Meeting Abstract
P1.134 Saturday, Jan. 4 15:30 RNA-seq analysis of stage-specific limb regenerates in the fiddler crab, Uca pugilator DAS, S.*; NAJAR, F.Z.; LAI, H.C.; ROE, B.A.; DURICA, D.S.; University of Oklahoma sunetra.das-1@ou.edu
Although an annotated genome of Daphnia pulex is available, crustacean genomic sequence data are exceedingly meager. While lack of genomic annotation is still a limiting factor in facilitating gene identification, with the advent of next generation sequencing technology, researchers have been able to generate transcriptomes in several arthropod models involved in developmental, evolutionary and ecological investigations. We study the hormonal basis of limb regeneration in Uca pugilator and have produced limb bud transcriptomes for three developmental phases using Illumina sequencing. Staging was based on time since limb loss, limb bud size, growth rate and circulating ecdysteroid titers: 1) early blastemal phase associated with cellular proliferation and differentiation; 2) early proecdysial phase associated with rapid limb bud growth and low hormone titers; 3) late proecdysial phase associated with plateau of growth seen just before molt and high circulating ecdysteroid titers. Following sequencing, de-novo assembly of quality reads was performed using the SOAP assembly program to generate 1,853,990 contigs (all libraries combined). Analyses of the sequence data are available online at http://www.genome.ou.edu/crab.html. Although 80% of these reads were not assignable in GenBank, these contigs could be mapped to a total of 144,593 metazoan sequences against the GenBank non-redundant protein database (E-value cutoff: e-3). Among the metazoan contigs, 44,959 were assigned to a KEGG metabolic pathway. DESeq analyses identified over 500 genes differentially expressed with a ≥ 5-fold change between blastema and early proecdysial growth phase. Further analyses were performed to obtain metabolic profiles using the KEGG database to study gene networks relevant to limb regeneration.
