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...
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| Format: | Article |
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Nature Portfolio
2024-03-01
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| Series: | Scientific Reports |
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| Online Access: | https://doi.org/10.1038/s41598-024-56705-y |
| _version_ | 1827310193704173568 |
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| author | 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 |
| author_facet | 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 |
| author_sort | Fabien Degalez |
| collection | DOAJ |
| description | 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 |
| first_indexed | 2024-04-24T19:55:45Z |
| format | Article |
| id | doaj.art-289590f9430a4752b5aaa9be20f46cfd |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-04-24T19:55:45Z |
| publishDate | 2024-03-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-289590f9430a4752b5aaa9be20f46cfd2024-03-24T12:20:49ZengNature PortfolioScientific Reports2045-23222024-03-0114111810.1038/s41598-024-56705-yEnriched atlas of lncRNA and protein-coding genes for the GRCg7b chicken assembly and its functional annotation across 47 tissuesFabien Degalez0Mathieu Charles1Sylvain Foissac2Haijuan Zhou3Dailu Guan4Lingzhao Fang5Christophe Klopp6Coralie Allain7Laetitia Lagoutte8Frédéric Lecerf9Hervé Acloque10Elisabetta Giuffra11Frédérique Pitel12Sandrine Lagarrigue13PEGASE, INRAE, Institut AgroINRAE, BioinfOmics, GenoToul Bioinformatics facility, Sigenae, Université Fédérale de ToulouseGenPhySE, Université de Toulouse, INRAE, ENVTUniversity of California DavisUniversity of California DavisAarhus UniversityINRAE, BioinfOmics, GenoToul Bioinformatics facility, Sigenae, Université Fédérale de ToulousePEGASE, INRAE, Institut AgroPEGASE, INRAE, Institut AgroPEGASE, INRAE, Institut AgroINRAE, AgroParisTech, GABI, Paris-Saclay UniversityINRAE, AgroParisTech, GABI, Paris-Saclay UniversityGenPhySE, Université de Toulouse, INRAE, ENVTPEGASE, INRAE, Institut AgroAbstract 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.orghttps://doi.org/10.1038/s41598-024-56705-yGene atlasLong non coding RNAsChickenGenome annotationTissue specificityCo-expression |
| spellingShingle | 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 Enriched atlas of lncRNA and protein-coding genes for the GRCg7b chicken assembly and its functional annotation across 47 tissues Scientific Reports Gene atlas Long non coding RNAs Chicken Genome annotation Tissue specificity Co-expression |
| title | Enriched atlas of lncRNA and protein-coding genes for the GRCg7b chicken assembly and its functional annotation across 47 tissues |
| title_full | Enriched atlas of lncRNA and protein-coding genes for the GRCg7b chicken assembly and its functional annotation across 47 tissues |
| title_fullStr | Enriched atlas of lncRNA and protein-coding genes for the GRCg7b chicken assembly and its functional annotation across 47 tissues |
| title_full_unstemmed | Enriched atlas of lncRNA and protein-coding genes for the GRCg7b chicken assembly and its functional annotation across 47 tissues |
| title_short | Enriched atlas of lncRNA and protein-coding genes for the GRCg7b chicken assembly and its functional annotation across 47 tissues |
| title_sort | enriched atlas of lncrna and protein coding genes for the grcg7b chicken assembly and its functional annotation across 47 tissues |
| topic | Gene atlas Long non coding RNAs Chicken Genome annotation Tissue specificity Co-expression |
| url | https://doi.org/10.1038/s41598-024-56705-y |
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