Life Sciences Commons^™

Transcriptome Deep-Sequencing And Clustering Of Expressed Isoforms From Favia Corals, Shaadi F. Pooyaei Mehr, Rob Desalle, Hung-Teh Kao, Apurva Narechania, Zhou Han, Dan Tchernov, Vincent A. Pieribone, David F. Gruber

Publications and Research

Background: Genomic and transcriptomic sequence data are essential tools for tackling ecological problems. Using an approach that combines next-generation sequencing, de novo transcriptome assembly, gene annotation and synthetic gene construction, we identify and cluster the protein families from Favia corals from the northern Red Sea.

Results: We obtained 80 million 75 bp paired-end cDNA reads from two Favia adult samples collected at 65 m (Fav1, Fav2) on the Illumina GA platform, and generated two de novo assemblies using ABySS and CAP3. After removing redundancy and filtering out low quality reads, our transcriptome datasets contained 58,268 (Fav1) and 62,469 (Fav2) contigs …

Edges And Overlaps In Northwest Atlantic Phylogeography, Safra Altman, John D. Robinson, James M. Pringle, James E. Byers, John P. Wares

Publications and Research

As marine environments change, the greatest ecological shifts—including resource usage and species interactions—are likely to take place in or near regions of biogeographic and phylogeographic transition. However, our understanding of where these transitional regions exist depends on the defining criteria. Here we evaluate phylogeographic transitions using a bootstrapping procedure that allows us to focus on either the strongest genetic transitions between a pair of contiguous populations, versus evaluation of transitions inclusive of the entire overlap between two intraspecific genetic lineages. We compiled data for the Atlantic coast of the United States, and evaluate taxa with short- and long-dispersing larval phases …