20210923

Contents
  1. 1. Working directories
  2. 2. URL
  3. 3. Philip White Board/TV
  4. 4. Swine genome
    1. 4.1. Swine Genome Project
    2. 4.2. Sus scrofa (pig) from NCBI Genome
      1. 4.2.0.1. Display Settings:
      2. 4.2.0.2. Send to:
  5. 4.3. Summary
  6. 4.4. Publications (limited to 20 most recent records)
  7. 4.5. Representative(genome information for reference and representative genomes)
  8. 4.6. Chromosomes
  9. 4.7. External Resources

Working directories

1
2
ls /media/ht/ht_5T_9/YouTubes/History/Wuhan/Video/US/NYT_20200527-1.mkv
i=/media/ht/ht_5T_9/YouTubes/History/Wuhan/Video/US/NYT_20200527-1.mkv

URL

Philip White Board/TV

  1. Manual
  2. Remote keyboard
  3. WiFi connection

Swine genome

Swine Genome Project

TheSwine Genome Sequencing Consortium (SGSC)was formed in September 2003 by academic,         government and industry representatives    to provide international coordination for sequencing the pig genome.

The SGSC’s mission is to advance biomedical research for animal production and health by the development of DNA based tools and products resulting from the sequencing of the swine genome.

A physical map of the swine genome was generated by an international collaboration of four laboratories, led by theWellcome Trust Sanger InstituteandDr. Lawrence Schookat the University of Illinois at Urbana-Champaign.  Both high-throughput fingerprinting and BAC-end sequencing were used to provide the template for an integrated physical map of the whole pig genome.

A high-quality draft genome sequence for the pig (Sus scrofa) was published in Nature in 2012. The paper entitled “Analyses of pig genomes provide insight into porcine demography and evolution“ described the sequencing, analysis, and annotation of the draft genome sequence.  In parallel, a series of companion papers was published in BMC journals.

The genome paper reports analyses not only of the reference genome of Duroc 2-14 (aka. TJ Tabasco), but also analyses of genomes of several wild boars and other domesticated pigs. The analyses revealed a deep phylogenetic split between European and Asian wild boars dating back ~1 million years. This observation, in part, provides final justification for the wide trait mapping crosses developed in the 1990s, especially between Western and Chinese breeds. It was argued at the time that Chinese and Western pigs were as genetically divergent as Mus musculus and Mus spretus, species of mice which had been extensively used in mouse genetics research. In effect, this judgment has been validated.

As observed in other genomes, genes encoding immune response functions show evidence of rapid evolution. The pig has the largest repertoire of functional olfactory receptor genes of any mammal sequenced to date – perhaps that is why they are effective hunters for truffles. There is evidence that genes involved in taste are located in pig evolutionary break points. Pigs can tolerate higher levels of substances that are distasteful to humans – perhaps the ability of pigs to eat material that is unpalatable to humans was one of the attractions when they were domesticated.

A comparison of multiple pig genomes and the comparison of pig and human genomes reveal several potentially disease-causing genetic variants which may extend the value of pigs in biomedical research.

The pig industry has an excellent track record for rapid and effective exploitation of new knowledge and technologies. The pig genome sequence is expected to enable the acceleration of pig genetics research, the results of which are expected to be translated into pig improvement in a timely manner. The pig industry support for the sequencing project is gratefully acknowledged by the Consortium.

This paper represents an important landmark for the Consortium. For many of the authors their collaborative research in pig genetics and genomics stretches back to the early 1990s and the European PiGMap project and USDA Pig Genome Coordinated activities in the US. The project has benefited from these long established collaborations and friendships. Trans-national funding was critical to the delivery of the project, including USDA funding to The Wellcome Trust Sanger Institute, European Commission and European Research Council funding, and significant contributions from Korean, Japanese, and Chinese national sources and many others.

