Genome-wide SNP data unravel the ancestry and signatures of divergent selection in Ghurrah pigs of India

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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Genomic characterization of coxsackievirus type B3 strains associated with acute flaccid paralysis in south-western India

Journal of General Virology ◽

10.1099/jgv.0.000391 ◽

2016 ◽

Vol 97 (3) ◽

pp. 694-705 ◽

Cited By ~ 6

Author(s):

Rongala Laxmivandana ◽

Sarah S. Cherian ◽

Prasanna Yergolkar ◽

Shobha D. Chitambar

Keyword(s):

Acute Flaccid Paralysis ◽

Flaccid Paralysis ◽

Western India ◽

Genomic Characterization

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Genomic characterization of Vibrio parahaemolyticus from Pacific white shrimp and rearing water in Malaysia reveals novel sequence types and structural variation in genomic regions containing the Photorhabdus insect-related (Pir) toxin-like genes

FEMS Microbiology Letters ◽

10.1093/femsle/fnz211 ◽

2019 ◽

Vol 366 (17) ◽

Cited By ~ 2

Author(s):

Chrystine Zou Yi Yan ◽

Christopher M Austin ◽

Qasim Ayub ◽

Sadequr Rahman ◽

Han Ming Gan

Keyword(s):

Vibrio Parahaemolyticus ◽

Illumina Miseq ◽

Pacific White Shrimp ◽

White Shrimp ◽

Phylogenomic Analysis ◽

Genomic Characterization ◽

Genomic Resource ◽

Acute Hepatopancreatic Necrosis Disease ◽

Genomic Regions

ABSTRACT The Malaysian and global shrimp aquaculture production has been significantly impacted by acute hepatopancreatic necrosis disease (AHPND) typically caused by Vibrio parahaemolyticus harboring the pVA plasmid containing the pirAVp and pirBVp genes, which code for Photorhabdus insect-related (Pir) toxin. The limited genomic resource for V. parahaemolyticus strains from Malaysian aquaculture farms precludes an in-depth understanding of their diversity and evolutionary relationships. In this study, we isolated shrimp-associated and environmental (rearing water) V. parahaemolyticus from three aquaculture farms located in Northern and Central Malaysia followed by whole-genome sequencing of 40 randomly selected isolates on the Illumina MiSeq. Phylogenomic analysis and multilocus sequence typing (MLST) reveal distinct lineages of V. parahaemolyticus that harbor the pirABVp genes. The recovery of pVA plasmid backbone devoid of pirAVp or pirABVp in some V. parahaemolyticus isolates suggests that the toxin genes are prone to deletion. The new insight gained from phylogenomic analysis of Asian V. parahaemolyticus, in addition to the observed genomic instability of pVa plasmid, will have implications for improvements in aquaculture practices to diagnose, treat or limit the impacts of this disease.

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

Virus Genes ◽

10.1007/s11262-013-0897-z ◽

2013 ◽

Vol 46 (3) ◽

pp. 479-486 ◽

Cited By ~ 5

Author(s):

Kun Li ◽

Lin-Qing Wang ◽

Yu-Yang Wu ◽

An-Jun Chao ◽

Quan-Wei Lu ◽

...

Keyword(s):

Molecular Detection ◽

Central China ◽

Domestic Pigs ◽

Genomic Characterization ◽

Torque Teno Sus Virus

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Near Full-Length Genomic Characterization of a Novel CRF 01_AE/C Recombinant from Western India

AIDS Research and Human Retroviruses ◽

10.1089/aid.2015.0228 ◽

2015 ◽

Vol 31 (12) ◽

pp. 1269-1273 ◽

Cited By ~ 4

Author(s):

Santosh Karade ◽

Sudhanshu Pandey ◽

Sheetal Gianchandani ◽

Swarali N. Kurle ◽

Manisha Ghate ◽

...

Keyword(s):

Full Length ◽

Western India ◽

Genomic Characterization

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Identification and genomic characterization of emerging goose astrovirus in central China, 2020

Transboundary and Emerging Diseases ◽

10.1111/tbed.14060 ◽

2021 ◽

Author(s):

Xiaozhan Zhang ◽

Tongwei Deng ◽

Yuzhen Song ◽

Jian Liu ◽

Zenghai Jiang ◽

...

