De novo transcriptome assembly for Pachygrapsus marmoratus, an intertidal brachyuran crab.

ABSTRACT

The marble crab Pachygrapsus marmoratus inhabits the rocky shores of the Mediterranean Sea, Black Sea and East Atlantic Ocean. As other intertidal species, it is considered a model species to study the effects of environmental stressors on natural populations. In this study, we performed Illumina next-generation sequencing on eleven P. marmoratus specimens with the aims to (i) reconstruct their whole transcriptome, (ii) perform a functional annotation of the assembled transcriptome and (iii) develop gene-based markers for future genetic and genomic studies on this as well as other brachyuran species. We obtained a transcriptome assembly constituted by 56,308 unigenes and covering about 60.3 Mbp. We detected 43,915 Simple Sequence Repeats (SSRs) and 192,631 high-quality Single Nucleotide Polymorphisms (SNPs). Due to the scarcity of genomic resources in decapods, and crabs in particular, our results constitute a valuable resource for future studies on brachyuran crabs. The present data also represent a sound resource to investigate biological responses to pollution in intertidal and marine populations.