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Doctoral thesis, 2017

Applying massive parallel sequencing technologies to unravel the genomic complexity in domestic species

Viluma, Agnese;


Massive parallel sequencing technologies have made a remarkable contribution in understanding the genomic complexity in human and other mammalian species. This thesis includes four studies illustrating the technology change from short-read to long-read massive parallel sequencing and the corresponding layers of genomic complexity resolved in dog and horse. In the first study, the Ion Proton sequencing platform was evaluated for whole-genome re-sequencing of four dog genomes. On average, 80 % of the genome and 77 % of the exome had at least 4-fold coverage. The obtained genotypes showed 90 % concordance with those using the CanineHD BeadChip. Next, whole-genome re-sequencing of a canine family trio was used as a proof-of-concept to map an autosomal recessive disorder termed hereditary footpad hyperkeratosis in the Kromfohrländer breed. This resulted in the identification and association of a single nucleotide variant in the FAM83G gene. In the third study, we generated the first long-read assembly of the horse MHC class II region (1.2 Mb) by assembling eight bacterial artificial chromosome clones sequenced with single molecule, real-time (SMRT) sequencing technology from Pacific Biosciences (PacBio). Detailed annotation of this assembly revealed 23 functional genes and 12 pseudogenes. In comparison to other mammals, the horse MHC showed an increased number of MHC class II genes in different relative positions and with different directionality. In the fourth study, “sequence self-similarity” of the equine MHC class II region was investigated to identify paralogous segments and to reconstruct the evolutionary history of duplication events. The results indicated a major expansion of class II loci 55-70 million years ago, coinciding with mammalian radiation. We showed that the high genomic structural diversity and plasticity of the mammalian MHC region may be a result of recurring segmental duplication events mediated either by unequal crossing-over between misaligned genomic regions or, possibly, by alternative transposition of long interspersed nuclear elements.


whole genome re-sequencing, trio sequencing, dog, hereditary footpad hyperkeratosis, horse, MHC, annotation, gene families, unequal crossing-over, transposable elements

Published in

Acta Universitatis Agriculturae Sueciae

2017, number: 2017:93
ISBN: 978-91-7760-076-3, eISBN: 978-91-7760-077-0
Publisher: Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences

Authors' information

Viluma, Agnese
Swedish University of Agricultural Sciences, Department of Animal Breeding and Genetics

UKÄ Subject classification

Animal and Dairy Science
Genetics and Breeding
Bioinformatics (Computational Biology)

URI (permanent link to this page)