Status of the Buffalo Genome Project

The draft assembly of the buffalo genome sequence was deposited with NCBI in November 2013 (GCF_000471725.1). This assembly was created from 70X Illumina mate-paired sequence and 1.5X Roche 454 long paired end sequence assembled using the MaSuRCA genome assembler. This draft sequence is 2,836 Mbp fragmented into 366,983 contigs with N50 of 1,412,388.   Using the bovine genome as a guide 32,766 overlaps between contigs that were not identified by the assembler were identified with an average overlap of 2635bp.  Following the manual merging of overlapping contigs the probability of ordering of buffalo contigs is being examined using genotype data from over 1000 Mediterranean buffalo genotyped with the Affymetrix 90K SNP panel. Finally contigs are being assigned to buffalo chromosomes based on RH and cytogenetic mapping information.

The genome sequence was annotated by NCBI (Annotation Release 100, 14^th March 2014) which identified 21,711 coding genes compared with 23,103 genes annotated in the cattle genome.  RNAseq data from 30 different buffalo tissues which was used for the buffalo annotation was assembled into transcripts, generating about 160k transcripts of a length greater than 1000bp corresponding to about 45k predicted genes of which  23k had a unique target in the genome. Blasting this dataset against the ENSEMBL bovine cDNA dataset produced 57k alignments to 16k bovine genes.  These data are being compared with transcripts from other species to remove background noise and identify potential missing genes and contribute to an improve buffalo annotation.