ArticleScientific reports2018
Single-molecule long-read sequencing facilitates shrimp transcriptome research.
Article in Scientific reports, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Multi-Omics Analysis Reveals the Regulatory Mechanism of Different Probiotics on Growth Performance and Intestinal Health ofMicroorganisms · 2024Article
- Transcriptomic Insights and the Development of Microsatellite Markers to Assess Genetic Diversity in the Broodstock Management ofAnimals : an open access journal from MDPI · 2024Article
- Article
- Genome-wide QTL and eQTL mapping reveal genes associated with growth rate trait of the Pacific white shrimp (Litopenaeus vannamei).BMC genomics · 2024Article
- Microbes and pathogens associated with shrimps - implications and review of possible control strategies.Frontiers in Marine Science · 2024Article
- Single-Molecule Real-Time Sequencing for Identifying Sexual-Dimorphism-Related Transcriptomes and Genes in the Chinese Soft-Shelled Turtle (Animals : an open access journal from MDPI · 2023Article
- Screening and Validation of p38 MAPK Involved in Ovarian Development ofFrontiers in veterinary science · 2022Article
- Full-length transcriptome sequencing and comparative transcriptome analysis ofFrontiers in cellular and infection microbiology · 2022Article
- Genome and transcriptome assemblies of the kuruma shrimp, Marsupenaeus japonicus.G3 (Bethesda, Md.) · 2021Article
- Comparative Analysis of PacBio and Oxford Nanopore Sequencing Technologies for Transcriptomic Landscape Identification ofLife (Basel, Switzerland) · 2021Article
- There and Back Again: Hox Clusters Use Both DNA Strands.Journal of developmental biology · 2021Review
- Full-length SMRT transcriptome sequencing and microsatellite characterization in Paulownia catalpifolia.Scientific reports · 2021Article
- A First Insight into the Gonad Transcriptome of Hong Kong Catfish (Animals : an open access journal from MDPI · 2021Article
- Single-Molecule Long-Read Sequencing of Purslane (Plants (Basel, Switzerland) · 2021Article
- Combined Transcriptome Analysis Reveals the Ovule Abortion Regulatory Mechanisms in the Female Sterile Line ofInternational journal of molecular sciences · 2021Article
- Full-length transcript sequencing accelerates the transcriptome research of Gymnocypris namensis, an iconic fish of the Tibetan Plateau.Scientific reports · 2020Article
- Single-molecule long-read sequencing of the full-length transcriptome of Rhododendron lapponicum L.Scientific reports · 2020Article
- Article
- Single-molecule real-time sequencing of the full-length transcriptome of loquat under low-temperature stress.PloS one · 2020Article
- The Single-molecule long-read sequencing of Scylla paramamosain.Scientific reports · 2019Article
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Authors and funding
12 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Although shrimp are of great economic importance, few full-length shrimp transcriptomes are available. Here, we used Pacific Biosciences single-molecule real-time (SMRT) long-read sequencing technology to generate transcripts from the Pacific white shrimp (Litopenaeus vannamei). We obtained 322,600 full-length non-chimeric reads, from which we generated 51,367 high-quality unique full-length transcripts. We corrected errors in the SMRT sequences by comparison with Illumina-produced short reads. We successfully annotated 81.72% of all unique SMRT transcripts against the NCBI non-redundant database, 58.63% against Swiss-Prot, 45.38% against Gene Ontology, 32.57% against Clusters of Orthologous Groups of proteins (COG), and 47.83% against Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Across all transcripts, we identified 3,958 long non-coding RNAs (lncRNAs) and 80,650 simple sequence repeats (SSRs). Our study provides a rich set of full-length cDNA sequences for L. vannamei, which will greatly facilitate shrimp transcriptome research.
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