title: Assembly and annotation of a non-model gastropod (Nerita melanotragus) transcriptome: a comparison of de novo assemblers.
abstract: BACKGROUND
  The sequencing, de novo assembly and annotation of transcriptome datasets generated with next generation sequencing (NGS) has enabled biologists to answer genomic questions in non-model species with unprecedented ease. Reliable and accurate de novo assembly and annotation of transcriptomes, however, is a critically important step for transcriptome assemblies generated from short read sequences. Typical benchmarks for assembly and annotation reliability have been performed with model species. To address the reliability and accuracy of de novo transcriptome assembly in non-model species, we generated an RNAseq dataset for an intertidal gastropod mollusc species, Nerita melanotragus, and compared the assembly produced by four different de novo transcriptome assemblers; Velvet, Oases, Geneious and Trinity, for a number of quality metrics and redundancy.
  
  
  RESULTS
  Transcriptome sequencing on the Ion Torrent PGM™ produced 1,883,624 raw reads with a mean length of 133 base pairs (bp). Both the Trinity and Oases de novo assemblers produced the best assemblies based on all quality metrics including fewer contigs, increased N50 and average contig length and contigs of greater length. Overall the BLAST and annotation success of our assemblies was not high with only 15-19% of contigs assigned a putative function.
  
  
  CONCLUSIONS
  We believe that any improvement in annotation success of gastropod species will require more gastropod genome sequences, but in particular an increase in mollusc protein sequences in public databases. Overall, this paper demonstrates that reliable and accurate de novo transcriptome assemblies can be generated from short read sequencers with the right assembly algorithms.
authors.forename: Shorash
authors.initials: S
authors.lastname: Amin
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Prentis
authors.forename: Edward K
authors.initials: EK
authors.lastname: Gilding
authors.affiliation: School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, GPO Box 2434, Brisbane, Qld 4001, Australia. a.pavasovic@qut.edu.au.
authors.forename: Ana
authors.initials: A
authors.lastname: Pavasovic
mesh_terms: D000818:Animals; D020451:Contig Mapping; D049851:Gastropoda / Q000235:genetics*; D063990:Gene Ontology; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction; D015203:Reproducibility of Results; D013045:Species Specificity; D059467:Transcriptome / Q000235:genetics*
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