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Swine Research Report, 2000 Animal Science Research Reports 2001 High-Resolution Radiation Hybrid Mapping of Human Chromosome 17 Genes to the Pig Genome Extends Gene Order Conservation with Pig Chromosome 12 and Limited Synteny with Pig Chromosome 2 X. W. Shi Iowa State University C. J. Fitzsimmons Iowa State University C. K. Tuggle Iowa State University C. Genêt Institut National de la Recherche Agronomique–Toulouse R. Prather University of Missouri–Columbia Recommended Citation Shi, X. W.; Fitzsimmons, C. J.; Tuggle, C. K.; Genêt, C.; Prather, R.; Whitworth, K.; and Green, J. A., "High-Resolution Radiation Hybrid Mapping of Human Chromosome 17 Genes to the Pig Genome Extends Gene Order Conservation with Pig Chromosome 12 and Limited Synteny with Pig Chromosome 2" (2001). Swine Research Report, 2000. 19. http://lib.dr.iastate.edu/swinereports_2000/19 This report is brought to you for free and open access by the Animal Science Research Reports at Iowa State University Digital Repository. It has been accepted for inclusion in Swine Research Report, 2000 by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. See next page for additional authors Follow this and additional works at: http://lib.dr.iastate.edu/swinereports_2000 Part of the Agriculture Commons, and the Animal Sciences Commons Extension Number: ASL R666 High-Resolution Radiation Hybrid Mapping of Human Chromosome 17 Genes to the Pig Genome Extends Gene Order Conservation with Pig Chromosome 12 and Limited Synteny with Pig Chromosome 2 Abstract A comparative study of human chromosome 17 (HSA17) and pig chromosome 12 (SSC12) and 2 (SSC2) was conducted using both somatic cell hybrid panel (SCHP) and radiation hybrid (RH) panel analysis. A cDNA library from an expressed sequence tag (EST) project in pig reproduction was examined and six genes and ESTs from HSA17 were selected for this study. The eg nes/ESTs were TATA box binding protein- associated factor (TAF2N/RBP56), plasmin inhibitor (PLI), H3 histone family 3B (H3F3B), aminopeptidase puromycin sensitive (NPEPPS/PSA), P311 protein (P311), and an expressed sequence tag (ESTMI015). SCHP analysis mapped five genes/ESTs (TAF2N , H3F3B, PLI, NPEPPS, and ESTMI015) to SSC12q11-q15 and SSC12p11-p15 with 100% concordance, and assigned P311 to SSC2 (1/2q24)-q29 with 100% concordance. RH analysis of all six genes confirmed the SCHP mapping results, with average retention frequency of 25%. An expanded comparative SSC12 RH map integrating the five new type I markers and 23 previously mapped loci was established using a LOD score threshold of 4.8. The eg ne order of the five genes/ ESTs on the SSC12 framework RH map (H3F3B-ESTMI015-PSA-RBP56-PLI) is identical to the HSA17 GB4 map but with map inversion. Although synteny conservation between HSA17 and SSC2 has not been detected by previous painting experiments, the mapping of P311 to SSC2 suggests that some synteny conservation exists between HSA17 and SSC2. Keywords ASL R666 Disciplines Agriculture | Animal Sciences Authors X. W. Shi, C. J. Fitzsimmons, C. K. Tuggle, C. Genêt, R. Prather, K. Whitworth, and J. A. Green This breeding/physiology is available at Iowa State University Digital Repository: http://lib.dr.iastate.edu/swinereports_2000/19 Iowa State University Breeding/Physiology High-Resolution Radiation Hybrid Mapping of Human Chromosome 17 Genes to the Pig Genome Extends Gene Order Conservation with Pig Chromosome 12 and Limited Synteny with Pig Chromosome 2 X. W. Shi, visiting scientist P311 to SSC2 suggests that some synteny conservation C. J. Fitzsimmons, research associate exists between HSA17 and SSC2. C. K. Tuggle, associate professor Introduction Department of Animal Science Comparative mapping is expected to be an efficient and powerful strategy in predicting gene location from the well- developed human genome map, and as a method for selecting C. Genêt, Ph.D student candidate genes for improvement of economically important Laboratoire de Genetique Cellulaire, traits in livestock species. Bidirectional painting has revealed INRA-Toulouse, 37 synteny groups conserved between the pig and human France (2). However, even within conserved synteny groups, rearrangement of gene order and distance discrepancy of adjacent loci have been documented (1, 4, 9, 13). R. Prather, professor Accumulation of comparative mapping information K. Whitworth, research associate between human and swine is helpful for understanding the J. A. Green, research assistant professor evolutionary relationship between the two genomes and in predicting gene order and location with increased certainty. Department of Animal Science, 128 linkage groups covering all porcine chromosomes (n = University of Missouri-Columbia 19) were established in a first-generation porcine whole- genome radiation hybrid (WG-RH) analysis (3). This useful map consists almost exclusively of microsatellites, thus RH ASL-R666 mapping of additional type I loci is