Open AccessGene Discovery Using Computational and Microarray Analysis of Transcription in the Drosophila melanogaster Testis
Author(s) -
Joseph Andrews,
Gerard G. Bouffard,
Chris Cheadle,
Jining Lü,
Kevin G. Becker,
Brian Oliver
Publication year - 2000
Publication title -
genome research
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 9.556
H-Index - 297
eISSN - 1549-5469
pISSN - 1088-9051
DOI - 10.1101/gr.159800
Subject(s) - biology , expressed sequence tag , gene , genetics , drosophila melanogaster , genome , complementary dna , microarray analysis techniques , cdna library , dna microarray , computational biology , gene expression
Identification and annotation of all the genes in the sequenced Drosophila genome is a work in progress. Wild-type testis function requires many genes and is thus of potentially high value for the identification of transcription units. We therefore undertook a survey of the repertoire of genes expressed in the Drosophila testis by computational and microarray analysis. We generated 3141 high-quality testis expressed sequence tags (ESTs). Testis ESTs computationally collapsed into 1560 cDNA set used for further analysis. Of those, 11% correspond to named genes, and 33% provide biological evidence for a predicted gene. A surprising 47% fail to align with existing ESTs and 16% with predicted genes in the current genome release. EST frequency and microarray expression profiles indicate that the testis mRNA population is highly complex and shows an extended range of transcript abundance. Furthermore, >80% of the genes expressed in the testis showed onefold overexpression relative to ovaries, or gonadectomized flies. Additionally, >3% showed more than threefold overexpression at p <0.05. Surprisingly, 22% of the genes most highly overexpressed in testis match Drosophila genomic sequence, but not predicted genes. These data strongly support the idea that sequencing additional cDNA libraries from defined tissues, such as testis, will be important tools for refined annotation of the Drosophila genome. Additionally, these data suggest that the number of genes in Drosophila will significantly exceed the conservative estimate of 13,601. [The sequence data described in this paper have been submitted to the dbEST data library under accession nos. AI944400 – AI947263 and BE661985 – BE662262 .] [The microarray data described in this paper have been submitted to the GEO data library under accession nos. GPLS, GSM3–GSM10.]