W113 The Buffalo Transcriptome

Date: Saturday, January 14, 2012
Time: 8:30 AM
Room: Pacific Salon 4-5 (2nd Floor)
Francesco Strozzi , Parco Tecnologico Padano, Lodi, Italy
Daniela Iamartino , Parco Tecnologico Padano, Lodi, Italy
Tommaso Biagini , CASPUR - Inter-University Consortium for the Application of Supercomputing for Universities and Research, Rome, Italy
Giordano Mancini , UniversitÓ della Tuscia, Viterbo, Italy
Giovanni Chillemi , CASPUR - Inter-University Consortium for the Application of Supercomputing for Universities and Research, Rome, Italy
John Williams , Fondazione Parco Technologico Padano, Lodi, Italy
Samples from male and female water buffalos (Bubalus bubalis) were selected to begin the transcriptome analysis as part of the International Water Buffalo Genome Project. The samples collected were representative of a wide range of tissues and cell types ranging from lymphocytes to heart, bone marrow, spleen and reproductive organs for a total of 31 different samples. All the samples were processed to extract both mRNAs and small RNAs and sequenced using Illumina Hi-Seq 2000. For mRNA the sequencing was targeted to generate around 20M paired end reads of 100bp for each sample. The bioinformatics analysis is ongoing and initial efforts were focused to process first all the mRNAs and reconstruct the buffalo transcriptome. Raw data have been processed using Illumina 1.9 pipeline to generate the set of FastQ files and each dataset was subsequently filtered and reads trimmed using quality scores. A de novo assembly of the transcriptome was selected as best strategy to analyse the data and provide a comprehensive picture of the transcript sequences in the different samples. A subset of samples coming from the reproductive tissues was chosen as initial dataset to assess the performance and overall results of different de novo transcriptome assembler, in particular the ABySS / Trans-ABySS and Trinity pipelines. Preliminary results on genes and transcripts that were reconstructed by this analysis will be presented and discussed along with the different approaches of the assembly methods.