required to fully use the RH panel for high-resolution comparative mapping. For Summary and Implications example, only a single type I locus, GH, was mapped to A comparative study of human chromosome 17 SSC12 by using the INRA-Minnesota porcine radiation (HSA17) and pig chromosome 12 (SSC12) and 2 (SSC2) hybrid (IMpRH) panel (3). Therefore, the objective in this was conducted using both somatic cell hybrid panel (SCHP) study was to provide additional comparative mapping and radiation hybrid (RH) panel analysis. A cDNA library references between human chromosome 17 (HSA17) and pig from an expressed sequence tag (EST) project in pig chromosome 12 (SSC12) using both somatic cell hybrid reproduction was examined and six genes and ESTs from panel (SCHP) and radiation hybrid (RH) panel analysis. HSA17 were selected for this study. The genes/ESTs were TATA box binding protein-associated factor (TAF2N /RBP56), plasmin inhibitor (PLI), H3 histone family 3B Materials and Methods (H3F3B), aminopeptidase puromycin sensitive As part of an expressed sequence tag (EST) project in (NPEPPS/PSA), P311 protein (P311), and an expressed pig reproduction (11), a directionally cloned cDNA library sequence tag (ESTMI015). SCHP analysis mapped five was produced from day 20 porcine embryos at University of genes/ESTs (TAF2N , H3F3B, PLI, NPEPPS, and Missouri-Columbia., The 3´-untranslated region of 220 ESTMI015) to SSC12q11-q15 and SSC12p11-p15 with clones was sequenced at Iowa State University. BLAST hits 100% concordance, and assigned P311 to SSC2 (1/2q24)-q29 were evaluated for 187 clones, and six genes/ESTs on with 100% concordance. RH analysis of all six genes HSA17 were selected for the present study (Table 1). The six confirmed the SCHP mapping results, with average genes/ESTs were TATA box binding protein-associated retention frequency of 25%. An expanded comparative factor (TAF2N), plasmin inhibitor (PLI), H3 histone family SSC12 RH map integrating the five new type I markers and 3B (H3F3B), aminopeptidase puromycin sensitive 23 previously mapped loci was established using a LOD (NPEPPS/PSA), P311 protein (P311), and an expressed tag score threshold of 4.8. The gene order of the five sequence (ESTMI015). genes/ESTs on the SSC12 framework RH map (H3F3B- The oligonucleotide primers for these genes/ESTs were ESTMI015-PSA-RBP56-PLI) is identical to the HSA17 designed using the OLIGO 5.0 program (NBI, Plymouth, GB4 map but with map inversion. Although synteny MN), and they were then PCR-tested on a panel of conservation between HSA17 and SSC2 has not been templates, including pig, mouse, and Chinese hamster detected by previous painting experiments, the mapping of genomic DNAs. All primer sets for these six genes/ESTs showed robust and porcine specific amplification. 96 Iowa State University Breeding/Physiology PCR was performed on an MJ Research PTC-200 was consistent with the recently published first-generation thermal cycler in a 15-µl reaction volume containing 1 × porcine whole-genome radiation hybrid map (3). However, PCR buffer (Promega, Madison, WI), 66 µM dNTP, 0.5 one discrepancy was observed between the two maps, µ M of each primer, 1.5 mM MgCl2, 0.25 U Taq polymerase involving Sw957, GH and Sw943. In the published map (Promega), and 25 ng of hybrid DNA. PCR reactions were (3), we notice that Sw957 and GH were inadvertently preheated at 94oC for 2 min and then followed by 35 cycles assigned to the second linkage group. The mapping of at 94oC for 30 s, 60-64oC for 30 s, and 72oC for 45 s and ESTMI015 allows us to localize GH and Sw957 to the first completed at 72oC for 5 min. The PCR products were size- linkage group. The results of our analysis are in agreement separated on a 3% agarose gel. Detailed information on with the two point analysis of the first generation map primer sequences, annealing temperature and product size for available from the Web site at each locus was submitted to http://imprh.toulouse.inra.fr/. http://fabctr.umn.edu/RHMaps/2ptdata/chr12-2pt.html A somatic cell hybrid panel (SCHP) comprised of 27 Eighteen type I genes or ESTs have been physically clones was used for regional assignments of the six mapped on SSC12 by SCHP and FISH analysis genes/ESTs on pig chromosomes (12; also see (http://www.toulouse.inra.fr/lgc/pig/cyto/gene/chromo/SSC http://www,toulouse.inra.fr/lgc/pig/pcr/pcr.htm). G12.htm). However, SSC12 gene order is unclear due to A WG-RH (whole-genome radiation hybrids) panel overlapping localizations for many of these loci. Radiation included 118 hybrid clones was used for determining the hybrid mapping can provide higher resolution, yet of these gene order. The panel was tested at least twice for each loci only GH has been mapped using the IMpRH panel (3). gene/EST. If a discrepancy occurred between the first two Assignment of these five genes/ESTs in the present study tests, then a third confirmation test was performed. thus significantly increases the density of type I markers on the SSC12 RH map.
