Research article

A cricket Gene Index: a genomic resource for studying neurobiology, speciation, and molecular evolution

Patrick D Danley¹ , Sean P Mullen¹ , Fenglong Liu² , Vishvanath Nene³ , John Quackenbush^2,4,5 and Kerry L Shaw¹

¹Department of Biology, University of Maryland, College Park, MD 20742, USA

²Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA

³The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA

⁴Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA

⁵Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA

author email corresponding author email

BMC Genomics 2007, 8:109doi:10.1186/1471-2164-8-109

Published:	25 April 2007

Abstract

Background

As the developmental costs of genomic tools decline, genomic approaches to non-model systems are becoming more feasible. Many of these systems may lack advanced genetic tools but are extremely valuable models in other biological fields. Here we report the development of expressed sequence tags (EST's) in an orthopteroid insect, a model for the study of neurobiology, speciation, and evolution.

Results

We report the sequencing of 14,502 EST's from clones derived from a nerve cord cDNA library, and the subsequent construction of a Gene Index from these sequences, from the Hawaiian trigonidiine cricket Laupala kohalensis. The Gene Index contains 8607 unique sequences comprised of 2575 tentative consensus (TC) sequences and 6032 singletons. For each of the unique sequences, an attempt was made to assign a provisional annotation and to categorize its function using a Gene Ontology-based classification through a sequence-based comparison to known proteins. In addition, a set of unique 70 base pair oligomers that can be used for DNA microarrays was developed. All Gene Index information is posted at the DFCI Gene Indices web page

Conclusion

Orthopterans are models used to understand the neurophysiological basis of complex motor patterns such as flight and stridulation. The sequences presented in the cricket Gene Index will provide neurophysiologists with many genetic tools that have been largely absent in this field. The cricket Gene Index is one of only two gene indices to be developed in an evolutionary model system. Species within the genus Laupala have speciated recently, rapidly, and extensively. Therefore, the genes identified in the cricket Gene Index can be used to study the genomics of speciation. Furthermore, this gene index represents a significant EST resources for basal insects. As such, this resource is a valuable comparative tool for the understanding of invertebrate molecular evolution. The sequences presented here will provide much needed genomic resources for three distinct but overlapping fields of inquiry: neurobiology, speciation, and molecular evolution.