Keyword(s):

Central China ◽

Genomic Characterization

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Genomic characterization of Vibrio parahaemolyticus from Pacific white shrimp and rearing water in Malaysia reveals novel sequence types and structural variation in genomic regions containing the Photorhabdus insect-related (Pir) toxin-like genes

10.1101/714626 ◽

2019 ◽

Cited By ~ 1

Author(s):

Chrystine Zou Yi Yan ◽

Christopher M. Austin ◽

Qasim Ayub ◽

Sadequr Rahman ◽

Han Ming Gan

Keyword(s):

Vibrio Parahaemolyticus ◽

Illumina Miseq ◽

Pacific White Shrimp ◽

White Shrimp ◽

Phylogenomic Analysis ◽

Genomic Characterization ◽

Genomic Resource ◽

Acute Hepatopancreatic Necrosis Disease ◽

Genomic Regions

AbstractThe Malaysian and global shrimp aquaculture production has been significantly impacted by acute hepatopancreatic necrosis disease (AHPND) typically caused by Vibrio parahaemolyticus harboring the pVA plasmid containing the pirAVpand pirBVpgenes which code for Photorhabdus insect-related (Pir) toxin. The limited genomic resource for V. parahaemolyticus strains from Malaysian aquaculture farms precludes an in-depth understanding of their diversity and evolutionary relationships. In this study, we isolated shrimp-associated and environmental (rearing water) V. parahaemolyticus from three aquaculture farms located in Northern and Central Malaysia followed by whole-genome sequencing of 40 randomly selected isolates on the Illumina MiSeq. Phylogenomic analysis and multilocus sequence typing (MLST) reveal distinct lineages of V. parahaemolyticus that harbor the pirABVpgenes. The recovery of pVA plasmid backbone devoid of pirAVp or pirABVp in some V. parahaemolyticus isolates suggests that the toxin genes are prone to deletion. The new insight gained from phylogenomic analysis of Asian V. parahaemolyticus, in addition to the observed genomic instability of pVa plasmid, will have implications for improvements in aquaculture practices to diagnose, treat or limit the impacts of this disease.

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A comparative genomic analysis of the barley pathogen Pyrenophora teres f. teres identifies sub-telomeric regions as drivers of virulence

10.1101/753202 ◽

2019 ◽

Author(s):

Nathan A. Wyatt ◽

Jonathan K. Richards ◽

Robert S. Brueggeman ◽

Timothy L. Friesen

Keyword(s):

Genomic Analysis ◽

Effector Proteins ◽

Comparative Genomic ◽

Pyrenophora Teres ◽

Structural Variations ◽

Evolution Of Virulence ◽

Reference Quality ◽

Genomic Characterization ◽

Genomic Regions

AbstractPyrenophora teres f. teres causes net form net blotch of barley and is an economically important pathogen throughout the world. However, P. teres f. teres is lacking in the genomic resources necessary to characterize the mechanisms of virulence. Recently a high quality reference genome was generated for P. teres f. teres isolate 0-1. Here, we present the reference quality sequence and annotation of four new isolates and we use the five available P. teres f. teres genomes for an in-depth comparison resulting in the generation of hypotheses pertaining to the potential mechanisms and evolution of virulence. Comparative analyses were performed between all five P. teres f. teres genomes examining genomic organization, structural variations, and core and accessory genomic content, specifically focusing on the genomic characterization of known virulence loci and the localization of genes predicted to encode secreted and effector proteins. We showed that 14 of 15 currently published virulence quantitative trait loci (QTL) span accessory genomic regions consistent with these accessory regions being important drivers of host adaptation. Additionally, these accessory genomic regions were frequently found in sub-telomeric regions of chromosomes with 10 of the 14 accessory region QTL localizing to sub-telomeric regions. Comparative analysis of the sub-telomeric regions of P. teres f. teres chromosomes revealed translocation events where homology was detected between non-homologous chromosomes at a significantly higher rate than the rest of the genome. These results indicate that the sub-telomeric accessory genomic compartments not only harbor most of the known virulence loci, but also that these regions have the capacity to rapidly evolve.

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