Zoological Research (动物学研究) 2010/31:2 PP.131-140
Microsatellites have been widely used in studies on population genetics, ecology and evolutionary biology. However, microsatellites are not always available for the species to be studied and their isolation could be time-consuming. In order to save time and effort researchers often rely on cross-species amplification. We revealed a new problem of microsatellite cross-species amplification in addition to size homoplasy by analyzing the sequences of electromorphs from seven catfish species belonging to three different families (Clariidae, Heteropneustidae and Pimelodidae). A total of 50 different electromorphs were amplified from the seven catfish species by using primers for 4 microsatellite loci isolated from the species Clarias batrachus. Two hundred and forty PCR-products representing all 50 electromorphs were sequenced and analyzed. Primers for two loci amplified specific products from orthologous loci in all species tested, whereas primers for the other two loci produced specific and polymorphic bands from some non-orthologous loci, even in closely related non-source species. Size homoplasy within the source species was not obvious, whereas extensive size homoplasy across species were detected at three loci, but not at the fourth one. These data suggest that amplification of products from non-orthologous loci and appearance of size homoplasy by cross-amplification are locus dependent, and do not reflect phylogenetic relationship. Amplification of non-orthologous loci and appearance of size homoplasy will lead to obvious complications in phylogenetic interference, population genetic and evolutionary studies. Therefore, we propose that sequence analysis of cross-amplification products should be conducted prior to application of cross-species amplification of microsatellites.
Funds：This study was supported financially by the internal research funding from Temasek Life Sciences Laboratory
Agnese, JF, Teugels, GG. Insight into the phylogeny of African Clariidae (Teleostei, Siluriformes): Implications for their body shape evolution, biogeography, and taxonomy [J]. Mol Phylogenet Evol,2005 36 (3): 546-553.
Angers B, Gharbi K, Estoup A. Evidence of gene conversion events between paralogous sequences produced by tetraploidization in Salmoninae fish [J]. J Mol Evol,2002 54 (4): 501-510.
Anmarkrud JA, Kleven O, Bachmann L, Lifjeld JT. Microsatellite evolution: Mutations, sequence variation, and homoplasy in the hypervariable avian microsatellite locus HrU10 [J]. BMC Evol Biol,2008 8: 138.
Chang CH, Hsieh LC, Chen TY, Chen HD, Luo L, Lee HC. Shannon information in complete genomes [J]. J Bioinform Comput Biol,2005 3 (3): 587-608.
Chang YM, Kuang YY, Liang LQ, Lu CY, He JG, Su XW. Searching for protein-coding genes using microsatellites in common carp by comparing to zebrafish EST database [J]. Zool Res,2008 29 (4): 373-378.
Chen X, Cho YG, McCouch SR. Sequence divergence of rice microsatellites in Oryza and other plant species [J]. Mol Genet Genomics,2002 268 (3): 331-343.
Culver M, Menotti-Raymond MA, O'Brien SJ. Patterns of size homoplasy at 10 microsatellite loci in pumas (Puma concolor) [J]. Mol Biol Evol,2001 18 (6): 1151-1156.
Di Gaspero G, Peterlunger E, Testolin R, Edwards KJ, Cipriani G. Conservation of microsatellite loci within the genus Vitis [J]. Theor Appl Genet,2000 101 (1-2): 301-308.
Estoup A, Jarne P, Cornuet JM. Homoplasy and mutation model at microsatellite loci and their consequences for population genetics analysis [J]. Mol Ecol,2002 11 (9): 1591-1604.
Estoup A, Tailliez C, Cornuet JM, Solignac M. Size homoplasy and mutational processes of interrupted microsatellites in two bee species, Apis mellifera and Bombus terrestris (Apidae) [J]. Mol Biol Evol,1995 12 (6): 1074-1084.
Garza JC, Slatkin M, Freimer NB. Microsatellite allele frequencies in humans and chimpanzees, with implications for constraints on allele size [J]. Mol Biol Evol,1995 12 (4): 594-603.
Goldstein DB, Schlotterer C. 1999. Microsatellites: Evolution and Applications [M]. Oxford: Oxford University Press.
Gonzalez-Martinez SC, Robledo-Arnuncio JJ, Collada C, Diaz A, Williams CG, Alia R, Cervera MT. Cross-amplification and sequence variation of microsatellite loci in Eurasian hard pines [J]. Theor Appl Genet,2004 109 (1): 103-111.
Harr B, Zangerl B, Brem G, Schlotterer C. Conservation of locus-specific microsatellite variability across species: A comparison of two Drosophila sibling species, D. melanogaster and D. simulans [J]. Mol Biol Evol,1998 15 (2): 176-184.
Hempel K, Peakall R. Cross-species amplification from crop soybean Glycine max provides informative microsatellite markers for the study of inbreeding wild relatives [J]. Genome,2003 46 (3): 382-393.
Housley DJ, Zalewski ZA, Beckett SE, Venta PJ. Design factors that influence PCR amplification success of cross-species primers among 1147 mammalian primer pairs [J]. BMC Genomics,2006 7: 253.
