ESTs from brain and testis of White Leghorn and red junglefowl: annotation, bioinformatic classification of unknown transcripts and analysis of expression levels

Vol. 111, No. 1, 2005

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Original Article

ESTs from brain and testis of White Leghorn and red junglefowl: annotation, bioinformatic classification of unknown transcripts and analysis of expression levels
P. Savolainen^a, C. Fitzsimmons^b, L. Arvestad^c, L. Andersson^b,d, J. Lundeberg^a

^aDepartment of Biotechnology, Royal Institute of Technology, Stockholm;
^bDepartment of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala;
^cStockholm Bioinformatics Center and Department of Numerical Analysis and Computing Science, Albanova, KTH, Stockholm;
^dDepartment of Medical Biochemistry and Microbiology, Uppsala University, Uppsala (Sweden)

Address of Corresponding Author

Cytogenet Genome Res 2005;111:79-87 (DOI: 10.1159/000085674)

Abstract.

We report the generation, assembly and annotation of expressed sequence tags (ESTs) from four chicken cDNA libraries, constructed from brain and testis tissue dissected from red junglefowl and White Leghorn. 21,285 5'-end ESTs were generated and assembled into 2,813 contigs and 9,737 singletons, giving 12,549 tentative unique transcripts. The transcripts were annotated using BLAST by matching to known chicken genes or to putative homologues in other species using the major gene/protein databases. The results for these similarity searches are available on www.sbc.su.se/~arve/chicken. 4,129 (32.9%) of the transcripts remained without a significant match to gene/protein databases, a proportion of unmatched transcripts similar to earlier non-mammalian EST studies. To estimate how many of these transcripts may represent novel genes, they were studied for the presence of coding sequence. It was shown that most of the unique chicken transcripts do not contain coding parts of genes, but it was estimated that at least 400 of the transcripts contain coding sequence, indicating that 3.2% of avian genes belong to previously unknown gene families. Further BLAST search against dbEST left 1,649 (13.1%) of the transcripts unmatched to any library. The number of completely unmatched transcripts containing coding sequence was estimated at 180, giving a measure of the number of putative novel chicken genes identified in this study. 84.3% of the identified transcripts were found only in testis tissue, which has been poorly studied in earlier chicken EST studies. Large differences in expression levels were found between the brain and testis libraries for a large number of transcripts, and among the 525 most frequently represented transcripts, there were at least 20 transcripts with significant difference in expression levels between red junglefowl and White Leghorn.

Author Contacts

Request reprints from Peter Savolainen, Department of Biotechnology
Royal Institute of Technology (KTH)
Albanova, SE-10691 Stockholm (Sweden)
telephone: +8 5537 8335, fax: +8 5537 8481, e-mail: savo@biotech.kth.se

Article Information

Supported by grants from Wallenberg Consortium North, the Foundation for Strategic Research and the AgriFunGen program at the Swedish University of Agricultural Sciences.

Manuscript received 26 April 2004;
accepted in revised form for publication by T. Shows 30 November 2004.
Number of Print Pages : 9
Number of Figures : 1, Number of Tables : 6, Number of References : 28

Medline Abstract (ID 16093725)

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