ArticleGenome research2012
RNA-seq analysis of the C. briggsae transcriptome.
Article in Genome research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
23 citing papers in PubMed, 28 citations in OpenAlex.
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- SLRanger: an integrated approach for spliced leader detection and operon prediction using long RNA reads.Briefings in bioinformatics · 2025Article
- High resolution of full-length RNA sequencing deciphers massive transcriptome complexity during zebrafish embryogenesis.BMC biology · 2025Article
- Genome annotation of Caenorhabditis briggsae by TEC-RED identifies new exons, paralogs, and conserved and novel operons.G3 (Bethesda, Md.) · 2022Article
- Conservation of Nematocida microsporidia gene expression and host response in Caenorhabditis nematodes.PloS one · 2022Article
- SLIDR and SLOPPR: flexible identification of spliced leader trans-splicing and prediction of eukaryotic operons from RNA-Seq data.BMC bioinformatics · 2021Article
- Resolution of polycistronic RNA by SL2RNA (New York, N.Y.) · 2020Article
- mRNA Editing, Processing and Quality Control inGenetics · 2020Review
- Direct full-length RNA sequencing reveals unexpected transcriptome complexity duringGenome research · 2020Article
- Genome editing in the nematodeBiology methods & protocols · 2020Article
- SL-quant: a fast and flexible pipeline to quantify spliced leader trans-splicing events from RNA-seq data.GigaScience · 2018Article
- Genomic basis of recombination suppression in the hybrid between Caenorhabditis briggsae and C. nigoni.Nucleic acids research · 2018Article
- Identification of potential genes for human ischemic cardiomyopathy based on RNA-Seq data.Oncotarget · 2016Article
- Improvement of genome assembly completeness and identification of novel full-length protein-coding genes by RNA-seq in the giant panda genome.Scientific reports · 2015Article
- A Genome-wide hybrid incompatibility landscape between Caenorhabditis briggsae and C. nigoni.PLoS genetics · 2015Article
- Genome-wide analysis of trans-splicing in the nematode Pristionchus pacificus unravels conserved gene functions for germline and dauer development in divergent operons.RNA (New York, N.Y.) · 2014Article
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- The multiplicity of alternative splicing decisions in Caenorhabditis elegans is linked to specific intronic regulatory motifs and minisatellites.BMC genomics · 2014Article
- Article
Corrections and comments
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Authors and funding
8 authors at 2 institutions in 1 country.
Funding
Abstract
Curation of a high-quality gene set is the critical first step in genome research, enabling subsequent analyses such as ortholog assignment, cis-regulatory element finding, and synteny detection. In this project, we have reannotated the genome of Caenorhabditis briggsae, the best studied sister species of the model organism Caenorhabditis elegans. First, we applied a homology-based gene predictor genBlastG to annotate the C. briggsae genome. We then validated and further improved the C. briggsae gene annotation through RNA-seq analysis of the C. briggsae transcriptome, which resulted in the first validated C. briggsae gene set (23,159 genes), among which 7347 genes (33.9% of all genes with introns) have all of their introns confirmed. Most genes (14,812, or 68.3%) have at least one intron validated, compared with only 3.9% in the most recent WormBase release (WS228). Of all introns in the revised gene set (103,083), 61,503 (60.1%) have been confirmed. Additionally, we have identified numerous trans-splicing leaders (SL1 and SL2 variants) in C. briggsae, leading to the first genome-wide annotation of operons in C. briggsae (1105 operons). The majority of the annotated operons (564, or 51.0%) are perfectly conserved in C. elegans, with an additional 345 operons (or 31.2%) somewhat divergent. Additionally, RNA-seq analysis revealed over 10 thousand small-size assembly errors in the current C. briggsae reference genome that can be readily corrected. The revised C. briggsae genome annotation represents a solid platform for comparative genomics analysis and evolutionary studies of Caenorhabditis species.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.