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Transcriptome Profiling of In-Vivo Produced Bovine Pre-implantation Embryos Using Two-color Microarray Platform

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The porcelain crab transcriptome and PCAD, the porcelain crab microarray and sequence database.

Abderrahmane Tagmount¹, Mei Wang, Erika Lindquist

¹Romberg Tiburon Center and Department of Biology, San Francisco State University, Tiburon, California, United States of America.

|February 23, 2010

Summary

This summary is machine-generated.

We generated a large expressed sequence tag (EST) dataset and cDNA microarray for the porcelain crab Petrolisthes cinctipes. This resource aids comparative genomics and environmental studies in crustaceans.

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Area of Science:

Marine biology
Genomics
Evolutionary physiology

Background:

Comparative genomics requires extensive sequence databases for crustaceans.
Porcelain crabs (Petrolisthes) are key models for thermal adaptation and climate change research.
A large-scale expressed sequence tag (EST) sequencing and cDNA microarray project was initiated for Petrolisthes cinctipes.

Purpose of the Study:

To create a comprehensive genomic-scale sequence database for Petrolisthes cinctipes.
To facilitate comparative genomics and annotation within crustacean research.
To support environmental and evolutionary physiology studies.

Main Methods:

Generated approximately 98,000 high-quality ESTs from Petrolisthes cinctipes.
Created ~30,000 unique sequences (UniSeqs) representing ~19,000 clusters.
Performed homology assessments using BLAST, InterProScan, Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases.

Main Results:

Approximately 66% of UniSeqs exhibited homology in at least one database.
Publicly accessible database (PCAD) created with EST, UniSeq, annotation, and microarray data.
The EST dataset is comparable in diversity to the Daphnia pulex genome project.

Conclusions:

This EST project is the third-largest for any crustacean and the largest for a crab species.
The data supports the pancrustacea hypothesis, suggesting Malacostraca's ancestral role.
The cDNA microarrays offer a valuable resource for environmental genomics research.