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The Genetic Origin of Short Tail in Endangered Korean Dog, DongGyeongi

Yoo, DongAhn ; Kim, Kwondo ; Kim, Hyaekang ; [et al.]

Springer Science and Business Media LLC ; 2017

In: Scientific Reports Vol. 7, No. 1 ( 2017-08-30)

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In: Scientific Reports, Springer Science and Business Media LLC, Vol. 7, No. 1 ( 2017-08-30)

Abstract: The tail of many animal species is responsible for various physiological functions. The functional importance of tail may have brought tail-loss to attention in many evolutionary and developmental studies. To provide a better explanation for the loss of tail, the current study aims to identify the evolutionary history and putative causal variants for the short tail in DongGyeongi (DG), an endangered dog breed, which is also the only dog in Korea that possesses a short tail. Whole genome sequencing was conducted on 22 samples of DG, followed by an investigation of population stratification with 10 other dog breeds. The genotypes, selective sweep and demography of DG were also investigated. As a result, we discovered the unique genetic structure of DG and suggested two possible ways in which the short tail phenotype developed. Moreover, this study suggested that selective sweep genes, ANKRD11 and ACVR2B may contribute to the reduction in tail length, and non-synonymous variant in the coding sequence of T gene and the CpG island variant of SFRP2 gene are the candidate causal variants for the tail-loss.

Type of Medium: Online Resource

ISSN: 2045-2322

URL: Article

DOI: 10.1038/s41598-017-10106-6

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2017

detail.hit.zdb_id: 2615211-3

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Inference of Admixture Origins in Indigenous African Cattle

Kim, Kwondo ; Kim, Donghee ; Hanotte, Olivier ; [et al.]

Oxford University Press (OUP) ; 2023

In: Molecular Biology and Evolution Vol. 40, No. 12 ( 2023-12-01)

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In: Molecular Biology and Evolution, Oxford University Press (OUP), Vol. 40, No. 12 ( 2023-12-01)

Abstract: Present-day African cattle retain a unique genetic profile composed of a mixture of the Bos taurus and Bos indicus populations introduced into the continent at different time periods. However, details of the admixture history and the exact origins of the source populations remain obscure. Here, we infer the source of admixture in the earliest domestic cattle in Africa, African taurine. We detect a significant contribution (up to ∼20%) from a basal taurine lineage, which might represent the now-extinct African aurochs. In addition, we show that the indicine ancestry of African cattle, although most closely related to so-far sampled North Indian indicine breeds, has a small amount of additional genetic affinity to Southeast Asian indicine breeds. Our findings support the hypothesis of aurochs introgression into African taurine and generate a novel hypothesis that the origin of indicine ancestry in Africa might be different indicine populations than the ones found in North India today.

Type of Medium: Online Resource

ISSN: 0737-4038 , 1537-1719

URL: Article

DOI: 10.1093/molbev/msad257

Language: English

Publisher: Oxford University Press (OUP)

Publication Date: 2023

detail.hit.zdb_id: 2024221-9

SSG: 12

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Complete genome of Vibrio parahaemolyticus FORC014 isolated from the toothfish

Ahn, Sojin ; Chung, Han Young ; Lim, Sooyeon ; [et al.]

Springer Science and Business Media LLC ; 2016

In: Gut Pathogens Vol. 8, No. 1 ( 2016-12)

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In: Gut Pathogens, Springer Science and Business Media LLC, Vol. 8, No. 1 ( 2016-12)

Type of Medium: Online Resource

ISSN: 1757-4749

URL: Article

DOI: 10.1186/s13099-016-0134-0

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2016

detail.hit.zdb_id: 2478277-4

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Genome sequence of pacific abalone (Haliotis discus hannai): the first draft genome in family Haliotidae

Nam, Bo-Hye ; Kwak, Woori ; Kim, Young-Ok ; [et al.]

