The water buffalo (Bubalus bubalis) is important for small-holder producers in developing countries and an important source of products for specialized markets. Knowledge of the buffalo genome will help to unravel the evolutionary relationships among different breeds and will contribute to understanding the genetic control of phenotypic variation. Resulting genomic tools will help the genetic improvement of animals for milk and meat production. The International Buffalo Genome Project has three main phases: 1) the complete sequencing and assembly of the buffalo genome and its annotation; 2) SNP and variation detection in river and swamp buffalo genomes; 3) analysis of genetic variation among buffalo populations. The project has produced sequence for a female Mediterranean buffalo genome using Illumina GAII and Roche 454 high throughput sequencing. These sequences were assembled using the MaSuRCA assembler, obtaining a contig N50 of 21Kb and a scaffold N50 of 1.4Mb organized in 367K scaffolds, giving an estimated genome size of 2.7 Gbp. Eighty-six buffaloes from 8 breeds were sequenced to a depth between 5 and 12X by Illumina PE reads, yielding a total of 470X genome coverage. Four of these breeds (Mediterranean, Murrah, Jaffarabady and Nili Ravi) were analysed to yield a total of 22.2M SNPs. The within and across breeds allele frequencies for these SNPs were calculated and the minimum allele frequencies (MAF) were determined. These data were used to design an Axiom Buffalo Genotyping 90K array (Affymetrix). Preliminary comparative analyses of the buffalo genome assembly with the bovine sequence, highlights extensive conservation between genomes of cattle and buffalo, including a high degree of between species conservation of genomic and transcribed sequence. However, detailed analysis of the largest buffalo genome scaffolds suggests a complex history of genomic rearrangements since divergence. Finally, current estimates suggest that 13-18% of the buffalo genomic sequence is unique.
Sequencing of the Water Buffalo Genome: results and perspectives / Iamartino, D.; Williams, J. L.; Ramunno, Luigi; AJMONE MARSAN, P.; Valentini, A.; Moioli, B.; Chillemi, G.; Strozzi, F.; Ferré, F.; Biagini, T.; Mancini, G.; Pasquariello, R.; Cosenza, Gianfranco; Coletta, A.; Castiglioni, B.; Zicarelli, Luigi; Iannuzzi, Leopoldo; Macciotta, N.; Matassino, D.; Pilla, F.; D’Andrea, M.; Corrado, F.; Peretti, Vincenzo. - In: ITALIAN JOURNAL OF ANIMAL SCIENCE. - ISSN 1594-4077. - 12:(2013), pp. 21-21. (Intervento presentato al convegno 20th ASPA CONGRESS Animal Science and Production Association tenutosi a Bologna (Italy) nel 11-13 June 2013) [10.4081/ijas.2013.s1].
Sequencing of the Water Buffalo Genome: results and perspectives
RAMUNNO, LUIGI;COSENZA, GIANFRANCO;ZICARELLI, LUIGI;IANNUZZI, LEOPOLDO;PERETTI, VINCENZO
2013
Abstract
The water buffalo (Bubalus bubalis) is important for small-holder producers in developing countries and an important source of products for specialized markets. Knowledge of the buffalo genome will help to unravel the evolutionary relationships among different breeds and will contribute to understanding the genetic control of phenotypic variation. Resulting genomic tools will help the genetic improvement of animals for milk and meat production. The International Buffalo Genome Project has three main phases: 1) the complete sequencing and assembly of the buffalo genome and its annotation; 2) SNP and variation detection in river and swamp buffalo genomes; 3) analysis of genetic variation among buffalo populations. The project has produced sequence for a female Mediterranean buffalo genome using Illumina GAII and Roche 454 high throughput sequencing. These sequences were assembled using the MaSuRCA assembler, obtaining a contig N50 of 21Kb and a scaffold N50 of 1.4Mb organized in 367K scaffolds, giving an estimated genome size of 2.7 Gbp. Eighty-six buffaloes from 8 breeds were sequenced to a depth between 5 and 12X by Illumina PE reads, yielding a total of 470X genome coverage. Four of these breeds (Mediterranean, Murrah, Jaffarabady and Nili Ravi) were analysed to yield a total of 22.2M SNPs. The within and across breeds allele frequencies for these SNPs were calculated and the minimum allele frequencies (MAF) were determined. These data were used to design an Axiom Buffalo Genotyping 90K array (Affymetrix). Preliminary comparative analyses of the buffalo genome assembly with the bovine sequence, highlights extensive conservation between genomes of cattle and buffalo, including a high degree of between species conservation of genomic and transcribed sequence. However, detailed analysis of the largest buffalo genome scaffolds suggests a complex history of genomic rearrangements since divergence. Finally, current estimates suggest that 13-18% of the buffalo genomic sequence is unique.I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
