The Buffalo Transcriptome

Samples from male and female water buffalos (Bubalus bubalis) were selected to generate a reference set of transcripts using RNA-seq, as part of the International Water Buffalo Genome Project. The samples were from 30 tissues ranging from lymphocytes to heart, bone marrow, spleen and reproductive organs representing a wide range of cell types. All the samples were processed to extract both mRNAs and small RNAs and sequenced using the Illumina Hi-Seq platform. A complete transcriptome analysis was performed by aligning the mRNA sequencing data, with the 367339 scaffolds of the first version of the assembly of the water buffalo genome generated within the Consortium. The raw reads of each sample were aligned with the reference genome using TopHat and the Cufflinks software to reconstruct full-length transcript sequences and isoforms. A total of 170855 putative transcripts were generated by the reference-assisted assembly across all the samples with a mean transcript length of 3800 nucleotides. These putative transcripts were processed using ORF prediction software to identify potential coding regions and predict amino acid sequences. The protein sequences of each putative transcript were then annotated using a pipeline to identify potential homologs present within databases such as UniProt or PFAM. The reference set of transcripts generated from this information will be used to annotate the Water Buffalo Genome.