title: A second generation integrated map of the rainbow trout (Oncorhynchus mykiss) genome: analysis of conserved synteny with model fish genomes.
abstract: DNA fingerprints and end sequences from bacterial artificial chromosomes (BACs) from two new libraries were generated to improve the first generation integrated physical and genetic map of the rainbow trout (Oncorhynchus mykiss) genome. The current version of the physical map is composed of 167,989 clones of which 158,670 are assembled into contigs and 9,319 are singletons. The number of contigs was reduced from 4,173 to 3,220. End sequencing of clones from the new libraries generated a total of 11,958 high quality sequence reads. The end sequences were used to develop 238 new microsatellites of which 42 were added to the genetic map. Conserved synteny between the rainbow trout genome and model fish genomes was analyzed using 188,443 BAC end sequence (BES) reads. The fractions of BES reads with significant BLASTN hits against the zebrafish, medaka, and stickleback genomes were 8.8%, 9.7%, and 10.5%, respectively, while the fractions of significant BLASTX hits against the zebrafish, medaka, and stickleback protein databases were 6.2%, 5.8%, and 5.5%, respectively. The overall number of unique regions of conserved synteny identified through grouping of the rainbow trout BES into fingerprinting contigs was 2,259, 2,229, and 2,203 for stickleback, medaka, and zebrafish, respectively. These numbers are approximately three to five times greater than those we have previously identified using BAC paired ends. Clustering of the conserved synteny analysis results by linkage groups as derived from the integrated physical and genetic map revealed that despite the low sequence homology, large blocks of macrosynteny are conserved between chromosome arms of rainbow trout and the model fish species.
authors.affiliation: National Center for Cool and Cold Water Aquaculture, ARS-USDA, 11861 Leetown Road, Kearneysville, WV 25430, USA. yniv.palti@ars.usda.gov
authors.forename: Yniv
authors.initials: Y
authors.lastname: Palti
authors.forename: Carine
authors.initials: C
authors.lastname: Genet
authors.forename: Guangtu
authors.initials: G
authors.lastname: Gao
authors.forename: Yuqin
authors.initials: Y
authors.lastname: Hu
authors.forename: Frank M
authors.initials: FM
authors.lastname: You
authors.forename: Mekki
authors.initials: M
authors.lastname: Boussaha
authors.forename: Caird E
authors.initials: CE
authors.lastname: Rexroad
authors.forename: Ming-Cheng
authors.initials: MC
authors.lastname: Luo
mesh_terms: D000818:Animals; D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D016678:Genome / Q000235:genetics*; D008969:Molecular Sequence Data; D017686:Oncorhynchus mykiss / Q000235:genetics*; D026801:Synteny / Q000235:genetics*
references.citation: J Hered. 2003 Jul-Aug;94(4):273-84
references.pmid: 12920098
references.citation: Cytogenet Genome Res. 2003;102(1-4):347-54
references.pmid: 14970727
references.citation: J Hered. 1996 Jan-Feb;87(1):77-80
references.pmid: 8742822
references.citation: Mol Ecol. 2012 Jan;21(2):237-49
references.pmid: 21988725
references.citation: BMC Genomics. 2009 Dec 10;10:592
references.pmid: 20003258
references.citation: J Dairy Sci. 2009 Jul;92(7):3431-6
references.pmid: 19528621
references.citation: BMC Genet. 2008 Nov 19;9:74
references.pmid: 19019240
references.citation: Genome Res. 2004 Mar;14(3):478-90
references.pmid: 14962987
references.citation: Anim Genet. 2004 Apr;35(2):130-3
references.pmid: 15025574
references.citation: Genetics. 2006 Nov;174(3):1661-70
references.pmid: 16951085
references.citation: BMC Genet. 2009 Aug 18;10:46
references.pmid: 19689812
references.citation: Proc Natl Acad Sci U S A. 1984 Jun;81(11):3443-6
references.pmid: 6587361
references.citation: Biotechniques. 2001 Jul;31(1):24-6, 28
references.pmid: 11464515
references.citation: Anim Genet. 2006 Aug;37(4):321-6
references.pmid: 16879340
references.citation: Dis Aquat Organ. 2003 Sep 24;56(2):145-54
references.pmid: 14598990
references.citation: Nat Genet. 1995 Dec;11(4):402-8
references.pmid: 7493020
