Dataset Information

Genome assembly and transcriptome resource for river buffalo, Bubalus bubalis (2n = 50).

ABSTRACT: Water buffalo is a globally important species for agriculture and local economies. A de novo assembled, well-annotated reference sequence for the water buffalo is an important prerequisite for studying the biology of this species, and is necessary to manage genetic diversity and to use modern breeding and genomic selection techniques. However, no such genome assembly has been previously reported. There are 2 species of domestic water buffalo, the river (2 n = 50) and the swamp (2 n = 48) buffalo. Here we describe a draft quality reference sequence for the river buffalo created from Illumina GA and Roche 454 short read sequences using the MaSuRCA assembler. The assembled sequence is 2.83 Gb, consisting of 366 983 scaffolds with a scaffold N50 of 1.41 Mb and contig N50 of 21 398 bp. Annotation of the genome was supported by transcriptome data from 30 tissues and identified 21 711 predicted protein coding genes. Searches for complete mammalian BUSCO gene groups found 98.6% of curated single copy orthologs present among predicted genes, which suggests a high level of completeness of the genome. The annotated sequence is available from NCBI at accession GCA_000471725.1.

SUBMITTER: Williams JL

PROVIDER: S-EPMC5737279 | biostudies-literature | 2017 Oct

REPOSITORIES: biostudies-literature

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Genome assembly and transcriptome resource for river buffalo, Bubalus bubalis (2n = 50).

Williams John L JL Iamartino Daniela D Pruitt Kim D KD Sonstegard Tad T Smith Timothy P L TPL Low Wai Yee WY Biagini Tommaso T Bomba Lorenzo L Capomaccio Stefano S Castiglioni Bianca B Coletta Angelo A Corrado Federica F Ferré Fabrizio F Iannuzzi Leopoldo L Lawley Cynthia C Macciotta Nicolò N McClure Matthew M Mancini Giordano G Matassino Donato D Mazza Raffaele R Milanesi Marco M Moioli Bianca B Morandi Nicola N Ramunno Luigi L Peretti Vincenzo V Pilla Fabio F Ramelli Paola P Schroeder Steven S Strozzi Francesco F Thibaud-Nissen Francoise F Zicarelli Luigi L Ajmone-Marsan Paolo P Valentini Alessio A Chillemi Giovanni G Zimin Aleksey A

GigaScience 20171001 10

Water buffalo is a globally important species for agriculture and local economies. A de novo assembled, well-annotated reference sequence for the water buffalo is an important prerequisite for studying the biology of this species, and is necessary to manage genetic diversity and to use modern breeding and genomic selection techniques. However, no such genome assembly has been previously reported. There are 2 species of domestic water buffalo, the river (2 n = 50) and the swamp (2 n = 48) buffalo ...[more]

PMID: 29048578

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Project description:BackgroundConsecutive homozygous fragments of a genome inherited by offspring from a common ancestor are known as runs of homozygosity (ROH). ROH can be used to calculate genomic inbreeding and to identify genomic regions that are potentially under historical selection pressure. The dataset of our study consisted of 254 Azeri (AZ) and 115 Khuzestani (KHZ) river buffalo genotyped for ~ 65,000 SNPs for the following two purposes: 1) to estimate and compare inbreeding calculated using ROH (FROH), excess of homozygosity (FHOM), correlation between uniting gametes (FUNI), and diagonal elements of the genomic relationship matrix (FGRM); 2) to identify frequently occurring ROH (i.e. ROH islands) for our selection signature and gene enrichment studies.ResultsIn this study, 9102 ROH were identified, with an average number of 21.2 ± 13.1 and 33.2 ± 15.9 segments per animal in AZ and KHZ breeds, respectively. On average in AZ, 4.35% (108.8 ± 120.3 Mb), and in KHZ, 5.96% (149.1 ± 107.7 Mb) of the genome was autozygous. The estimated inbreeding values based on FHOM, FUNI and FGRM were higher in AZ than they were in KHZ, which was in contrast to the FROH estimates. We identified 11 ROH islands (four in AZ and seven in KHZ). In the KHZ breed, the genes located in ROH islands were enriched for multiple Gene Ontology (GO) terms (P ≤ 0.05). The genes located in ROH islands were associated with diverse biological functions and traits such as body size and muscle development (BMP2), immune response (CYP27B1), milk production and components (MARS, ADRA1A, and KCTD16), coat colour and pigmentation (PMEL and MYO1A), reproductive traits (INHBC, INHBE, STAT6 and PCNA), and bone development (SUOX).ConclusionThe calculated FROH was in line with expected higher inbreeding in KHZ than in AZ because of the smaller effective population size of KHZ. Thus, we find that FROH can be used as a robust estimate of genomic inbreeding. Further, the majority of ROH peaks were overlapped with or in close proximity to the previously reported genomic regions with signatures of selection. This tells us that it is likely that the genes in the ROH islands have been subject to artificial or natural selection.

Dataset Information

Genome assembly and transcriptome resource for river buffalo, Bubalus bubalis (2n = 50).

Publications

Genome assembly and transcriptome resource for river buffalo, Bubalus bubalis (2n = 50).

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