title: Generation of physical map contig-specific sequences.
abstract: Rapid advances of the next-generation sequencing technologies have allowed whole genome sequencing of many species. However, with the current sequencing technologies, the whole genome sequence assemblies often fall in short in one of the four quality measurements: accuracy, contiguity, connectivity, and completeness. In particular, small-sized contigs and scaffolds limit the applicability of whole genome sequences for genetic analysis. To enhance the quality of whole genome sequence assemblies, particularly the scaffolding capabilities, additional genomic resources are required. Among these, sequences derived from known physical locations offer great powers for scaffolding. In this mini-review, we will describe the principles, procedures and applications of physical-map-derived sequences, with the focus on physical map contig-specific sequences.
authors.affiliation: Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences Beijing, China.
authors.forename: Yanliang
authors.initials: Y
authors.lastname: Jiang
authors.affiliation: Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences Beijing, China.
authors.forename: Peng
authors.initials: P
authors.lastname: Xu
authors.affiliation: Aquatic Genomics Unit, The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, and Program of Cell and Molecular Biosciences, Auburn University AL, USA.
authors.forename: Zhanjiang
authors.initials: Z
authors.lastname: Liu
keywords: BAC end sequences; assembly; physical map contig-specific sequences; scaffolding; whole genome sequencing
references.citation: Nature. 2012 Oct 4;490(7418):49-54
references.pmid: 22992520
references.citation: Mar Biotechnol (NY). 2007 Nov-Dec;9(6):701-11
references.pmid: 17671813
references.citation: Genome Res. 2003 Aug;13(8):1966-72
references.pmid: 12902387
references.citation: Nature. 2012 Nov 29;491(7426):711-6
references.pmid: 23075845
references.citation: Science. 2002 Apr 5;296(5565):79-92
references.pmid: 11935017
references.citation: Genome Res. 2000 Jan;10(1):129-36
references.pmid: 10645957
references.citation: Proc Natl Acad Sci U S A. 2004 Oct 5;101(40):14349-54
references.pmid: 15388850
references.citation: Nature. 2001 Feb 15;409(6822):860-921
references.pmid: 11237011
references.citation: Genome Res. 2012 Nov;22(11):2241-9
references.pmid: 22800726
references.citation: Bioinformatics. 2012 Jun 1;28(11):1429-37
references.pmid: 22492642
references.citation: PLoS One. 2010 Jun 08;5(6):e10922
references.pmid: 20544019
references.citation: Genome Res. 2001 Oct;11(10):1736-45
references.pmid: 11591651
references.citation: PLoS One. 2012;7(2):e30087
references.pmid: 22347999
references.citation: Nature. 2000 Dec 14;408(6814):796-815
references.pmid: 11130711
references.citation: Anim Genet. 2006 Aug;37(4):321-6
references.pmid: 16879340
references.citation: Nature. 2007 Jun 7;447(7145):714-9
references.pmid: 17554307
references.citation: PLoS One. 2013 Oct 24;8(10):e78872
references.pmid: 24205335
references.citation: Nature. 2013 May 30;497(7451):579-84
references.pmid: 23698360
references.citation: Bioinformatics. 2011 Feb 15;27(4):578-9
references.pmid: 21149342
references.citation: Nucleic Acids Res. 2000 Sep 15;28(18):3636-41
references.pmid: 10982886
references.citation: Science. 2002 Apr 5;296(5565):92-100
references.pmid: 11935018
references.citation: BMC Genomics. 2011 Dec 22;12:629
references.pmid: 22192763
references.citation: Genome Res. 2009 Nov;19(11):1925-8
references.pmid: 19596977
references.citation: Nat Genet. 2014 Mar;46(3):270-8
references.pmid: 24441736
references.citation: Nature. 2004 Dec 9;432(7018):695-716
references.pmid: 15592404
references.citation: G3 (Bethesda). 2014 Apr 16;4(4):669-79
references.pmid: 24531727
references.citation: BMC Biol. 2006 Jun 06;4:16
references.pmid: 16756667
references.citation: Proc Natl Acad Sci U S A. 1999 Aug 17;96(17):9739-44
references.pmid: 10449764
references.citation: Genome Res. 2010 Dec;20(12):1740-7
references.pmid: 20980554
references.citation: Bioessays. 2005 Sep;27(9):937-45
references.pmid: 16108068
references.citation: Nature. 2010 Jan 21;463(7279):311-7
references.pmid: 20010809
references.citation: BMC Genomics. 2011 Nov 02;12:537
references.pmid: 22044723
references.citation: Genetics. 2014 Mar;196(3):875-90
references.pmid: 24653210
references.citation: BMC Genomics. 2011 Apr 14;12:188
references.pmid: 21492448
references.citation: Genome Res. 2003 Dec;13(12):2754-8
references.pmid: 14656976
references.citation: J Fish Biol. 2011 Sep;79(3):561-74
references.pmid: 21884100
references.citation: Genome Biol. 2014 Mar 03;15(3):R42
references.pmid: 24581555
references.citation: Genome Res. 1999 Mar;9(3):297-307
references.pmid: 10077536
references.citation: Nature. 2004 Oct 21;431(7011):946-57
references.pmid: 15496914
references.citation: Trends Plant Sci. 2011 Feb;16(2):77-88
references.pmid: 21081278
references.citation: IEEE/ACM Trans Comput Biol Bioinform. 2013 Mar-Apr;10(2):352-60
references.pmid: 23929859
references.citation: Nat Genet. 2013 Jan;45(1):59-66
references.pmid: 23179022
references.citation: J Comput Biol. 2011 Nov;18(11):1681-91
references.pmid: 21929371
references.citation: BMC Genomics. 2009 Dec 10;10:592
references.pmid: 20003258
references.citation: Genome Biol. 2013 Jun 17;14(6):R60
references.pmid: 23773524
references.citation: BMC Genomics. 2008 Aug 28;9:404
references.pmid: 18755037
references.citation: Genome Res. 2014 Aug;24(8):1384-95
references.pmid: 24755901
references.citation: Genomics. 2007 Sep;90(3):380-8
references.pmid: 17582737
references.citation: Nature. 2013 Apr 25;496(7446):498-503
references.pmid: 23594743
references.citation: Nature. 2005 Aug 11;436(7052):793-800
references.pmid: 16100779
references.citation: Nature. 2002 Dec 5;420(6915):520-62
references.pmid: 12466850