Küpper C, Burke T, Székely T, Dawson DA. Enhanced cross-species utility of conserved microsatellite markers in shorebirds [J]. BMC Genomics,2008 9: 502.
Kayang BB, Inoue-Murayama M, Hoshi T, Matsuo K, Takahashi H, Minezawa M, Mizutani M, Ito S. Microsatellite loci in Japanese quail and cross-species amplification in chicken and guinea fowl [J]. Genet Sel Evol,2002 34 (2): 233-253.
Kayser M, Ritter H, Bercovitch F, Mrug M, Roewer L, Nurnberg P. Identification of highly polymorphic microsatellites in the rhesus macaque Macaca mulatta by cross-species amplification [J]. Mol Ecol,1996 5 (1): 157-159.
Kijas JM, Fowler JC, Thomas MR. An evaluation of sequence tagged microsatellite site markers for genetic analysis within Citrus and related species [J]. Genome,1995 38 (2): 349-355.
Koskinen MT, Primmer CR. Cross-species amplification of salmonid microsatellites which reveal polymorphism in European and Arctic grayling, Salmonidae: Thymallus spp [J]. Hereditas,1999 131 (2): 171-176.
Kumar S, Tamura K, Jakobsen IB, Nei M. MEGA2: molecular evolutionary genetics analysis software [J]. Bioinformatics,2001 17: 1244-1245.
Lin G, Chang A, Yap W, Yue GH. Characterization and cross-species amplification of microsatellites from the endangered Hawksbill turtle (Eretmochelys imbricate) [J]. Conserv Genet,2008 9: 1071-1073.
Makova KD, Nekrutenko A, Baker RJ. Evolution of microsatellite alleles in four species of mice (genus Apodemus) [J]. J Mol Evol,2000 51 (2): 166-172.
Meyer A, Schartl M. Gene and genome duplications in vertebrates: the one-to-four (- to-eight in fish) rule and the evolution of novel gene functions [J]. Curr Opin Cell Biol,1999 11 (6): 699-704.
Peakall R, Gilmore S, Keys W, Morgante M, Rafalski A. Cross-species amplification of soybean (Glycine max) simple sequence repeats (SSRs) within the genus and other legume genera: Implications for the transferability of SSRs in plants [J]. Mol Biol Evol,1998 15 (10): 1275-1287.
Postlethwait JH, Woods IG, Ngo-Hazelett P, Yan YL, Kelly PD, Chu F, Huang H, Hill-Force A, Talbot WS. Zebrafish comparative genomics and the origins of vertebrate chromosomes [J]. Genome Res,2000 10 (12): 1890-1902.
Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools [J]. Nucleic Acids Res,1997 25 (24): 4876-4882.
van Oppen MJH, Rico C, Turner GF, Hewitt GM. Extensive homoplasy, nonstepwise mutations, and shared ancestral polymorphism at a complex microsatellite locus in Lake Malawi cichlids [J]. Mol Biol Evol,2000 17 (4): 489-498.
Viard F, Franck P, Dubois MP, Estoup A, Jarne P. Variation of microsatellite size homoplasy across electromorphs, loci, and populations in three invertebrate species [J]. J Mol Evol,1998 47 (1): 42-51.
Wang HZ, Yin QQ, Feng ZG, Li, DY, Sun XW, Li C. Construction of fractional genomic libraries and screening microsatellites DNA of Esox reieherti Dybowski [J]. Zool Res,2008 29 (3): 245-252.
Weber JL, May PE. Abundant class of human DNA polymorphisms which can be typed using the polymerase chain-reaction [J]. Am J Hum Genet,1989 44 (3): 388-396.
Yue GH, Chen F, Orban L. Rapid isolation and characterization of microsatellites from the genome of Asian arowana (Scleropages formosus, Osteoglossidae, Pisces) [J]. Mol Ecol,2000 9 (7): 1007-1009.
Yue GH, David L, Orban L. Mutation rate and pattern of microsatellites in common carp (Cyprinus carpio L.) [J]. Genetica,2007 129 (3): 329-31.
Yue GH, Ho MY, Orban L, Komen J. Microsatellites within genes and ESTs of common carp and their applicability in silver crucian carp [J]. Aquaculture,2004 234 (1-4): 85-98.
Yue GH, Kovacs B, Orban L. Microsatellites from Clarias batrachus and their polymorphism in seven additional catfish species [J]. Mol Ecol Notes,2003 3 (3): 465-468.
Yue GH, Orban L. Rapid isolation of DNA from fresh and preserved fish scales for polymerase chain reaction [J]. Mar Biotechnol,2001 3 (3): 199-204.
Zane L, Bargelloni L, Patarnello T. Strategies for microsatellite isolation: a review [J]. Mol Ecol,2002 11 (1): 1-16.
Zhang YW, Zhang YP, Aryder O. Microsatellites and its application [J]. Zool Res,2001 22 (4): 315-320.