ArticleGenome research2010
Scaffolding a Caenorhabditis nematode genome with RNA-seq.
Article in Genome research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 papers.
What it found
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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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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
65 citing papers in PubMed.
- Article
- Phylogenomic Analysis of 155 Helminth Species Reveals Widespread Absence of Oxygen Metabolic Capacity.Genome biology and evolution · 2023Article
- The GATA factor ELT-3 specifies endoderm in Caenorhabditis angaria in an ancestral gene network.Development (Cambridge, England) · 2022Article
- Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies.BMC biology · 2020Article
- Diversification of theeLife · 2019Article
- Selection and gene flow shape niche-associated variation in pheromone response.Nature ecology & evolution · 2019Article
- Evolution of Yin and Yang isoforms of a chromatin remodeling subunit precedes the creation of two genes.eLife · 2019Article
- Modern technologies and algorithms for scaffolding assembled genomes.PLoS computational biology · 2019Review
- The Long Non-Coding RNA lep-5 Promotes the Juvenile-to-Adult Transition by Destabilizing LIN-28.Developmental cell · 2019Article
- Comparative genomics of 10 newEvolution letters · 2019Article
- P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads.BMC genomics · 2018Article
- Genomic basis of recombination suppression in the hybrid between Caenorhabditis briggsae and C. nigoni.Nucleic acids research · 2018Article
- A Model for Evolutionary Ecology of Disease: The Case forJournal of nematology · 2017Article
- Comparative Transcriptomics of Steinernema and Caenorhabditis Single Embryos Reveals Orthologous Gene Expression Convergence during Late Embryogenesis.Genome biology and evolution · 2017Article
- Transcriptomic Analysis of C. elegans RNA Sequencing Data Through the Tuxedo Suite on the Galaxy Project.Journal of visualized experiments : JoVE · 2017Article
- Nematophagous funguseLife · 2017Article
- Article
- Integrating transcriptomic and proteomic data for accurate assembly and annotation of genomes.Genome research · 2017Article
- Extensive ceRNA-ceRNA interaction networks mediated by miRNAs regulate development in multiple rhesus tissues.Nucleic acids research · 2016Article
- PEP_scaffolder: using (homologous) proteins to scaffold genomes.Bioinformatics (Oxford, England) · 2016Article
5 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
Abstract
Efficient sequencing of animal and plant genomes by next-generation technology should allow many neglected organisms of biological and medical importance to be better understood. As a test case, we have assembled a draft genome of Caenorhabditis sp. 3 PS1010 through a combination of direct sequencing and scaffolding with RNA-seq. We first sequenced genomic DNA and mixed-stage cDNA using paired 75-nt reads from an Illumina GAII. A set of 230 million genomic reads yielded an 80-Mb assembly, with a supercontig N50 of 5.0 kb, covering 90% of 429 kb from previously published genomic contigs. Mixed-stage poly(A)(+) cDNA gave 47.3 million mappable 75-mers (including 5.1 million spliced reads), which separately assembled into 17.8 Mb of cDNA, with an N50 of 1.06 kb. By further scaffolding our genomic supercontigs with cDNA, we increased their N50 to 9.4 kb, nearly double the average gene size in C. elegans. We predicted 22,851 protein-coding genes, and detected expression in 78% of them. Multigenome alignment and data filtering identified 2672 DNA elements conserved between PS1010 and C. elegans that are likely to encode regulatory sequences or previously unknown ncRNAs. Genomic and cDNA sequencing followed by joint assembly is a rapid and useful strategy for biological analysis.
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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.