Despite dramatic reduction in sequencing costs with the advent of next generation sequencing technologies, obtaining a complete mammalian genome sequence at sufficient depth is still costly. An alternative is partial sequencing. Here, we have sequenced a reduced representation library of an Iberian sow from the Guadyerbas strain, a highly inbred strain that has been used in numerous QTL studies because of its extreme phenotypic characteristics. Using the Illumina Genome Analyzer II (San Diego, CA, USA), we resequenced ∼ 1\% of the genome with average 4 × depth, identifying 68,778 polymorphisms. Of these, 55,457 were putative fixed differences with respect to the assembly, based on the genome of a Duroc pig, and 13,321 were heterozygous positions within Guadyerbas. Despite being highly inbred, the estimate of heterozygosity within Guadyerbas was ∼ 0.78 kb(-1) in autosomes, after correcting for low depth. Nucleotide variability was consistently higher at the telomeric regions than on the rest of the chromosome, likely a result of increased recombination rates. Further, variability was 50\% lower in the X-chromosome than in autosomes, which may be explained by a recent bottleneck or by selection. We divided the whole genome in 500 kb windows and we analyzed overrepresented gene ontology terms in regions of low and high variability. Multi organism process, pigmentation and cell killing were overrepresented in high variability regions and metabolic process ontology, within low variability regions. Further, a genome wide Hudson-Kreitman-Aguadé test was carried out per window; overall, variability was in agreement with neutral expectations.
@article{esteve-codina_partial_2011,
Author = {Esteve-Codina, A. and Kofler, R. and Himmelbauer, H.
and Ferretti, L. and Vivancos, A. P. and Groenen, M. a.
M. and Folch, J. M. and Rodríguez, M. C. and
Pérez-Enciso, M.},
Title = {Partial short-read sequencing of a highly inbred
{Iberian} pig and genomics inference thereof},
Journal = {Heredity},
Volume = {107},
Number = {3},
Pages = {256--264},
abstract = {Despite dramatic reduction in sequencing costs with
the advent of next generation sequencing technologies,
obtaining a complete mammalian genome sequence at
sufficient depth is still costly. An alternative is
partial sequencing. Here, we have sequenced a reduced
representation library of an Iberian sow from the
Guadyerbas strain, a highly inbred strain that has been
used in numerous QTL studies because of its extreme
phenotypic characteristics. Using the Illumina Genome
Analyzer II (San Diego, CA, USA), we resequenced ∼
1\% of the genome with average 4 × depth, identifying
68,778 polymorphisms. Of these, 55,457 were putative
fixed differences with respect to the assembly, based
on the genome of a Duroc pig, and 13,321 were
heterozygous positions within Guadyerbas. Despite being
highly inbred, the estimate of heterozygosity within
Guadyerbas was ∼ 0.78 kb(-1) in autosomes, after
correcting for low depth. Nucleotide variability was
consistently higher at the telomeric regions than on
the rest of the chromosome, likely a result of
increased recombination rates. Further, variability was
50\% lower in the X-chromosome than in autosomes, which
may be explained by a recent bottleneck or by
selection. We divided the whole genome in 500 kb
windows and we analyzed overrepresented gene ontology
terms in regions of low and high variability. Multi
organism process, pigmentation and cell killing were
overrepresented in high variability regions and
metabolic process ontology, within low variability
regions. Further, a genome wide Hudson-Kreitman-Aguadé
test was carried out per window; overall, variability
was in agreement with neutral expectations.},
doi = {10.1038/hdy.2011.13},
issn = {1365-2540},
language = {eng},
month = sep,
pmcid = {PMC3183945},
pmid = {21407255},
year = 2011
}
