ArticleBMC genomics2019
Improved annotation of the domestic pig genome through integration of Iso-Seq and RNA-seq data.
Article in BMC genomics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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47 citing papers in PubMed, 100 citations in OpenAlex.
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- Human and porcine IgG subclasses differentially engage porcine Fc receptors.Discovery immunology · 2026Article
- Verification and comparison of pig, mouse, and human genome similarities: use of manual assembly and analyses.BMC genomics · 2025Article
- A multimodal cross-species comparison of pancreas development.Nature communications · 2025Article
- Long-read sequencing uncovers key regulatory genes involved in the differentiation of preadipocytes of Chinese red steppe cattle.Scientific reports · 2025Article
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- Landscape of alternative splicing and polyadenylation during growth and development of muscles in pigs.Communications biology · 2024Article
- A genome assembly and transcriptome atlas of the inbred Babraham pig to illuminate porcine immunogenetic variation.Immunogenetics · 2024Article
- Integrative analysis of Iso-Seq and RNA-seq data reveals transcriptome complexity and differential isoform in skin tissues of different hair length Yak.BMC genomics · 2024Article
- Selection of Catechin Biosynthesis-Related Genes and Functional Analysis from Chromosome-Level Genome Assembly inInternational journal of molecular sciences · 2024Article
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- Enhanced bovine genome annotation through integration of transcriptomics and epi-transcriptomics datasets facilitates genomic biology.GigaScience · 2024Article
- Long- and short-read RNA sequencing from five reproductive organs of boar.Scientific data · 2023Article
- TAGET: a toolkit for analyzing full-length transcripts from long-read sequencing.Nature communications · 2023Article
- Pangenome obtained by long-read sequencing of 11 genomes reveal hidden functional structural variants in pigs.iScience · 2023Article
- Deciphering the roles of unknown/uncharacterized genes in plant development and stress responses.Frontiers in plant science · 2023Review
- RNA-Seq and Iso-Seq Reveal the Important Role ofGenes · 2022Article
- Intestinal single-cell atlas reveals novel lymphocytes in pigs with similarities to human cells.Life science alliance · 2022Article
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Authors and funding
8 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundOur understanding of the pig transcriptome is limited. RNA transcript diversity among nine tissues was assessed using poly(A) selected single-molecule long-read isoform sequencing (Iso-seq) and Illumina RNA sequencing (RNA-seq) from a single White cross-bred pig.
resultsAcross tissues, a total of 67,746 unique transcripts were observed, including 60.5% predicted protein-coding, 36.2% long non-coding RNA and 3.3% nonsense-mediated decay transcripts. On average, 90% of the splice junctions were supported by RNA-seq within tissue. A large proportion (80%) represented novel transcripts, mostly produced by known protein-coding genes (70%), while 17% corresponded to novel genes. On average, four transcripts per known gene (tpg) were identified; an increase over current EBI (1.9 tpg) and NCBI (2.9 tpg) annotations and closer to the number reported in human genome (4.2 tpg). Our new pig genome annotation extended more than 6000 known gene borders (5' end extension, 3' end extension, or both) compared to EBI or NCBI annotations. We validated a large proportion of these extensions by independent pig poly(A) selected 3'-RNA-seq data, or human FANTOM5 Cap Analysis of Gene Expression data. Further, we detected 10,465 novel genes (81% non-coding) not reported in current pig genome annotations. More than 80% of these novel genes had transcripts detected in > 1 tissue. In addition, more than 80% of novel intergenic genes with at least one transcript detected in liver tissue had H3K4me3 or H3K36me3 peaks mapping to their promoter and gene body, respectively, in independent liver chromatin immunoprecipitation data.
conclusionsThese validated results show significant improvement over current pig genome annotations.
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