Oxford University Press (OUP) ; 2017

In: GigaScience Vol. 6, No. 5 ( 2017-05-01)

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In: GigaScience, Oxford University Press (OUP), Vol. 6, No. 5 ( 2017-05-01)

Type of Medium: Online Resource

ISSN: 2047-217X

URL: Article

DOI: 10.1093/gigascience/gix014

Language: English

Publisher: Oxford University Press (OUP)

Publication Date: 2017

detail.hit.zdb_id: 2708999-X

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Genetic and phenotypic characterization of the novel mouse substrain C57BL/6N Korl with increased body weight

Choi, Kyung-Min ; Jung, Jaehoon ; Cho, Young Min ; [et al.]

Springer Science and Business Media LLC ; 2017

In: Scientific Reports Vol. 7, No. 1 ( 2017-10-27)

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In: Scientific Reports, Springer Science and Business Media LLC, Vol. 7, No. 1 ( 2017-10-27)

Abstract: In inbred mouse lines, there is generally little genetic difference between individuals. This small genetic variability facilitates carrying out research on minute changes of various traits and the gene pool. Also, characterizing the diversity and detecting selective genetic and phenotypic signatures are crucial to understanding the genomic basis of a population and to identify specific patterns of evolutionary change. In this study, we investigated the underlying genetic profiles of a newly developed mouse strain, C57BL/6NKorl (Korl), established through sibling mating over 30 generations. To analyse the distinctive genomic features of Korl mice, we used whole-genome sequencing from six samples, which were compared to those of other C57BL/6N-based mouse strains. Korl strain-specific polymorphisms were identified and signatures of a selective sweep were detected. In particular, the candidate genes related to the increased body weight of the Korl strain were identified. Establishment of the genetic profile of Korl mice can provide insight into the inbreeding-induced changes to the gene pool, and help to establish this strain as a useful model for practical and targeted research purposes.

Type of Medium: Online Resource

ISSN: 2045-2322

URL: Article

DOI: 10.1038/s41598-017-14196-0

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2017

detail.hit.zdb_id: 2615211-3

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Artificial selection increased body weight but induced increase of runs of homozygosity in Hanwoo cattle

Kim, Kwondo ; Jung, Jaehoon ; Caetano-Anollés, Kelsey ; [et al.]

Public Library of Science (PLoS) ; 2018

In: PLOS ONE Vol. 13, No. 3 ( 2018-3-21), p. e0193701-

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In: PLOS ONE, Public Library of Science (PLoS), Vol. 13, No. 3 ( 2018-3-21), p. e0193701-

Type of Medium: Online Resource

ISSN: 1932-6203

URL: Article

DOI: 10.1371/journal.pone.0193701

DOI: 10.1371/journal.pone.0193701.g001

DOI: 10.1371/journal.pone.0193701.g002

DOI: 10.1371/journal.pone.0193701.g003

DOI: 10.1371/journal.pone.0193701.t001

DOI: 10.1371/journal.pone.0193701.t002

DOI: 10.1371/journal.pone.0193701.s001

DOI: 10.1371/journal.pone.0193701.s002

DOI: 10.1371/journal.pone.0193701.s003

DOI: 10.1371/journal.pone.0193701.s004

DOI: 10.1371/journal.pone.0193701.s005

DOI: 10.1371/journal.pone.0193701.s006

DOI: 10.1371/journal.pone.0193701.s007

DOI: 10.1371/journal.pone.0193701.s008

Language: English

Publisher: Public Library of Science (PLoS)

Publication Date: 2018

detail.hit.zdb_id: 2267670-3

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Comparative genomic analysis reveals genetic features related to the virulence of Bacillus cereus FORC_013

Koo, Hyun-Jin ; Ahn, Sojin ; Chung, Han Young ; [et al.]

