Mining non-model genomic libraries for microsatellites: BAC versus EST libraries and the generation of allelic richness.

BMC Genomics
Christopher K Ellison, Kerry L Shaw

Abstract

Simple sequence repeats (SSRs) are tandemly repeated sequence motifs common in genomic nucleotide sequence that often harbor significant variation in repeat number. Frequently used as molecular markers, SSRs are increasingly identified via in silico approaches. Two common classes of genomic resources that can be mined are bacterial artificial chromosome (BAC) libraries and expressed sequence tag (EST) libraries. 288 SSR loci were screened in the rapidly radiating Hawaiian swordtail cricket genus Laupala. SSRs were more densely distributed and contained longer repeat structures in BAC library-derived sequence than in EST library-derived sequence, although neither repeat density nor length was exceptionally elevated despite the relatively large genome size of Laupala. A non-random distribution favoring AT-rich SSRs was observed. Allelic diversity of SSRs was positively correlated with repeat length and was generally higher in AT-rich repeat motifs. The first large-scale survey of Orthopteran SSR allelic diversity is presented. Selection contributes more strongly to the size and density distributions of SSR loci derived from EST library sequence than from BAC library sequence, although all SSRs likely are subject to similar physic...Continue Reading

References

May 25, 1984·Nucleic Acids Research·D Tautz, M Renz
Mar 1, 1996·Genome Research·J C Garza, N B Freimer
Feb 4, 1997·Proceedings of the National Academy of Sciences of the United States of America·R ChakrabortyR Deka
Aug 27, 1998·Molecular Biology and Evolution·C R Primmer, H Ellegren
Oct 27, 1998·Molecular Biology and Evolution·W Stephan, Y Kim
Mar 5, 1999·Molecular Ecology·R H CrozierY C Crozier
Mar 31, 1999·Trends in Biochemical Sciences·M F Perutz
May 21, 1999·Molecular Biology and Evolution·D BachtrogC Schlötterer
Feb 11, 2000·Science·D A PetrovK L Shaw
Jul 26, 2000·Molecular Biology and Evolution·M PascualC F Aquadro
Mar 7, 2001·Molecular Biology and Evolution·J Wilder, H Hollocher
Mar 10, 2001·Nature·E S LanderUNKNOWN International Human Genome Sequencing Consortium
Jun 23, 2001·Molecular Biology and Evolution·M V KattiV S Gupta
Oct 30, 2001·Evolution; International Journal of Organic Evolution·B D Neff, M R Gross
Jan 19, 2002·Nature Genetics·Michele MorganteWayne Powell
Jun 5, 2003·Molecular Biology and Evolution·Charles L RossTherese A Markow
Nov 8, 2003·Gene·Paola AstolfiVittorio Sgaramella
Dec 11, 2003·Nature Reviews. Genetics·Christian Schlötterer
May 29, 2004·Genetics·Michel SolignacJean-Marie Cornuet
Jan 5, 2005·Trends in Biotechnology·Rajeev K VarshneyMark E Sorrells
Jan 28, 2005·Nature·Tamra C Mendelson, Kerry L Shaw
Feb 14, 2006·Journal of Molecular Evolution·Jana UstinovaFrieder Mayer
May 11, 2007·BioTechniques·Helena KorpelainenViivi Virtanen
Oct 20, 2007·Trends in Biotechnology·Prakash C SharmaGünter Kahl
Jul 16, 2008·Briefings in Bioinformatics·Angelika Merkel, Neil Gemmell
Sep 27, 2008·The Journal of Parasitology·Nicholas D TemperleyPaul C D Johnson
Nov 21, 2008·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Shalu ChoudharySabhyata Bhatia
Oct 7, 2009·Proceedings of the National Academy of Sciences of the United States of America·Jean PeccoudNancy A Moran

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Methods Mentioned

BETA
PCR

Software Mentioned

BioEdit
PERL
SPSS11
Msatfinder
Primer3
SPSS

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