NDLI: Lessons learned from the initial sequencing of the pig genome: comparative analysis of an 8 Mb region of pig chromosome 17

Content Provider	Springer Nature : BioMed Central
Author	Hart, Elizabeth A Caccamo, Mario Harrow, Jennifer L Humphray, Sean J Gilbert, James GR Trevanion, Steve Hubbard, Tim Rogers, Jane Rothschild, Max F
Abstract	Background We 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. Results Within 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. Conclusion We 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.
Related Links	https://genomebiology.biomedcentral.com/counter/pdf/10.1186/gb-2007-8-8-r168.pdf
Ending Page	12
Page Count	12
Starting Page	1
File Format	HTM / HTML
DOI	10.1186/gb-2007-8-8-r168
Journal	Genome Biology
Issue Number	8
Volume Number	8
Language	English
Publisher	BioMed Central
Publisher Date	2007-08-17
Access Restriction	Open
Subject Keyword	Animal Genetics and Genomics Human Genetics Plant Genetics and Genomics Microbial Genetics and Genomics Bioinformatics Evolutionary Biology Bacterial Artificial Chromosome Bacterial Artificial Chromosome Clone Bacterial Artificial Chromosome Library Syntenic Region Wellcome Trust Sanger Institute
Content Type	Text
Resource Type	Article
Subject	Biotechnology Genetics
Journal Impact Factor	10.1/2023
5-Year Journal Impact Factor	16.5/2023

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4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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