references.citation: Genetics. 2008 Jul;179(3):1559-75
references.pmid: 18562654
references.citation: Mar Biotechnol (NY). 2008 Sep-Oct;10(5):579-92
references.pmid: 18491191
references.citation: BMC Genomics. 2011 Apr 07;12:180
references.pmid: 21473775
references.citation: Methods Mol Biol. 2000;132:365-86
references.pmid: 10547847
references.citation: Genome Res. 2004 Jun;14(6):1199-205
references.pmid: 15140834
references.citation: Genome Res. 2000 Nov;10(11):1772-87
references.pmid: 11076862
references.citation: BMC Genomics. 2009 Oct 08;10:462
references.pmid: 19814815
references.citation: Mar Biotechnol (NY). 2010 Aug;12(4):410-29
references.pmid: 19816740
references.citation: Immunogenetics. 2004 Mar;55(12):825-35
references.pmid: 14968267
references.citation: Comp Biochem Physiol B Biochem Mol Biol. 2002 Dec;133(4):609-46
references.pmid: 12470823
references.citation: Proc Natl Acad Sci U S A. 1987 Apr;84(8):2363-7
references.pmid: 3470801
references.citation: Plant Physiol. 2005 Sep;139(1):27-38
references.pmid: 16166258
references.citation: BMC Genomics. 2007 Feb 06;8:40
references.pmid: 17284319
references.citation: BMC Genomics. 2010 Oct 13;11:564
references.pmid: 20942956
references.citation: J Hered. 2001 Jan-Feb;92(1):16-22
references.pmid: 11336224
references.citation: Nat Genet. 1994 Apr;6(4):384-90
references.pmid: 8054979
references.citation: Heredity (Edinb). 2001 Mar;86(Pt 3):333-41
references.pmid: 11488970
references.citation: BMC Genomics. 2011 Aug 11;12:408
references.pmid: 21831322
references.citation: Genome Res. 2003 Aug;13(8):1966-72
references.pmid: 12902387
references.citation: Nucleic Acids Res. 1999 Jan 15;27(2):573-80
references.pmid: 9862982
references.citation: BMC Genomics. 2006 Aug 03;7:196
references.pmid: 16887034
references.citation: Genetics. 2000 Jul;155(3):1331-45
references.pmid: 10880492
references.citation: Genome Biol. 2010;11(9):403
references.pmid: 20887641
references.citation: J Biomed Biotechnol. 2011;2011:329025
references.pmid: 21049003
references.citation: BMC Genomics. 2006 Nov 30;7:302
references.pmid: 17137492
references.citation: BMC Genomics. 2011 Apr 14;12:188
references.pmid: 21492448
references.citation: Fish Shellfish Immunol. 2007 May;22(5):510-9
references.pmid: 17085058
references.citation: Genome Res. 1998 Mar;8(3):186-94
references.pmid: 9521922
references.citation: BMC Genomics. 2008 Nov 25;9:557
references.pmid: 19032764
references.citation: Genome Biol. 2007;8(7):R152
references.pmid: 17663790
references.citation: BMC Bioinformatics. 2010 Jan 20;11:38
references.pmid: 20089148
references.citation: Anim Genet. 2001 Aug;32(4):200-4
references.pmid: 11531698
references.citation: Mol Genet Genomics. 2001 Mar;265(1):23-31
references.pmid: 11370869
references.citation: Genomics. 2005 Oct;86(4):396-404
references.pmid: 16026963
references.citation: BMC Genomics. 2010 Jan 27;11:68
references.pmid: 20105308
references.citation: Am J Hum Genet. 1998 Jul;63(1):259-66
references.pmid: 9634505
references.citation: J Hered. 2005 Mar-Apr;96(2):97-107
references.pmid: 15653562
references.citation: Nucleic Acids Res. 1997 Sep 1;25(17):3389-402
references.pmid: 9254694
references.citation: Genomics. 2003 Sep;82(3):378-89
references.pmid: 12906862
references.citation: Anim Genet. 2003 Apr;34(2):102-15
references.pmid: 12648093
references.citation: Heredity (Edinb). 2011 Jun;106(6):920-6
references.pmid: 21048672
references.citation: Nucleic Acids Res. 2009 Apr;37(5):e36
references.pmid: 19181701
references.citation: Genetics. 1998 Feb;148(2):839-50
references.pmid: 9504929
references.citation: Genome. 2005 Dec;48(6):1037-51
references.pmid: 16391673
references.citation: Comput Appl Biosci. 1997 Oct;13(5):523-35
references.pmid: 9367125
references.citation: BMC Genet. 2011 May 14;12:46
references.pmid: 21569550
references.citation: J Hered. 2002 Jan-Feb;93(1):77-8
references.pmid: 12011185
references.citation: Genetics. 2007 Jan;175(1):335-47
references.pmid: 17057232
references.citation: J Mol Biol. 1990 Oct 5;215(3):403-10
references.pmid: 2231712
references.citation: BMC Genomics. 2011 Jun 14;12:314
references.pmid: 21672188