Email updates

Keep up to date with the latest news and content from BMC Genomics and BioMed Central.

Open Access Methodology article

A new procedure for determining the genetic basis of a physiological process in a non-model species, illustrated by cold induced angiogenesis in the carp

John MJ Herbert1, Francesca M Buffa2, Henrik Vorschmitt1, Stuart Egginton3 and Roy Bicknell1*

Author Affiliations

1 Cancer Research UK Angiogenesis Group, Institute for Biomedical Research, Schools of Immunity and Infection and Cancer studies, College of Medicine and Dentistry, University of Birmingham, Birmingham, B15 2TT, UK

2 Cancer Research UK, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK

3 Division of Medical Sciences, Medical School, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK

For all author emails, please log on.

BMC Genomics 2009, 10:490  doi:10.1186/1471-2164-10-490

Published: 23 October 2009

Abstract

Background

Physiological processes occur in many species for which there is yet no sequenced genome and for which we would like to identify the genetic basis. For example, some species increase their vascular network to minimise the effects of reduced oxygen diffusion and increased blood viscosity associated with low temperatures. Since many angiogenic and endothelial genes have been discovered in man, functional homolog relationships between carp, zebrafish and human were used to predict the genetic basis of cold-induced angiogenesis in Cyprinus Carpio (carp). In this work, carp sequences were collected and built into contigs. Human-carp functional homolog relationships were derived via zebrafish using a new Conditional Stepped Reciprocal Best Hit (CSRBH) protocol. Data sources including publications, Gene Ontology and cDNA libraries were then used to predict the identity of known or potential angiogenic genes. Finally, re-analyses of cold carp microarray data identified carp genes up-regulated in response to low temperatures in heart and muscle.

Results

The CSRBH approach outperformed all other methods and attained 8,726 carp to human functional homolog relationships for 16,650 contiguous sequences. This represented 3,762 non-redundant genes and 908 of them were predicted to have a role in angiogenesis. The total number of up-regulated differentially expressed genes was 698 and 171 of them were putatively angiogenic. Of these, 5 genes representing the functional homologs NCL, RHOA, MMP9, GRN and MAPK1 are angiogenesis-related genes expressed in response to low temperature.

Conclusion

We show that CSRBH functional homologs relationships and re-analyses of gene expression data can be combined in a non-model species to predict genes of biological interest before a genome sequence is fully available. Programs to run these analyses locally are available from http://www.cbrg.ox.ac.uk/~jherbert/ webcite.