Identification and analysis of a prepro-chicken gonadotropin releasing hormone II (preprocGnRH-II) precursor in the Asian seabass, Lates calcarifer, based on an EST-based assessment of its brain transcriptome

Tan, Sik-Loo; Mohd-Adnan, Adura; Mohd-Yusof, Nurul Yuziana; Forstner, Michael R. J.; Wan, Kiew Lian

doi:10.1016/j.gene.2008.01.008

Cited by 8 publications

(10 citation statements)

References 46 publications

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“…At the start of the transcriptome project, the dbEST database contained 5637 Asian seabass ESTs (gi:169659332–169664968), originated from a brain cDNA library 32 and two subtracted spleen cDNA libraries (2887 ESTs; gi: GT219120–GT222006). 28 In order to enrich the existing transcriptome data sets and analyze genes that expressed in different organs of the Asian seabass, we sequenced ESTs from nine normalized cDNA libraries from various tissues of the Asian seabass (Supplementary Table S1).…”

Section: Resultsmentioning

confidence: 99%

“…To create a large global collection of the Asian seabass ESTs, the published 8524 ESTs 28,32 were retrieved from the dbEST database and included in the following clustering and annotation. After combining these data, a total of 19 975 high-quality ESTs were obtained and used to identify EST clusters representing redundant transcripts under high stringency (95% similarity; Supplementary Table S10).…”

Section: Resultsmentioning

confidence: 99%

“…EST sequences from the nine cDNA libraries constructed by our laboratory and sequences of ESTs 28,32 of Asian seabass from GenBank were included in the following analysis. Base calling from chromatogram traces and trimming of vector and adaptor sequences and low-quality regions from EST sequences were performed by using commercial software Sequencher 4.9 (Gene Codes, Ann Arbor, USA).…”

Section: Methodsmentioning

confidence: 99%

“…These include a large number of microsatellites, 21–23 a genetic linkage map, 24,25 a bacterial artificial chromosome (BAC) library, 26 a physical map based on BAC fingerprinting, 27 some ESTs related to immune responses, 28 microRNAs 29 and quantitative trait loci for growth 30 and an adaptive trait. 31 So far, the EST resource of the Asian seabass presented in the public NCBI dbEST database has grown to over 8000 ESTs (5637 ESTs from the brain 32 and 2887 immune-related ESTs from the spleen 28 ). However, to date, the large-scale EST data for the Asian seabass are lacking.…”

Section: Introductionmentioning

confidence: 99%

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Analysis of the Asian Seabass Transcriptome Based on Expressed Sequence Tags

Xia

Bai

et al. 2011

DNA Research

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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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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Analysis of the Asian Seabass Transcriptome Based on Expressed Sequence Tags

Xia

Bai

et al. 2011

DNA Research

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“…As the pleonal SSH cDNA library constructed in this work was not normalized, the EST abundance or cluster size is more likely to indicate the relative mRNA population or gene expression level (Tan et al 2008). PCR detection and analysis of the constructed libraries show that the SSH technique is efficient in adaptor ligation.…”

Section: Efficiency Of the Ssh Methodsmentioning

confidence: 98%

Identification of Differentially Expressed Genes During the Brachyurization of the Chinese Mitten Crab Eriocheir japonica sinensis

Zha

Sun

et al. 2011

Biochem Genet

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Expressed sequence tags (ESTs) obtained from two-directional suppression subtractive hybridization (SSH) of cDNA libraries derived from the pleon of the Chinese mitten crab were analyzed using mRNA subtractive hybridization. After cDNA cloning and sequencing, gene expression profiles were examined, focusing on brachyurization. We assembled 211 non-redundant ESTs from SSH library 1 (yielding 130 unique transcripts: 25 consensi, 105 singletons) and 669 from SSH library 2 (195: 51 consensi, 144 singletons). Functional analysis shows that these genes are putatively involved in various cellular processes (33%), ribosomal RNA/proteins (30%), molting (12%), signal transduction (6%), immune factor and stress proteins (6%), development (4%), energy metabolism (3%), and mitochondrial membrane protein, hormone metabolizing, and chaperone (1% each) of other organisms. Some 3% are of unknown function in SSH library 1. The results facilitate the functional study of candidate genes involved in early developmental processes, especially the regulation of brachyurization in this crab.

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