First comprehensive multi-tissue transcriptome of Cherax quadricarinatus (Decapoda: Parastacidae) reveals unexpected diversity of endogenous cellulase

The Australian freshwater crayfish species, Cherax quadricarinatus Von Martens, 1868, is an important commercial and invasive species that is also being increasingly used as a model organism to address important and interesting questions in crustacean biology. Through deep sequencing of the transcriptome of C. quadricarinatus from the hepatopancreas and four other tissues, we examine the evolution of endogenously transcribed cellulase genes and provide new insights into controversial issues regarding the nutritional biology of crayfishes. A cluster assembly approach yielded one of the highest quality transcriptome assemblies for a decapod crustacean to date. A total of 206,341,872 reads with an average read length of 80 bp were generated from sequencing the transcriptomes from the heart, kidney, hepatopancreas, nerve, and testis tissues. The assembled transcriptome contains a total of 44,525 transcripts. A total of 65 transcripts coding for carbohydrate-active enzymes (CAZy) were identified based on hidden Markov model (HMM), and a majority of them display high relative transcript abundance in the hepatopancreas tissue, supporting their role in nutrient digestion. Comprehensive phylogenetic analyses of proteins belonging to two main glycosyl hydrolase families (GH9 and GH5) suggest shared ancestry of C. quadricarinatus cellulases with other characterized crustacean cellulases. Our study significantly expands the number of known crustacean-derived CAZy-coding transcripts. More importantly, the surprising level of evolutionary diversification of these proteins in C. quadricarinatus suggests that these enzymes may have been of critical importance in the adaptation of freshwater crayfishes to new plant-based food sources as part of their successful invasion of freshwater systems from marine ancestors.

Experiences with an Object-Oriented, Multi-Stage Language

Metaphor is a multi-stage programming language extension to an imperative, object-oriented language in the style of C# or Java. This paper discusses some issues we faced when applying multi-stage language design concepts to an imperative base language and run-time environment. The issues range from dealing with pervasive references and open code to garbage collection and implementing cross-stage persistence.