Comparative Genomics

One of the particular advantages of the sea urchin as an experimental system lies in the well defined phylogeny that surrounds it. A deep and diverse fossil record and extensive biochemical studies together establish confident divergence times for many points in the phylogenetic tree for echinoderms (see figure). Sea urchins have diverged from the reference species at intervals covering 265 million years. Sea stars, hemichordates and the chordate branch to which humans belong diverged earlier.

This character has been especially useful for the description of gene regulatory networks (GRN) and the cis-regulatory modules (CRM) of which they are made. One of the most comprehensive examples of a GRN sufficiently mature to demonstrate their full range of predictive and explanatory power are at present those worked out experimentally for the embryo of the sea urchin (Strongylocentrotus purpuratusSp).

Genomic comparisons with another echinoid (sea urchin) species Lytechinus variegatus (Lv) identifies conserved non-coding regions that include CRMs. The full genomic sequence of this species will lead to the first algorithms (that work) for large scale prediction of overall GRN structure from genomic sequence. Acquisition of the genome sequence of the asteroid (sea star) Patiria miniata (Pm) will produce direct evidence, and provide predictive principles, for assessing what types of GRN subcircuit are flexible in evolution and thus could be reorganized or altered, and which are virtually unchanging and inflexible.

A species of intermediate divergence (Eucidaris tribuloides (Et) exhibits interesting variation in developmental pattern which can also be used to contrast with that of the reference.

We presently have available two sets of transcriptome data that can be used for gene discovery. One comes from embryos of Eucidaris tribuloides. It is a single run of Illumina sequences, assembled with Velvet and blasted against the purple sea urchin gene sequences.

The second is the Roche 454 sequences made from mRNAs of the sea star Patiria miniata pooled from before and after gastrulation. The latter sequences were read and assembled by the Baylor College of Medicine, Human Genome Sequencing Center using material from the CCRG. This set is archived in the nucelotide database at Genbank under accession numbers HP081117-HP139644. We performed the BLAST analysis locally.