title: Evaluation ofde novoassembly technique in the South African abaloneHaliotis midaetranscriptome: A comparison from Illumina and 454 systems.
abstract: Next generation sequencing platforms have recently been used to rapidly characterize transcriptome sequences from a number of non-model organisms. The present study compares two of the most frequently used platforms, the Roche 454-pyrosequencing and the Illumina sequencing-by-synthesis (SBS), on the same RNA sample obtained from an intertidal gastropod mollusc species,Haliotis midae. All the sequencing reads were deposited in the Short Read Archive (SRA) database are retrievable under the accession number [SRR071314 (Illumina Genome Analyzer II)] and [SRR1737738, SRR1737737, SRR1737735, SRR1737734 (454 GS FLX)] in the SRA database of NCBI. Three transcriptomes, composed of either pure 454 or Illumina reads or a mixture of read types (Hybrid), were assembled using CLC Genomics Workbench software. Illumina assemblies performed the bestde novotranscriptome characterization in terms of contig length, whereas the 454 assemblies tended to improve the complete assembly of gene transcripts. Both the Hybrid and Illumina assemblies produced longer contigs covering more of the transcriptome than 454 assemblies. However, the addition of 454 significantly increased the number of genes annotated.
authors.affiliation: Department of Genetics, Stellenbosch University, van der Bijl Street, JC Smuts Building, Private Bag X1, Matieland 7602, South Africa.
authors.forename: Barbara
authors.initials: B
authors.lastname: Picone
authors.affiliation: Department of Genetics, Stellenbosch University, van der Bijl Street, JC Smuts Building, Private Bag X1, Matieland 7602, South Africa.
authors.forename: Clint
authors.initials: C
authors.lastname: Rhode
authors.affiliation: Department of Genetics, Stellenbosch University, van der Bijl Street, JC Smuts Building, Private Bag X1, Matieland 7602, South Africa.
authors.forename: Rouvay
authors.initials: R
authors.lastname: Roodt-Wilding
keywords: Abalone; Haliotis midae; Hybrid assembly; Transcriptome