Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Record number 562716
Title Pig Genome Evolution: De Novo Assembly and Annotation of the Genome of the Visayan Warty Pig (Sus cebifrons)
Author(s) Liu, Langqing; Madsen, Ole; Huang, Q.; Derks, Martijn; Megens, Hendrik-Jan; Crooijmans, Richard; Groenen, Martien
Event Plant and Animal Genome XXVIII, San Diego, 2020-01-11/2020-01-15
Department(s) Animal Breeding and Genomics
WIAS
Aquaculture and Fisheries
Publication type Unpublished lecture
Publication year 2020
Abstract The Visayan warty pig (Sus cebifrons) is a critically endangered species in the pig genus (Sus). We generated a de novo genome assembly of Visayan warty pig using linked-read sequencing (10x Genomics) and Hi-C-based chromatin interaction maps (Dovetail Genomics). The resulting chromosome level assembly consists of 17 chromosomes and 1,568 unplaced scaffolds. The scaffold N50 length is 141,782,568 bp while the contig N50 length is 159,621 bp. BUSCO analysis suggests the assembly is highly complete, with 95.7% of BUSCOs complete. The alignment of the Sus cebifrons and the Sus scrofa (Sscrofa11.1) assemblies reveals a high degree of collinearity. We reveal chromosome rearrangements during Suidae evolution, involving chromosome fusion and fission events involving Sus scofa chromosomes 13, 14 ,16 and 18. Annotation was done using Braker2 and included RNA-seq data from 6 different tissues. Identification of repetitive sequences was done using Repeatmasker and Repeatmodeler. In total, 38,300 protein-coding genes and 788.86 Mb of repetitive sequences were identified. This highly contiguous assembly provides a comparative framework to common pigs (S. scrofa), extending our understanding of the genome evolution. A comparison of the HiC data of S. cebifrons and S. scrofa revealed a high degree of conservation of the 3D chromatin structure in these two species that diverged approximately 4 million years ago.
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