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Neotropical Ichthyology

Print version ISSN 1679-6225

Neotrop. ichthyol. vol.11 no.3 Porto Alegre Sept. 2013 

Original Articles

Development and characterization of microsatellite loci of Microglanis cottoides (Siluriformes: Pseudopimelodidae) and cross-species amplification

Lenice  Souza-Shibatta1 

Dhiego Gomes  Ferreira2 

Claudio  Oliveira3 

Fernanda Simões de  Almeida2 

Oscar Akio  Shibatta1 

Silvia Helena  Sofia1  2 

1Universidade Estadual de Londrina, Programa de Pós-Graduação em Ciências Biológicas, Departamento de Biologia Animal e Vegetal, Centro de Ciências Biológicas, 86051-990 Londrina, PR, Brazil. (LSS); (OAS)

2Universidade Estadual de Londrina, Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Biologia Geral, Centro de Ciências Biológicas, 86051-990 Londrina, PR, Brazil. (SHS)

3Universidade Paulista Júlio Mesquita Filho, Instituto de Biociências, Departamento de Biociências. Distrito de Rubião Júnior s/n, 18618- 970 Botucatu, SP, Brazil.


Thirteen microsatellite loci were isolated and characterized in Microglanis cottoides. Of these, two were monomorphic and 11 were polymorphic. These polymorphic loci tested on 24 individuals from a wild population produced a total of 108 different alleles, with levels of variability high, ranging from 2 to 20, with an average of 8.3 alleles per locus. The observed and expected heterozygosity ranged from 0.125 to 0.958 and from 0.119 to 0.931, respectively. A high combined probability of paternity exclusion value and a low probability combined genetic identity value obtained show that the set of loci described herein displays good suitability for paternity studies and differentiation of M. cottoides. Additionally, all thirteen microsatellite primers developed for M. cottoides were tested in four other Pseudopimelodidae species and successful cross-species amplification was achieved for the majority of loci.

Key words: Brazilian Eastern basin; Catfish; Enriched genomic library; Genetic marker; SSR


Treze loci microssatélites foram isolados e caracterizados em Microglanis cottoides. Destes, dois foram monomórficos e 11 foram polimórficos. Estes loci polimórficos foram testados em 24 indivíduos de uma população selvagem e produziram um total de 108 alelos diferentes, com níveis de variabilidade alta, variando de 2 a 20, com uma média de 8,3 alelos por locus. A heterozigosidade observada e esperada variou de 0,125 a 0,958 e 0,119 a 0,931, respectivamente. Um elevado valor de exclusão de paternidade e um baixo valor de identidade genética foram obtidos, demostrando que o conjunto de loci descritos no presente trabalho exibe boa aplicabilidade no estudo de parentesco e diferenciação populacional em M. cottoides. Adicionalmente, os treze primers de microssatélites desenvolvidos para M. cottoides foram testados em outras quatro espécies de Pseudopimelodidae e a transferabilidade foi obtida para a maioria dos loci.


Microglanis Eigenmann 1912, also known as bumblebee catfishes (Shibatta, 2003a), is a genus of small South American catfishes that do not exceed over 110 mm in standard length (Shibatta, 2003a; Shibatta & Benine, 2005). Initially regarded as a member of the pimelodids (Eigenmann, 1912), this genus was subsequently included in the small Pseudopimelodidae family (Shibatta, 2003b), which is considered a monophyletic group (Lundberg et al., 1991).

With 21 valid species described to date (Ruiz & Shibatta, 2011), the genus Microglanis is also characterized by its wide mouth (gape width same as head width), short maxillary barbel (occasionally reaching pectoral-fin origin) and small eye without free orbital margin, among other particular characters (Shibatta, 2003a, 2003b). These small catfishes are widely distributed across South America, occurring from Guyana to the Rio de La Plata basin in Argentina (Shibatta & Benine, 2005; Sarmento-Soares et al., 2006).

Although our knowledge of the number of Microglanis species has increased in the last decade (Shibatta, 2003a, 2003b; Bertaco & Cardoso, 2005; Shibatta & Benine, 2005; Sarmento-Soares et al., 2006; Alcaraz et al., 2008; Ottoni et al., 2010; Shibatta & Ruiz, 2010; Shibatta & Ruiz, 2011), the biology of Microglanis still remains poorly known (Shibatta, 2003a). Recently, it has been shown that some species can occur in small populations patchily distributed along the river basins where they are found (Esguícero & Arcifa, 2010). According to these authors, such conditions which may be associated with the progressive environmental degradation of freshwater habitats could represent threats to populations of some Microglanis species. Despite this fact, up to this moment population genetic studies involving Microglanis species are still lacking.

Among the known species, Microglanis cottoides (Boulenger 1891) is especially interesting for phylogeographic and genetic population studies, owing to its geographical distribution in the Brazilian Atlantic Forest, being present in the Uruguay River basin and along the eastern coast of Brazil, with records of their occurrence in drainages across the southern and southeastern regions (Malabarba & Mahler, 1998; Shibatta, 2003b, 2007; Mori & Shibatta, 2006). These regions can be considered of great biogeographical significance, not only for the high degree of endemism of its fish fauna (Bizerril, 1994, 1995), but also for being a very populated area with high environmental degradation due to human activities.

Studies on geographic distribution of genealogical lineages have been widely used to describe historical events, such as habitat fragmentation or expansion of the range of species and populations. These studies also serve to understand migration events, vicariance and extinction of gene lineages, and other processes that affect the population structure or generate speciation in a spatial and temporal context (Avise, 2001, 2009; Hardy et al., 2002).

