common function. The annotated atlas is available at gega.sigenae.org",

keywords = "Chicken, Co-expression, Gene atlas, Genome annotation, Long non coding RNAs, miRNA, Tissue specificity",

author = "Fabien Degalez and Mathieu Charles and Sylvain Foissac and Haijuan Zhou and Dailu Guan and Lingzhao Fang and Christophe Klopp and Coralie Allain and Laetitia Lagoutte and Fr{\'e}d{\'e}ric Lecerf and Herv{\'e} Acloque and Elisabetta Giuffra and Fr{\'e}d{\'e}rique Pitel and Sandrine Lagarrigue",

note = "Publisher Copyright: {\textcopyright} The Author(s) 2024.",

year = "2024",

month = mar,

doi = "10.1038/s41598-024-56705-y",

language = "English",

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Degalez, F, Charles, M, Foissac, S, Zhou, H, Guan, D, Fang, L, Klopp, C, Allain, C, Lagoutte, L, Lecerf, F, Acloque, H, Giuffra, E, Pitel, F & Lagarrigue, S 2024, 'Enriched atlas of lncRNA and protein-coding genes for the GRCg7b chicken assembly and its functional annotation across 47 tissues', Scientific Reports, vol. 14, no. 1, 6588. https://doi.org/10.1038/s41598-024-56705-y

Enriched atlas of lncRNA and protein-coding genes for the GRCg7b chicken assembly and its functional annotation across 47 tissues. / Degalez, Fabien; Charles, Mathieu; Foissac, Sylvain et al.
In: Scientific Reports, Vol. 14, No. 1, 6588, 03.2024.

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaper › Journal article › Research › peer-review

TY - JOUR

T1 - Enriched atlas of lncRNA and protein-coding genes for the GRCg7b chicken assembly and its functional annotation across 47 tissues

AU - Degalez, Fabien

AU - Charles, Mathieu

AU - Foissac, Sylvain

AU - Zhou, Haijuan

AU - Guan, Dailu

AU - Fang, Lingzhao

AU - Klopp, Christophe

AU - Allain, Coralie

AU - Lagoutte, Laetitia

AU - Lecerf, Frédéric

AU - Acloque, Hervé

AU - Giuffra, Elisabetta

AU - Pitel, Frédérique

AU - Lagarrigue, Sandrine

N1 - Publisher Copyright: © The Author(s) 2024.

PY - 2024/3

Y1 - 2024/3

N2 - Gene atlases for livestock are steadily improving thanks to new genome assemblies and new expression data improving the gene annotation. However, gene content varies across databases due to differences in RNA sequencing data and bioinformatics pipelines, especially for long non-coding RNAs (lncRNAs) which have higher tissue and developmental specificity and are harder to consistently identify compared to protein coding genes (PCGs). As done previously in 2020 for chicken assemblies galgal5 and GRCg6a, we provide a new gene atlas, lncRNA-enriched, for the latest GRCg7b chicken assembly, integrating "NCBI RefSeq", "EMBL-EBI Ensembl/GENCODE" reference annotations and other resources such as FAANG and NONCODE. As a result, the number of PCGs increases from 18,022 (RefSeq) and 17,007 (Ensembl) to 24,102, and that of lncRNAs from 5789 (RefSeq) and 11,944 (Ensembl) to 44,428. Using 1400 public RNA-seq transcriptome representing 47 tissues, we provided expression evidence for 35,257 (79%) lncRNAs and 22,468 (93%) PCGs, supporting the relevance of this atlas. Further characterization including tissue-specificity, sex-differential expression and gene configurations are provided. We also identified conserved miRNA-hosting genes with human counterparts, suggesting common function. The annotated atlas is available at gega.sigenae.org

AB - Gene atlases for livestock are steadily improving thanks to new genome assemblies and new expression data improving the gene annotation. However, gene content varies across databases due to differences in RNA sequencing data and bioinformatics pipelines, especially for long non-coding RNAs (lncRNAs) which have higher tissue and developmental specificity and are harder to consistently identify compared to protein coding genes (PCGs). As done previously in 2020 for chicken assemblies galgal5 and GRCg6a, we provide a new gene atlas, lncRNA-enriched, for the latest GRCg7b chicken assembly, integrating "NCBI RefSeq", "EMBL-EBI Ensembl/GENCODE" reference annotations and other resources such as FAANG and NONCODE. As a result, the number of PCGs increases from 18,022 (RefSeq) and 17,007 (Ensembl) to 24,102, and that of lncRNAs from 5789 (RefSeq) and 11,944 (Ensembl) to 44,428. Using 1400 public RNA-seq transcriptome representing 47 tissues, we provided expression evidence for 35,257 (79%) lncRNAs and 22,468 (93%) PCGs, supporting the relevance of this atlas. Further characterization including tissue-specificity, sex-differential expression and gene configurations are provided. We also identified conserved miRNA-hosting genes with human counterparts, suggesting common function. The annotated atlas is available at gega.sigenae.org

KW - Chicken

KW - Co-expression

KW - Gene atlas

KW - Genome annotation

KW - Long non coding RNAs

KW - miRNA

KW - Tissue specificity

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U2 - 10.1038/s41598-024-56705-y

DO - 10.1038/s41598-024-56705-y

M3 - Journal article

C2 - 38504112

AN - SCOPUS:85188156983

SN - 2045-2322

VL - 14

JO - Scientific Reports

JF - Scientific Reports

IS - 1

M1 - 6588

ER -

Enriched atlas of lncRNA and protein-coding genes for the GRCg7b chicken assembly and its functional annotation across 47 tissues

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Keywords

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