Sus scrofa (pig) from NCBI Genome

Sequence data:

genome assemblies: 22; sequence reads: 35

(See Genome Assembly and Annotation report)

Statistics:

median total length (Mb): 2459.03

median protein count: 63577

median GC%: 41.5

NCBI Annotation Release:

106

Sus scrofa (pig)
Representative genome:Sus scrofa (assembly Sscrofa11.1)
Download sequences in FASTA format forgenome,transcript,protein
Download genome annotation inGFF,GenBankortabularformat
BLAST against Sus scrofagenome,transcript,protein
All 22 genomes for species:
Browse thelist
Download sequence and annotation fromRefSeqorGenBank
TryNCBI Datasets- a new way to download genome sequence and annotation we’re testing in NCBI Labs

Display Settings:

Send to:

ID: 84

Organism Overview;Genome Assembly and Annotation report [22];Organelle Annotation Report [6]
Organism Image Sus scrofa (pig)

pig

Lineage:Eukaryota[8059];Metazoa[3802];Chordata[1811];Craniata[1789];Vertebrata[1789];Euteleostomi[1773];Mammalia[480];Eutheria[455];Laurasiatheria[259];Artiodactyla[125];Suina[3];Suidae[2];Sus[1];Sus scrofa[1]

The pig (Sus scrofa) is a member of the artiodactyls, or cloven-hoofed mammals, which are an evolutionary clade distinct from the primates and rodents. Pigs exist in both feral and domesticated populations that have distinct phenotypes and karyotypes. The haploid genome of the domesticated pig is estimated to be 2800 Mb. The diploid genome isMore…

Summary

| Sequence data: | genome assemblies: 22; sequence reads: 35 | (See Genome Assembly and Annotation report) |
Statistics: median total length (Mb): 2459.03
median protein count: 63577
median GC%: 41.5
**NCBI Annotation Release: ** 106

Publications (limited to 20 most recent records)

  1. The Meishan pig genome reveals structural variation-mediated gene expression and phenotypic divergence underlying Asian pig domestication.Zhou R, et al. Mol Ecol Resour 2021 Aug
  2. An improved pig reference genome sequence to enable pig genetics and genomics research.Warr A, et al. Gigascience 2020 Jun 1
  3. Molecular characterization of the complete mitochondrial genome sequence of Indian wild pig (Sus scrofa cristatus).Kumar Jadav K, et al. Anim Biotechnol 2019 Apr

More…

Representative(genome information for reference and representative genomes)

Reference genome:

Chromosomes

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Chr1: chromosome

2

Chr2: chromosome

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Chr3: chromosome

4

Chr4: chromosome

5

Chr5: chromosome

6

Chr6: chromosome

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Chr7: chromosome

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Chr8: chromosome

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Chr9: chromosome

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Chr10: chromosome

11

Chr11: chromosome

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Chr12: chromosome

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Chr13: chromosome

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Chr14: chromosome

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Chr15: chromosome

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Chr16: chromosome

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Chr17: chromosome

18

Chr18: chromosome

X

ChrX: chromosome

Y

ChrY: chromosome

Click on chromosome name to open Genome Data Viewer

External Resources

  1. Breeds of Livestock - Swine
  2. DFCI Pig Gene Index
  3. National Swine Registry
  4. National Swine Resource and Research Center (NSRRC)
  5. Online Mendelian Inheritance in Animals (OMIA)
  6. Porcine Immunology and Nutrition (PIN) Database
  7. Rare Breeds Survival Trust
  8. The Swine Genome Sequencing Consortium
  9. Porcine Genome Sequencing and Mapping - Sanger Institute
  10. The Sino-Danish Pig Genome Project
  11. NAGRP Pig Genome Coordination Program
  12. Pigbase
  13. ArkDB - Pig
  14. Pig Genome Mapping, Roslin Institute
  15. Porcine Sequencing White Paper
  16. NISC Comparative Vertebrate Sequencing
  17. PigEST - University of Copenhagen
  18. Pig Expression Data Explorer (PEDE)
  19. PigQTLdb
  20. USDA/MARC Linkage Map
  21. INRA Cytogenetic Map
  22. INRA/UM Radiation Hybrid Map
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