The complete swine olfactory subgenome: expansion of the olfactory gene repertoire in the pig genome

Nguyen, Dinh-Truong; Lee, Kyooyeol; Choi, Hojun; Choi, Mi Hyun; Le, Minh-Tri; Song, Ning; Kim, Jin‐Hoi; Seo, Han Geuk; Oh, Jae-Wook; Lee, Kyungtae; Kim, Tae-Hun; Park, Chankyu

doi:10.1186/1471-2164-13-584

Cited by 77 publications

(91 citation statements)

References 47 publications

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“…The olfactory receptor gene family, one of the largest gene families in the porcine genome [25,33], is over-represented with 353 out of 545 genes overlapping with CNVRs (Additional file 5: Table S3D). Genes involved in immune response, for instance IFN (Alpha-8, 11, 14; Delta-2), IFNW1 , IGK ( V1D - 43 , V2 - 28 , V8 - 61 ), IL1B and PG3I , were often observed as variable in CN between individuals.…”

Section: Resultsmentioning

confidence: 99%

Evolutionary dynamics of copy number variation in pig genomes in the context of adaptation and domestication

et al. 2013

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Background: Copy number variable regions (CNVRs) can result in drastic phenotypic differences and may therefore be subject to selection during domestication. Studying copy number variation in relation to domestication is highly relevant in pigs because of their very rich natural and domestication history that resulted in many different phenotypes. To investigate the evolutionary dynamic of CNVRs, we applied read depth method on next generation sequence data from 16 individuals, comprising wild boars and domestic pigs from Europe and Asia. Results: We identified 3,118 CNVRs with an average size of 13 kilobases comprising a total of 39.2 megabases of the pig genome and 545 overlapping genes. Functional analyses revealed that CNVRs are enriched with genes related to sensory perception, neurological process and response to stimulus, suggesting their contribution to adaptation in the wild and behavioral changes during domestication. Variations of copy number (CN) of antimicrobial related genes suggest an ongoing process of evolution of these genes to combat food-borne pathogens. Likewise, some genes related to the omnivorous lifestyle of pigs, like genes involved in detoxification, were observed to be CN variable. A small portion of CNVRs was unique to domestic pigs and may have been selected during domestication. The majority of CNVRs, however, is shared between wild and domesticated individuals, indicating that domestication had minor effect on the overall diversity of CNVRs. Also, the excess of CNVRs in non-genic regions implies that a major part of these variations is likely to be (nearly) neutral. Comparison between different populations showed that larger populations have more CNVRs, highlighting that CNVRs are, like other genetic variation such as SNPs and microsatellites, reflecting demographic history rather than phenotypic diversity.

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Section: Resultsmentioning

confidence: 99%

Evolutionary dynamics of copy number variation in pig genomes in the context of adaptation and domestication

et al. 2013

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“…The olfactory receptor gene superfamily is the largest in vertebrate genomes, which function in the reception of innumerable odour molecules in the environment. Previous studies have showed that CNVs are highly prevalent among human and other vertebrate OR genes [40], [41], [42]. Two qPCR assays with primers located in two defensins genes ( BD114 and DEFB110 ) were used for CNVR#50 validation.…”

Section: Discussionmentioning

confidence: 99%

Identification of Genome-Wide Copy Number Variations among Diverse Pig Breeds Using SNP Genotyping Arrays

Wang

Jiang

et al. 2013

PLoS ONE

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Copy number variations (CNVs) are important forms of genetic variation complementary to SNPs, and can be considered as promising markers for some phenotypic and economically important traits or diseases susceptibility in domestic animals. In the present study, we performed a genome-wide CNV identification in 14 individuals selected from diverse populations, including six types of Chinese indigenous breeds, one Asian wild boar population, as well as three modern commercial foreign breeds. We identified 63 CNVRs in total, which covered 9.98 Mb of polymorphic sequence and corresponded to 0.36% of the genome sequence. The length of these CNVRs ranged from 3.20 to 827.21 kb, with an average of 158.37 kb and a median of 97.85 kb. Functional annotation revealed these identified CNVR have important molecular function, and may play an important role in exploring the genetic basis of phenotypic variability and disease susceptibility among pigs. Additionally, to confirm these potential CNVRs, we performed qPCR for 12 randomly selected CNVRs and 8 of them (66.67%) were confirmed successfully. CNVs detected in diverse populations herein are essential complementary to the CNV map in the pig genome, which provide an important resource for studies of genomic variation and the association between various economically important traits and CNVs.

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“…Twenty-two of these coding genes and five novel pseudogenes are in olfactory gene clusters. Pigs are known to have a large olfactory receptor repertoire (Nguyen et al 2012), and this adds to the reported collection. Supplemental Figure S4 shows the improved assembly and annotation around one of the olfactory region clusters on Xq.…”

Section: Comparative X Alignmentsmentioning

confidence: 96%

The pig X and Y Chromosomes: structure, sequence, and evolution

et al. 2015

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We have generated an improved assembly and gene annotation of the pig X Chromosome, and a first draft assembly of the pig Y Chromosome, by sequencing BAC and fosmid clones from Duroc animals and incorporating information from optical mapping and fiber-FISH. The X Chromosome carries 1033 annotated genes, 690 of which are protein coding. Gene order closely matches that found in primates (including humans) and carnivores (including cats and dogs), which is inferred to be ancestral. Nevertheless, several protein-coding genes present on the human X Chromosome were absent from the pig, and 38 pig-specific X-chromosomal genes were annotated, 22 of which were olfactory receptors. The pig Y-specific Chromosome sequence generated here comprises 30 megabases (Mb). A 15-Mb subset of this sequence was assembled, revealing two clusters of male-specific low copy number genes, separated by an ampliconic region including the HSFY gene family, which together make up most of the short arm. Both clusters contain palindromes with high sequence identity, presumably maintained by gene conversion. Many of the ancestral X-related genes previously reported in at least one mammalian Y Chromosome are represented either as active genes or partial sequences. This sequencing project has allowed us to identify genes-both single copy and amplified-on the pig Y Chromosome, to compare the pig X and Y Chromosomes for homologous sequences, and thereby to reveal mechanisms underlying pig X and Y Chromosome evolution.

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The complete swine olfactory subgenome: expansion of the olfactory gene repertoire in the pig genome

Cited by 77 publications

References 47 publications

Evolutionary dynamics of copy number variation in pig genomes in the context of adaptation and domestication

Evolutionary dynamics of copy number variation in pig genomes in the context of adaptation and domestication

Identification of Genome-Wide Copy Number Variations among Diverse Pig Breeds Using SNP Genotyping Arrays

The pig X and Y Chromosomes: structure, sequence, and evolution

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