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    OriGene Technologies, Inc. 9620 Medical Center Drive, Ste 200 Rockville, MD 20850, US Phone: +1-888-267-4436 [email protected] EU: [email protected] CN: [email protected] Product datasheet for RC209037 NPEPPS (NM_006310) Human Tagged ORF Clone Product data: Product Type: Expression Plasmids Product Name: NPEPPS (NM_006310) Human Tagged ORF Clone Tag: Myc-DDK Symbol: NPEPPS Synonyms: AAP-S; MP100; PSA Vector: pCMV6-Entry (PS100001) E. coli Selection: Kanamycin (25 ug/mL) Cell Selection: Neomycin This product is to be used for laboratory only. Not for diagnostic or therapeutic use. View online » ©2021 OriGene Technologies, Inc., 9620 Medical Center Drive, Ste 200, Rockville, MD 20850, US 1 / 5 NPEPPS (NM_006310) Human Tagged ORF Clone – RC209037 ORF Nucleotide >RC209037 representing NM_006310 Sequence: Red=Cloning site Blue=ORF Green=Tags(s) TTTTGTAATACGACTCACTATAGGGCGGCCGGGAATTCGTCGACTGGATCCGGTACCGAGGAGATCTGCC GCCGCGATCGCC ATGTGGCTGGCAGCTGCCGCCCCCTCCCTCGCTCGCCGCCTGCTCTTCCTCGGCCCTCCGCCTCCTCCCC TCCTCCTTCTCGTCTTCAGCCGCTCCTCTCGCCGCCGCCTCCACAGCCTGGGCCTCGCCGCGATGCCGGA GAAGAGGCCCTTCGAGCGGCTGCCTGCCGATGTCTCCCCCATCAACTACAGCCTTTGCCTCAAGCCCGAC TTGCTGGACTTCACCTTCGAGGGCAAGCTGGAGGCCGCCGCCCAGGTGAGGCAGGCGACTAATCAGATTG TGATGAATTGTGCTGATATTGATATTATTACAGCTTCATATGCACCAGAAGGAGATGAAGAAATACATGC TACAGGATTTAACTATCAGAATGAAGATGAAAAAGTCACCTTGTCTTTCCCTAGTACTCTGCAAACAGGT ACGGGAACCTTAAAGATAGATTTTGTTGGAGAGCTGAATGACAAAATGAAAGGTTTCTATAGAAGTAAAT ATACTACCCCTTCTGGAGAGGTGCGCTATGCTGCTGTAACACAGTTTGAGGCTACTGATGCCCGAAGGGC TTTTCCTTGCTGGGATGAGCCTGCTATCAAAGCAACTTTTGATATCTCATTGGTTGTTCCTAAAGACAGA
  • Li Et Al: Comprehensive Variation Discovery and Recovery of Missing Sequence in the Pig Genome Using Multiple De Novo Assemblies

    Li Et Al: Comprehensive Variation Discovery and Recovery of Missing Sequence in the Pig Genome Using Multiple De Novo Assemblies

    Li et al: Comprehensive variation discovery and recovery of missing sequence in the pig genome using multiple De Novo assemblies Supplemental references 1 Wang LY, Wang AG, Wang LX, Li K, Yang GS, He RG, Qian L, Xu NY, Huang RH, Peng ZZ, et al. 2011. Animal genetic resources in China: pigs. (ed. China National Commission of Animal Genetic Resources) , pp. 18-470. China Agricultural Press, Beijing. 2 Chen, K., Baxter, T., Muir, W. M., Groenen, M. A. & Schook, L. B. Genetic resources, genome mapping and evolutionary genomics of the pig (Sus scrofa). Int. J. Biol. Sci. 3, 153-165 (2007). 3 Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078-2079 (2009). 4 McKenna, A. et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297-1303 (2010). 5 Saeed, A. I. et al. TM4: a free, open-source system for microarray data management and analysis. Biotechniques 34, 374-378 (2003). 6 Tajima, F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123, 585-595 (1989). 7 Maillet, N., Lemaitre, C., Chikhi, R., Lavenier, D. & Peterlongo, P. Compareads: comparing huge metagenomic experiments. BMC Bioinformatics 13 Suppl 19, S10 (2012). 8 Sennoune, S. R. & Martinez-Zaguilan, R. Vacuolar H(+)-ATPase signaling pathway in cancer. Curr. Protein Pept. Sc. 13, 152-163 (2012). 9 Yang, D. Q. et al. V-ATPase subunit ATP6AP1 (Ac45) regulates osteoclast differentiation, extracellular acidification, lysosomal trafficking, and protease exocytosis in osteoclast‐mediated bone resorption. J. Bone Miner. Res.