ArticleGenome biology2007
Lessons learned from the initial sequencing of the pig genome: comparative analysis of an 8 Mb region of pig chromosome 17.
Article in Genome biology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
What it found
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Who cites it
29 citing papers in PubMed, 47 citations in OpenAlex.
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- Environmental stressors affect intestinal permeability and repair responses in a pig intestinal ischemia model.Tissue barriers · 2020Article
- BOARD INVITED REVIEW: The pig microbiota and the potential for harnessing the power of the microbiome to improve growth and health1.Journal of animal science · 2019Review
- Melatonin and its derivatives counteract the ultraviolet B radiation-induced damage in human and porcine skin ex vivo.Journal of pineal research · 2018Article
- Oral administration of inactivated porcine epidemic diarrhea virus activate DCs in porcine Peyer's patches.BMC veterinary research · 2018Article
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- Genetically Induced Tumors in the Oncopig Model Invoke an Antitumor Immune Response Dominated by Cytotoxic CD8βFrontiers in immunology · 2018Article
- Molecular Characterization of Barrier Properties in Follicle-Associated Epithelium of Porcine Peyer's Patches Reveals Major Sealing Function of Claudin-4.Frontiers in physiology · 2017Article
- Port d'Entrée for Respiratory Infections - Does the Influenza A Virus Pave the Way for Bacteria?Frontiers in microbiology · 2017Review
- Large Animal Models: The Key to Translational Discovery in Digestive Disease Research.Cellular and molecular gastroenterology and hepatology · 2016Article
- Large animal models of cardiovascular disease.Cell biochemistry and function · 2016Review
- Mechanism of Cell Culture Adaptation of an Enteric Calicivirus, the Porcine Sapovirus Cowden Strain.Journal of virology · 2016Article
- Extensive error in the number of genes inferred from draft genome assemblies.PLoS computational biology · 2014Article
Corrections and comments
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Authors and funding
9 authors at 2 institutions in 2 countries.
Funding
Abstract
backgroundWe describe here the sequencing, annotation and comparative analysis of an 8 Mb region of pig chromosome 17, which provides a useful test region to assess coverage and quality for the pig genome sequencing project. We report our findings comparing the annotation of draft sequence assembled at different depths of coverage.
resultsWithin this region we annotated 71 loci, of which 53 are orthologous to human known coding genes. When compared to the syntenic regions in human (20q13.13-q13.33) and mouse (chromosome 2, 167.5 Mb-178.3 Mb), this region was found to be highly conserved with respect to gene order. The most notable difference between the three species is the presence of a large expansion of zinc finger coding genes and pseudogenes on mouse chromosome 2 between Edn3 and Phactr3 that is absent from pig and human. All of our annotation has been made publicly available in the Vertebrate Genome Annotation browser, VEGA. We assessed the impact of coverage on sequence assembly across this region and found, as expected, that increased sequence depth resulted in fewer, longer contigs. One-third of our annotated loci could not be fully re-aligned back to the low coverage version of the sequence, principally because the transcripts are fragmented over several contigs.
conclusionWe have demonstrated the considerable advantages of sequencing at increased read depths and discuss the implications that lower coverage sequence may have on subsequent comparative and functional studies, particularly those involving complex loci such as GNAS.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.