Gene discovery in the hamster: a comparative genomics approach for gene annotation by sequencing of hamster testis cDNAs.

SriTulasi Karri,Simon C Williams,Shafiq A Khan,Janee L Campbell,William J Hendry,Sreedhar Oduru

doi:10.1186/1471-2164-4-22

Abstract

BackgroundComplete genome annotation will likely be achieved through a combination of computer-based analysis of available genome sequences combined with direct experimental characterization of expressed regions of individual genomes. We have utilized a comparative genomics approach involving the sequencing of randomly selected hamster testis cDNAs to begin to identify genes not previously annotated on the human, mouse, rat and Fugu (pufferfish) genomes.Results735 distinct sequences were analyzed for their relatedness to known sequences in public databases. Eight of these sequences were derived from previously unidentified genes and expression of these genes in testis was confirmed by Northern blotting. The genomic locations of each sequence were mapped in human, mouse, rat and pufferfish, where applicable, and the structure of their cognate genes was derived using computer-based predictions, genomic comparisons and analysis of uncharacterized cDNA sequences from human and macaque.ConclusionThe use of a comparative genomics approach resulted in the identification of eight cDNAs that correspond to previously uncharacterized genes in the human genome. The proteins encoded by these genes included a new member of the kinesin superfamily, a SET/MYND-domain protein, and six proteins for which no specific function could be predicted. Each gene was expressed primarily in testis, suggesting that they may play roles in the development and/or function of testicular cells.

Highlights

Complete genome annotation will likely be achieved through a combination of computer-based analysis of available genome sequences combined with direct experimental characterization of expressed regions of individual genomes
Current estimates suggest that the human genome encodes approximately 35,000 to 38,000 the final number must await the complete annotation of each genome sequence
The search for additional genes not discovered during early annotation attempts has involved the use of several different approaches. These have included the sequencing of randomly selected cDNAs from various tissue sources, the development of computer-based prediction programs of ever-increasing accuracy, and the direct comparison between the human genome and the genome sequences of other vertebrates and invertebrates [3,4,5,6,7,8,9]

Summary

Introduction

Complete genome annotation will likely be achieved through a combination of computer-based analysis of available genome sequences combined with direct experimental characterization of expressed regions of individual genomes. The search for additional genes not discovered during early annotation attempts has involved the use of several different approaches These have included the sequencing of randomly selected cDNAs from various tissue sources, the development of computer-based prediction programs of ever-increasing accuracy, and the direct comparison between the human genome and the genome sequences of other vertebrates and invertebrates [3,4,5,6,7,8,9]. Using these (page number not for citation purposes). Sequence information from any hamster species should complement information gained from other closely related species

Methods

Results

Conclusion