An EST Resource for Tilapia Based on 17 Normalized Libraries and Assembly of 116,899 Sequence Tags

Overview

Journal BMC Genomics

Publisher Biomed Central

Specialty Genetics

Date 2010 May 4

PMID 20433739

Citations 24

Authors

Bo-Young Lee

Aimee E Howe

Matthew A Conte

Helena DCotta

Elodie Pepey

Jean-Francois Baroiller

Federica Di Palma

Karen L Carleton

Thomas D Kocher

Affiliations

Soon will be listed here.

Abstract

Background: Large collections of expressed sequence tags (ESTs) are a fundamental resource for analysis of gene expression and annotation of genome sequences. We generated 116,899 ESTs from 17 normalized and two non-normalized cDNA libraries representing 16 tissues from tilapia, a cichlid fish widely used in aquaculture and biological research.

Results: The ESTs were assembled into 20,190 contigs and 36,028 singletons for a total of 56,218 unique sequences and a total assembled length of 35,168,415 bp. Over the whole project, a unique sequence was discovered for every 2.079 sequence reads. 17,722 (31.5%) of these unique sequences had significant BLAST hits (e-value < 10(-10)) to the UniProt database.

Conclusion: Normalization of the cDNA pools with double-stranded nuclease allowed us to efficiently sequence a large collection of ESTs. These sequences are an important resource for studies of gene expression, comparative mapping and annotation of the forthcoming tilapia genome sequence.

Citing Articles

Mapping QTL for Sex and Growth Traits in Salt-Tolerant Tilapia (Oreochromis spp. X O. mossambicus).

Lin G, Chua E, Orban L, Yue G PLoS One. 2016; 11(11):e0166723.

PMID: 27870905 PMC: 5117716. DOI: 10.1371/journal.pone.0166723.

Signatures of selection in tilapia revealed by whole genome resequencing.

Xia J, Bai Z, Meng Z, Zhang Y, Wang L, Liu F Sci Rep. 2015; 5:14168.

PMID: 26373374 PMC: 4570987. DOI: 10.1038/srep14168.

Living without DAT: Loss and compensation of the dopamine transporter gene in sauropsids (birds and reptiles).

Lovell P, Kasimi B, Carleton J, Velho T, Mello C Sci Rep. 2015; 5:14093.

PMID: 26364979 PMC: 4894405. DOI: 10.1038/srep14093.

Transcriptome of the Deep-Sea Black Scabbardfish, Aphanopus carbo (Perciformes: Trichiuridae): Tissue-Specific Expression Patterns and Candidate Genes Associated to Depth Adaptation.

Stefanni S, Bettencourt R, Pinheiro M, De Moro G, Bongiorni L, Pallavicini A Int J Genomics. 2014; 2014:267482.

PMID: 25309900 PMC: 4182897. DOI: 10.1155/2014/267482.

Identification of male-specific amh duplication, sexually differentially expressed genes and microRNAs at early embryonic development of Nile tilapia (Oreochromis niloticus).

Eshel O, Shirak A, Dor L, Band M, Zak T, Markovich-Gordon M BMC Genomics. 2014; 15:774.

PMID: 25199625 PMC: 4176596. DOI: 10.1186/1471-2164-15-774.

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