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

Marine Genomics. Bd. 28. Elsevier BV 2016 S. 7 - 10

Erscheinungsjahr: 2016

ISBN/ISSN: 1874-7787

Publikationstyp: Zeitschriftenaufsatz

Sprache: Englisch

Doi/URN: 10.1016/j.margen.2016.02.006

Volltext über DOI/URN

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Inhaltszusammenfassung


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 w...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.» weiterlesen» einklappen

  • Aphanomyces astaci
  • Genomics
  • RNA-seq data
  • Trinity
  • Transrate
  • BUSCO

Autoren


Falckenhayn, Cassandra (Autor)
Blande, Daniel (Autor)
Toljamo, Anna (Autor)
Gutekunst, Julian (Autor)
Makkonen, Jenny (Autor)
Jussila, Japo (Autor)
Lyko, Frank (Autor)
Schrimpf, Anne (Autor)
Kokko, Harri (Autor)

Klassifikation


DFG Fachgebiet:
Zoologie

DDC Sachgruppe:
Biowissenschaften, Biologie

Verknüpfte Personen