Biomaterial Database

De Novo assembly and annotation of the freshwater crayfish Astacus astacus transcriptome. 2016

Kathrin Theissinger, and Cassandra Falckenhayn, and Daniel Blande, and Anna Toljamo, and Julian Gutekunst, and Jenny Makkonen, and Japo Jussila, and Frank Lyko, and Anne Schrimpf, and Ralf Schulz, and Harri Kokko

University of Koblenz-Landau, Institute for Environmental Sciences, Fortstrasse 7, 76829 Landau, Germany. Electronic address: theissinger@uni-landau.de.

We generated RNA-seq data to assemble the transcriptome of the noble crayfish (Astacus astacus) from four combined tissues (abdominal muscle, hepatopancreas, ovaries, green glands). A total of 194 million read pairs with a length of 100 bp were generated. The transcriptome was assembled de novo using Trinity software, producing 158,649 non-redundant transcripts. Lowly expressed transcripts were filtered out leaving 45,415 transcripts of which 14,559 were found to contain open reading frames with predicted gene function. The Transrate software revealed that 91% of the total reads were realigned to the assembly. Furthermore, BUSCO analysis indicated that our assembly is 64% complete. A total of 13,770 transcripts were assigned at least one GO term. This first de novo transcriptome assembly is an important foundation for future genomic research on the noble crayfish and adds to the general knowledge and further characterization of transcriptomes of non-model organisms.

UI	MeSH Term	Description	Entries
D003400	Astacoidea	A superfamily of various freshwater CRUSTACEA, in the infraorder Astacidea, comprising the crayfish. Common genera include Astacus and Procambarus. Crayfish resemble lobsters, but are usually much smaller.	Astacus,Crayfish,Procambarus,Astacoideas,Crayfishs
D005260	Female		Females
D005618	Fresh Water	Water containing no significant amounts of salts, such as water from RIVERS and LAKES.	Freshwater,Fresh Waters,Freshwaters,Water, Fresh,Waters, Fresh
D000818	Animals	Unicellular or multicellular, heterotrophic organisms, that have sensation and the power of voluntary movement. Under the older five kingdom paradigm, Animalia was one of the kingdoms. Under the modern three domain model, Animalia represents one of the many groups in the domain EUKARYOTA.	Animal,Metazoa,Animalia
D017423	Sequence Analysis, RNA	A multistage process that includes cloning, physical mapping, subcloning, sequencing, and information analysis of an RNA SEQUENCE.	RNA Sequence Analysis,Sequence Determination, RNA,Analysis, RNA Sequence,Determination, RNA Sequence,Determinations, RNA Sequence,RNA Sequence Determination,RNA Sequence Determinations,RNA Sequencing,Sequence Determinations, RNA,Analyses, RNA Sequence,RNA Sequence Analyses,Sequence Analyses, RNA,Sequencing, RNA
D059467	Transcriptome	The pattern of GENE EXPRESSION at the level of genetic transcription in a specific organism or under specific circumstances in specific cells.	Transcriptomes,Gene Expression Profiles,Gene Expression Signatures,Transcriptome Profiles,Expression Profile, Gene,Expression Profiles, Gene,Expression Signature, Gene,Expression Signatures, Gene,Gene Expression Profile,Gene Expression Signature,Profile, Gene Expression,Profile, Transcriptome,Profiles, Gene Expression,Profiles, Transcriptome,Signature, Gene Expression,Signatures, Gene Expression,Transcriptome Profile