ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2011
Analysis of the Asian seabass transcriptome based on expressed sequence tags.
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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15 citing papers in PubMed.
- Scale Drop Disease Virus (SDDV) andFrontiers in genetics · 2021Article
- Toward Genome-Based Selection in Asian Seabass: What Can We Learn From Other Food Fishes and Farm Animals?Frontiers in genetics · 2021Review
- Construction of a high-density linkage map and fine mapping of QTL for growth in Asian seabass.Scientific reports · 2015Article
- Transcriptomic Analysis of Metabolic Pathways in Milkfish That Respond to Salinity and Temperature Changes.PloS one · 2015Article
- Analysis of immune-related ESTs and differential expression analysis of few important genes in lines of rohu (Labeo rohita) selected for resistance and susceptibility to Aeromonas hydrophila infection.Molecular biology reports · 2014Article
- The intestinal microbiome of fish under starvation.BMC genomics · 2014Article
- Mapping quantitative trait loci for omega-3 fatty acids in Asian seabass.Marine biotechnology (New York, N.Y.) · 2014Article
- Gene discovery through transcriptome sequencing for the invasive mussel Limnoperna fortunei.PloS one · 2014Article
- Analysis of stress-responsive transcriptome in the intestine of Asian seabass (Lates calcarifer) using RNA-seq.DNA research : an international journal for rapid publication of reports on genes and genomes · 2013Article
- Whole genome scanning and association mapping identified a significant association between growth and a SNP in the IFABP-a gene of the Asian seabass.BMC genomics · 2013Article
- Analysis of two lysozyme genes and antimicrobial functions of their recombinant proteins in Asian seabass.PloS one · 2013Article
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- Characterization of Liaoning cashmere goat transcriptome: sequencing, de novo assembly, functional annotation and comparative analysis.PloS one · 2013Article
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Authors and funding
5 authors.
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Abstract
Analysis of transcriptomes is of great importance in genomic studies. Asian seabass is an important fish species. A number of genomic tools in it were developed, while large expressed sequence tag (EST) data are lacking. We sequenced ESTs from nine normalized cDNA libraries and obtained 11 431 high-quality ESTs. We retrieved 8524 ESTs from dbEST database and analyzed all 19 975 ESTs using bioinformatics tools. After clustering, we obtained 8837 unique sequences (2838 contigs and 5999 singletons). The average contig length was 574 bp. Annotation of these unique sequences revealed that 48.9% of them showed significant homology to RNA sequences in GenBank. Functional classification of the unique ESTs identified a broad range of genes involved in different functions. We identified 6114 putative single-nucleotide polymorphisms and 634 microsatellites in ESTs. We discovered different temporal and spatial expression patterns of some immune-related genes in the Asian seabass after challenging with a pathogen Vibrio harveyi. The unique EST sequences are being used in developing a cDNA microarray to examine global gene expression and will also facilitate future whole-genome sequence assembly and annotation of Asian seabass and comparative genomics.
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