Molecular detection and genomic characterization of Torque teno sus virus 1 and 2 from domestic pigs in central China

SummaryThe evolution and domestication of pigs is a complex and ongoing process. Despite its rich biodiversity and proximity to the geographical origins of Sus scrofa domesticus, the place of Indian pigs in the global phylogeny is unclear. Using microarray-derived (porcine 60K SNP chip) genotypes of 11 Ghurrah pigs from North-Western India and a public dataset comprising 2113 pigs of 146 breeds, we determined the genomic ancestry of Ghurrah pigs and compared their genetic constitution to European and Asian breeds to ascertain signatures of divergent selection. Results showed that Ghurrah pigs contain genes of Asian and European ancestry with signs of inter-species introgression. Using Admixture LD – decay statistics, the European admixture event was dated to the recent past, coinciding with the start of cross-breeding efforts in India. The complex Asian ancestry pattern of the breed resembled that of wild boars of South – Central China and Thailand, possibly suggesting introgression from an Indian wild boar relative. FST and XP – EHH comparisons with Asian breeds highlighted divergent selection in genomic regions associated with odontogenesis and skeletal muscle development. Comparisons with European commercial breeds revealed that genomic regions governing olfaction and response to sensory stimulation were under selection in Ghurrah pigs. QTL for meat and carcass traits also showed divergent selection between European breeds and Ghurrah pigs. Our results present the first genomic characterization of an Indian pig breed using dense microarray-derived genotypes and highlight the importance of further genomic characterization of Indian domestic and wild pigs.

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A comparative genomics and immunoinformatics approach to identify epitope-based peptide vaccine candidates against bovine hemoplasmosis

10.1101/2020.09.21.305987 ◽

2020 ◽

Author(s):

Rosa Estela Quiroz-Castañeda ◽

Hugo Aguilar-Díaz ◽

Diana Laura Flores-García ◽

Fernando Martínez-Ocampo ◽

Itzel Amaro-Estrada

Keyword(s):

Comparative Genomics ◽

Molecular Detection ◽

Peptide Vaccine ◽

Detection Methods ◽

Cattle Production ◽

Vaccine Candidates ◽

Mycoplasma Wenyonii ◽

Alignment Coverage ◽

Genomic Characterization

AbstractMycoplasma wenyonii and ‘Candidatus Mycoplasma haemobos’ have been described as major hemoplasmas that infect cattle worldwide. Currently, three bovine hemoplasma genomes are known. The aim of this work was to know the main genomic characteristics and the evolutionary relationships between hemoplasmas, as well as to provide a list of epitopes identified by immunoinformatics that could be used as vaccine candidates against bovine hemoplasmosis. So far, there is not a vaccine to prevent this disease that impact economically in cattle production around the world.In this work, we used comparative genomics to analyze the genomes of the hemoplasmas so far reported. As a result, we confirm that ‘Ca. M haemobos’ INIFAP01 is a divergent species from M. wenyonii INIFAP02 and M. wenyonii Massachusetts. Although both strains of M. wenyonii have genomes with similar characteristics (length, G+C content, tRNAs and position of rRNAs) they have different structures (alignment coverage and identity of 51.58 and 79.37%, respectively).The correct genomic characterization of bovine hemoplasmas, never studied before, will allow to develop better molecular detection methods, to understand the possible pathogenic mechanisms of these bacteria and to identify epitopes sequences that could be used in the vaccine design.

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Morphological and Mitochondrial Genomic Characterization of Eyeworms (Thelazia callipaeda) from Clinical Cases in Central China

Frontiers in Microbiology ◽

10.3389/fmicb.2017.01335 ◽

2017 ◽

Vol 8 ◽

Cited By ~ 4

Author(s):

Xi Zhang ◽

Ya L. Shi ◽

Zhong Q. Wang ◽

Jiang Y. Duan ◽

Peng Jiang ◽

...

Keyword(s):

Central China ◽

Thelazia Callipaeda ◽

Genomic Characterization ◽

Clinical Cases

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Molecular detection and genomic characterization of porcine circovirus 3 in pigs from Northeast China

BMC Veterinary Research ◽

10.1186/s12917-018-1634-6 ◽

2018 ◽

Vol 14 (1) ◽

Cited By ~ 17

Author(s):

Zhuo Ha ◽

Chang-zhan Xie ◽

Jin-feng Li ◽

Shu-bo Wen ◽

Ke-long Zhang ◽

...

Keyword(s):

Northeast China ◽

Molecular Detection ◽

Porcine Circovirus ◽

Genomic Characterization ◽

Porcine Circovirus 3

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Molecular detection and characterization of Porcine Kobuvirus in domestic pigs and wild boars in Serbia

Research in Veterinary Science ◽

10.1016/j.rvsc.2020.07.028 ◽

2020 ◽

Vol 132 ◽

pp. 404-406

Author(s):

Vesna Milićević ◽

Branislav Kureljušić ◽

Jelena Maksimović-Zorić ◽

Božidar Savić ◽

Ljiljana Spalević ◽

...

Keyword(s):

Molecular Detection ◽

Porcine Kobuvirus ◽

Wild Boars ◽

Domestic Pigs

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Molecular Detection of Torque Teno Sus Virus and Coinfection with African Swine Fever Virus in Blood Samples of Pigs from Some Slaughterhouses in Nigeria

Advances in Virology ◽

10.1155/2016/6341015 ◽

2016 ◽

Vol 2016 ◽

pp. 1-6 ◽

Cited By ~ 3

Author(s):

Pam D. Luka ◽

Joseph Erume ◽

Bitrus Yakubu ◽

Olajide A. Owolodun ◽

David Shamaki ◽

...

Keyword(s):

Molecular Detection ◽

African Swine Fever Virus ◽

African Swine Fever ◽

Comparative Sequence Analysis ◽

Fever Virus ◽

Nucleic Acid Detection ◽

Viral Nucleic Acid ◽

Blood Samples ◽

Domestic Pigs ◽

Torque Teno Sus Virus

Torque teno sus virus 1 (TTSuV1a/TTSuV1b) infection is present in pig herds worldwide. This study investigated the prevalence of TTSuV1a/TTSuV1b infections in domestic pigs from some slaughterhouses in Nigeria as well as coinfection with African swine fever virus (ASFV) and described the phylogeny in relation to global strains. One hundred and eighty-one (181) blood samples from four slaughterhouses were used for the study and viral nucleic acid detection was carried out by PCR. Comparative sequence analysis was carried out to infer phylogeny. The overall prevalence of TTSuV1a/b was 17.7%. Prevalence of individual genotypes was 10.5% and 7.2% for TTSuV1a and TTSuV1b, respectively. Coinfection of ASFV/TTSuV1a/b was 7.7% while that of TTSuV1a and TTSuV1b was 1.7%. ASFV alone was detected in 11.91% of the total samples. The Nigerian TTSuV1a and TTSuV1b shared a sequence identity of 91–100% and 95–100%, respectively, among each other. The ASFV sequences were 100% identical to members of genotype 1. This is the first report on the presence of TTSuV1a/b in domestic pigs in Nigeria and coinfection with ASFV. Although the prevalence of TTSuV1a/b in Nigeria was low, we recommend further studies to establish the trend and possible role in the pathogenesis of ASFV.

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