RT Journal Article SR Electronic T1 First near complete haplotype phased genome assembly of River buffalo (Bubalus bubalis) JF bioRxiv FD Cold Spring Harbor Laboratory SP 618785 DO 10.1101/618785 A1 Sudhakar Ananthasayanam A1 Harish Kothandaraman A1 Nilesh Nayee A1 Sujit Saha A1 Dushyant Singh Baghel A1 Kishore Gopalakrishnan A1 Sathish Peddamma A1 Ram Bahadur Singh A1 Michael Schatz YR 2019 UL http://biorxiv.org/content/early/2019/04/26/618785.abstract AB This study reports the first haplotype phased reference quality genome assembly of ‘Murrah’ an Indian breed of river buffalo. A mother-father-progeny trio was used for sequencing so that the individual haplotypes could be assembled in the progeny. Parental DNA samples were sequenced on the Illumina platform to generate a total of 274 Gb paired-end data. The progeny DNA sample was sequenced using PacBio long reads and 10x Genomics linked reads at 166x coverage along with 802Gb of optical mapping data. Trio binning based FALCON assembly of each haplotype was scaffolded with 10x Genomics reads and superscaffolded with BioNano Maps to build reference quality assembly of sire and dam haplotypes of 2.63Gb and 2.64Gb with just 59 and 64 scaffolds and N50 of 81.98Mb and 83.23Mb, respectively. BUSCO single copy core gene set coverage was > 91.25%, and gVolante-CEGMA completeness was >96.14% for both haplotypes. Finally, RaGOO was used to order and build the chromosomal level assembly with 25 scaffolds and N50 of 117.48 Mb (sire haplotype) and 118.51 Mb (dam haplotype). The improved haplotype phased genome assembly of river buffalo may provide valuable resources to discover molecular mechanisms related to milk production and reproduction traits.