Research article
An Sp185/333 gene cluster from the purple sea urchin and putative microsatellite-mediated gene diversification
-
* Corresponding author: L Courtney Smith csmith@gwu.edu
- † Equal contributors
1 Genomics and Bioinformatics Program, Department of Biochemistry, School of Medicine, The George Washington University, Washington DC, 20037, USA
2 Department of Biological Sciences, George Washington University, Washington, DC, 20052, USA
3 Department of Biology, Boston College, Boston, MA, USA
4 Department of Immunology, Sunnybrook Research Institute, University of Toronto, Toronto, ON, Canada
5 TECHLAB Inc, Blacksburg, VA, USA
BMC Genomics 2010, 11:575 doi:10.1186/1471-2164-11-575
Published: 18 October 2010Abstract
Background
The immune system of the purple sea urchin, Strongylocentrotus purpuratus, is complex and sophisticated. An important component of sea urchin immunity is the Sp185/333 gene family, which is significantly upregulated in immunologically challenged animals. The Sp185/333 genes are less than 2 kb with two exons and are members of a large diverse family composed of greater than 40 genes. The S. purpuratus genome assembly, however, contains only six Sp185/333 genes. This underrepresentation could be due to the difficulties that large gene families present in shotgun assembly, where multiple similar genes can be collapsed into a single consensus gene.
Results
To understand the genomic organization of the Sp185/333 gene family, a BAC insert containing Sp185/333 genes was assembled, with careful attention to avoiding artifacts resulting from collapse or artificial duplication/expansion of very similar genes. Twelve candidate BAC assemblies were generated with varying parameters and the optimal assembly was identified by PCR, restriction digests, and subclone sequencing. The validated assembly contained six Sp185/333 genes that were clustered in a 34 kb region at one end of the BAC with five of the six genes tightly clustered within 20 kb. The Sp185/333 genes in this cluster were no more similar to each other than to previously sequenced Sp185/333 genes isolated from three different animals. This was unexpected given their proximity and putative effects of gene homogenization in closely linked, similar genes. All six genes displayed significant similarity including both 5' and 3' flanking regions, which were bounded by microsatellites. Three of the Sp185/333 genes and their flanking regions were tandemly duplicated such that each repeated segment consisted of a gene plus 0.7 kb 5' and 2.4 kb 3' of the gene (4.5 kb total). Both edges of the segmental duplications were bounded by different microsatellites.
Conclusions
The high sequence similarity of the Sp185/333 genes and flanking regions, suggests that the microsatellites may promote genomic instability and are involved with gene duplication and/or gene conversion and the extraordinary sequence diversity of this family.