Springer Science and Business Media LLC ; 2017

In: Gut Pathogens Vol. 9, No. 1 ( 2017-12)

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In: Gut Pathogens, Springer Science and Business Media LLC, Vol. 9, No. 1 ( 2017-12)

Type of Medium: Online Resource

ISSN: 1757-4749

URL: Article

DOI: 10.1186/s13099-017-0175-z

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2017

detail.hit.zdb_id: 2478277-4

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Deciphering the evolutionary signatures of pinnipeds using novel genome sequences: The first genomes of Phoca largha, Callorhinus ursinus, and Eumetopias jubatus

Park, Jung Youn ; Kim, Kwondo ; Sohn, Hawsun ; [et al.]

Springer Science and Business Media LLC ; 2018

In: Scientific Reports Vol. 8, No. 1 ( 2018-11-15)

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In: Scientific Reports, Springer Science and Business Media LLC, Vol. 8, No. 1 ( 2018-11-15)

Abstract: The pinnipeds, which comprise seals, sea lions, and walruses, are a remarkable group of marine animals with unique adaptations to semi-aquatic life. However, their genomes are poorly characterized. In this study, we sequenced and characterized the genomes of three pinnipeds ( Phoca largha , Callorhinus ursinus , and Eumetopias jubatus ), focusing on site-wise sequence changes. We detected rapidly evolving genes in pinniped lineages and substitutions unique to pinnipeds associated with amphibious sound perception. Phenotypic convergence-related sequence convergences are not common in marine mammals. For example, FASN , KCNA5 , and IL17RA contain substitutions specific to pinnipeds, yet are potential candidates of phenotypic convergence (blubber, response to hypoxia, and immunity to pathogens) in all marine mammals. The outcomes of this study will provide insight into targets for future studies of convergent evolution or gene function.

Type of Medium: Online Resource

ISSN: 2045-2322

URL: Article

DOI: 10.1038/s41598-018-34758-0

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2018

detail.hit.zdb_id: 2615211-3

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Cattle genome-wide analysis reveals genetic signatures in trypanotolerant N’Dama

Kim, Soo-Jin ; Ka, Sojeong ; Ha, Jung-Woo ; [et al.]

Springer Science and Business Media LLC ; 2017

In: BMC Genomics Vol. 18, No. 1 ( 2017-12)

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In: BMC Genomics, Springer Science and Business Media LLC, Vol. 18, No. 1 ( 2017-12)

Type of Medium: Online Resource

ISSN: 1471-2164

URL: Article

DOI: 10.1186/s12864-017-3742-2

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2017

detail.hit.zdb_id: 2041499-7

SSG: 12

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Application of LogitBoost Classifier for Traceability Using SNP Chip Data

Kim, Kwondo ; Seo, Minseok ; Kang, Hyunsung ; [et al.]

Public Library of Science (PLoS) ; 2015

In: PLOS ONE Vol. 10, No. 10 ( 2015-10-5), p. e0139685-

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In: PLOS ONE, Public Library of Science (PLoS), Vol. 10, No. 10 ( 2015-10-5), p. e0139685-

Type of Medium: Online Resource

ISSN: 1932-6203

URL: Article

DOI: 10.1371/journal.pone.0139685

DOI: 10.1371/journal.pone.0139685.g001

DOI: 10.1371/journal.pone.0139685.g002

DOI: 10.1371/journal.pone.0139685.g003

DOI: 10.1371/journal.pone.0139685.g004

DOI: 10.1371/journal.pone.0139685.g005

DOI: 10.1371/journal.pone.0139685.t001

DOI: 10.1371/journal.pone.0139685.t002

DOI: 10.1371/journal.pone.0139685.s001

DOI: 10.1371/journal.pone.0139685.s002

DOI: 10.1371/journal.pone.0139685.s003

DOI: 10.1371/journal.pone.0139685.s004

DOI: 10.1371/journal.pone.0139685.s005

DOI: 10.1371/journal.pone.0139685.s006

DOI: 10.1371/journal.pone.0139685.s007

Language: English

Publisher: Public Library of Science (PLoS)

Publication Date: 2015

detail.hit.zdb_id: 2267670-3

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