| Literature DB >> 17625002 |
Sean J Humphray1, Carol E Scott, Richard Clark, Brandy Marron, Clare Bender, Nick Camm, Jayne Davis, Andrew Jenks, Angela Noon, Manish Patel, Harminder Sehra, Fengtang Yang, Margarita B Rogatcheva, Denis Milan, Patrick Chardon, Gary Rohrer, Dan Nonneman, Pieter de Jong, Stacey N Meyers, Alan Archibald, Jonathan E Beever, Lawrence B Schook, Jane Rogers.
Abstract
BACKGROUND: The domestic pig is being increasingly exploited as a system for modeling human disease. It also has substantial economic importance for meat-based protein production. Physical clone maps have underpinned large-scale genomic sequencing and enabled focused cloning efforts for many genomes. Comparative genetic maps indicate that there is more structural similarity between pig and human than, for example, mouse and human, and we have used this close relationship between human and pig as a way of facilitating map construction.Entities:
Mesh:
Year: 2007 PMID: 17625002 PMCID: PMC2323232 DOI: 10.1186/gb-2007-8-7-r139
Source DB: PubMed Journal: Genome Biol ISSN: 1474-7596 Impact factor: 13.583
Fingerprint and BAC end sequence summary
| Library | Fingerprinted clones | Genome complexity | BES passed reads | Paired ends | Average GC % | Average Phred Q20 length (bp) |
| CHORI-242 | 101,434 | 6.7 | 340,484 | 93% | 41 | 705 |
| PigEBAC | 73,863 | 4.2 | 144,870 | 93% | 42 | 700 |
| RPCI-44 | 61,225 | 3.8 | 71,847 | 87% | 40 | 521 |
| INRA | 28,465 | 1.5 | 62,888 | 94% | 42 | 613 |
| All | 264,987 | 16.2* | 620,089 | 92% | 41 | 635 |
*Based on a genome size of 2.6 to 2.7 Gb [30].
Summary of pig BAC end sequence alignments to NCBI build 35 of the human genome
| Human-pig sequence matches | Homologous crosslink matches | Matches to human exons | |||||
| Human chromosome | Available human sequence (Mb) | Total | Per Mb | Total | Per Mb | Total | Per Mb |
| 1 | 222.8 | 24,510 | 110 | 14,393 | 65 | 3,049 | 13.7 |
| 2 | 237.5 | 27,269 | 115 | 15,755 | 66 | 2,279 | 9.6 |
| 3 | 194.6 | 23,691 | 122 | 13,991 | 72 | 1,949 | 10.0 |
| 4 | 187.2 | 20,347 | 109 | 11,449 | 61 | 1,272 | 6.8 |
| 5 | 177.7 | 20,497 | 115 | 11,950 | 67 | 1,509 | 8.5 |
| 6 | 167.3 | 18,898 | 113 | 10,856 | 65 | 1,586 | 9.5 |
| 7 | 154.8 | 15,036 | 97 | 8,736 | 57 | 1,270 | 8.2 |
| 8 | 142.6 | 14,344 | 101 | 8,251 | 58 | 1,048 | 7.3 |
| 9 | 117.8 | 12,597 | 107 | 7,286 | 62 | 1,092 | 9.3 |
| 10 | 131.6 | 13,709 | 104 | 8,073 | 61 | 1,281 | 9.7 |
| 11 | 131.1 | 14,893 | 114 | 8,375 | 64 | 1,573 | 12.0 |
| 12 | 130.3 | 14,817 | 114 | 8,427 | 65 | 1,778 | 13.6 |
| 13 | 95.6 | 9,873 | 103 | 5,765 | 60 | 628 | 6.6 |
| 14 | 88.3 | 10,414 | 118 | 6,185 | 70 | 1,070 | 12.1 |
| 15 | 81.3 | 9,176 | 113 | 5,505 | 68 | 1,021 | 12.6 |
| 16 | 78.9 | 7,129 | 91 | 4,233 | 54 | 959 | 12.2 |
| 17 | 77.8 | 6,949 | 89 | 3,969 | 51 | 1,365 | 17.5 |
| 18 | 74.7 | 8,098 | 111 | 5,038 | 68 | 521 | 7.0 |
| 19 | 55.8 | 2,926 | 53 | 1,629 | 29 | 1,095 | 19.6 |
| 20 | 59.5 | 5,893 | 99 | 3,417 | 57 | 701 | 11.8 |
| 21 | 34.2 | 3,328 | 98 | 1,849 | 54 | 289 | 8.5 |
| 22 | 34.8 | 2,462 | 71 | 1,319 | 38 | 499 | 14.3 |
| X | 150.4 | 10,824 | 72 | 5,716 | 38 | 763 | 5.0 |
| Y | 24.9 | 62 | 3 | 2 | 0.1 | 0 | 0 |
| All | 2,851.5 | 297,742 | 97 | 172,169 | 56.3 | 28,597 | 10.2 |
Figure 1Alignment between human chromosome 6 tilepath and pig chromosome 7 physical map via porcine BES matches. (a) Mb scale; (b) human sequence tilepath; (c) BES matches to human; (d) sequenced clone EMBL:CR956379 (CH242-196P11); (e) pig clone map - green indicate clones with BAC end sequence match to human; (f) UIUC RH map; (g) estimated Mb.
Figure 2Blocks of conserved synteny between pig and human. (a) Pig SSC7 to human chromosomes 6, 14 and 15. (b) HSA13 compared to pig chromosome 11. Block inversions between pig and human are denoted with broken lines. Contig coverage is depicted by bars in the center of SSC7 and HSA13.
Distribution of contigs across pig chromosomes
| Total | Ordered on UIUC RH map | |||
| Pig chromosome | Contigs | Coverage (kb) | Contigs | Coverage (kb) |
| 1 | 12 | 300,977 | 3 | 295,553 |
| 2 | 15 | 159,169 | 8 | 149,047 |
| 3 | 14 | 146,851 | 9 | 144,675 |
| 4 | 9 | 143,919 | 8 | 143,453 |
| 5 | 8 | 102,515 | 4 | 99,497 |
| 6 | 12 | 167,617 | 11 | 166,045 |
| 7 | 10 | 136,596 | 5 | 132,447 |
| 8 | 5 | 146,803 | 4 | 146,495 |
| 9 | 6 | 155,323 | 4 | 151,750 |
| 10 | 14 | 80,643 | 7 | 75,116 |
| 11 | 4 | 86,158 | 3 | 84,555 |
| 12 | 7 | 64,461 | 6 | 64,189 |
| 13 | 1 | 218,109 | 1 | 218,109 |
| 14 | 4 | 139,903 | 3 | 138,960 |
| 15 | 7 | 173,355 | 3 | 169,770 |
| 16 | 3 | 86,660 | 2 | 86,055 |
| 17 | 6 | 67,521 | 5 | 67,043 |
| 18 | 2 | 61,577 | 2 | 60,404 |
| X | 27 | 127,979 | 20 | 125,475 |
| Y | 6 | 1,760 | - | - |
| All | 172 | 2,567,896 | 108 | 2,518,638 |
Figure 3Comparison of homologous annotation between pig and human. Pig clone CH242-196P11 was aligned to HSA6 by BES matches, and the clone was then sequenced [EMBL:CR956379]. The resulting annotation showed the expected homologues to known human genes present in the pig sequence as in human sequences [EMBL:AL035587, EMBL:AL158815, EMBL:AL136304]. Full gene annotation for CH242-196P11 is available in the EMBL entry. Red lines indicate regions of sequence homology with a 75% sequence similarity over the whole region. Figure generated using Artemis Comparison Tool [57].