A good way to study the genetic structure of natural fish populations is through the use of molecular markers such as microsatellite (SSR-Simple Sequence Repeats) (O'Connell & Wright, 1997). In fact, SSR are considered a class of molecular markers highly polymorphic and useful for population studies (Zane et al., 2002). Therefore, the current work describes 13 SSR markers developed for Microglanis cottoides and tests their applicability for four other Pseudopimelodidae species.

Material and Methods

Microsatellites were isolated and characterized following the protocol of Billotte et al. (1999), with some minor modifications. Total genomic DNA was extracted from muscle tissue preserved in 95% ethanol. The DNA was isolated according to Almeida et al. (2001). Genomic DNA (5 °g) was digested with RsaI and the blunt-ended fragments were ligated to the adaptors Rsa 21 and Rsa 25 (Edwards et al., 1996). Fragments were selected with (AGA)5, (CT)8 and (GT)8 probes, and then cloned into the pGem(r)-T (Promega) vector. Such recombinant plasmids were used to transform the E. coli DH5- α lineage. The recombinant clones were selected and sequenced using the BigDye Terminator(tm) kit (v. 3.1 - Applied Biosystems). Sequencing was performed on an ABI 3500 XL automated sequencer. Sequences were analyzed using BioEdit v.7.0 software (Hall, 1999) and primers were designed using Primer 3 software (Rozen & Skaletsky, 2000). The selected forward primers were labelled with the M13 sequence (5'-TGTAAAACGACGGCCAGT-3') at the 5' end (Schuelke, 2000). The AutoDimer software (Vallone & Butler, 2004) was used to test the potential presence of hairpin structures and primer-dimer problems. The individual genotyping was performed on an ABI 3500 XL automated sequencer.

PCR amplifications were carried out on 24 individuals of M. cottoides (MZUEL 7453), collected in the arroio Divisa (30º54'5.6"S 52º05'18.0"W), municipality of Cristal, Rio Grande do Sul State, southern Brazil. Cross-species amplification tests were performed using four other pseudopimelodid species, as follows: Microglanis cibelae Malabarba & Mahler, 1998 (MZUEL 7452), from the rio Maquiné (Rio Grande do Sul State, 29º37'2.1"S 50º15'51.8"W); M. garavelloi Shibatta & Benine, 2005 (MZUEL 7878), from the Couro de Boi Stream (Paraná State, 23º05'41.4"S 50º59'49.5"W); M. parahybae Steindachner, 1880 (LBP 10741), from the rio Paraíba do Sul (Rio de Janeiro State, 22º04'07.8"S 41º54'36.2"W) and Pseudopimelodus pulcher Boulenger, 1887 (MZUEL 6039), from rio Laranjinha (Paraná State, 23º24'52.98"S 50º27'8.55"W), using five individuals of each species.

Reactions were performed in 5 °L reaction volume containing 1× GoTaq Master Mix (Promega), 10 ng of template DNA, 1% glycerol, 0.125 °M forward labeled primer (FAM, HEX or NED, Applied Biosystems, CA), 0.125 °M reverse primer, 0.0125 °M forward primer. Amplifications were performed with an initial denaturation step at 94ºC for 4 min, followed by 35 cycles at 94ºC for 40 s, 48ºC, 54ºC or 60ºC (according to Table 1) for 1 min, 72ºC for 1 min, and a final extension at 72ºC for 30 min. The PCR products were submitted to electrophoresis on an automated sequencer (Applied Biosystems 3500 Genetic Analyzer) and the GeneScan 600 Liz (Applied Biosystems) was used as the molecular weight standard.

Table 1 Description of 13 microsatellite loci (11 polymorphic and two monomorphic) isolated from the Neotropical fish Microglanis cottoides. Flanking primers, Ta = optimal annealing temperatures, k = number of alleles, allele size range (bp), Ho = observed heterozigosity, He = expected heterozygosity estimated from 30 individuals, Q = paternity exclusion probability, I = probability of genetic identity, FIS = endogamy coefficient, PIC = polymorphic information content, GenBank accession numbers. * Significant deviations from Hardy-Weinberg equilibrium (P < 0.05). ** Significant value for the endogamy coefficient (FIS). 

Locus Sequence Primers (5'- 3') Ta (ºC) k Allele size range (pb) Ho He (Q) (I) PIC F IS GenBank
Mcot01 (GT) 7 F: TCATGATGGCGACTGAACTC 48 1 244 0.000 0.000 0.000 1.000 0.000 - KF134914
Mcot02 (AC)9 F: AACTGCCTGCAAAACAACC 54 8 110 - 126 0.792 0.786 0.593 0.074 0.758 0.014 KF134915
Mcot03 (TG)16 F: AGCCCAATCTGTCTGAGAGC 54 17 183 - 221 0.917 0.915 0.828 0.013 0.909 0.019 KF134916
Mcot04 (TG)18 F: AGCGGCTGTAATAGGCTGTG 48 20 159 - 211 0.917 0.931 0.861 0.008 0.927 0.037 KF134917
Mcot05 (GTAAAA)3 F: CGTTGAAGAGTAACACAGACGTG 54 2 126 - 132 0.458 0.430 0.168 0.417 0.337 -0.045 KF134918
Mcot06 (GT)7 F: TCATGATGGCGACTGAACTC 48 1 245 0.000 0.000 0.000 1.000 0.000 - KF134919
Mcot07 (GT)10 F: TTCACTCAAGAGGCAGCTGTAG 54 15 127 - 183 0.917 0.875 0.759 0.025 0.865 -0.026 KF134920
Mcot08 (AC)19 F: CGCAGCACACCAGACTTATG 54 17 156 - 204 *0.792 0.908 0.815 0.015 0.901 **0.148 KF134921
Mcot09 (TGAA)4 F: CAGGTGGGTTCCGGATTAAC 54 7 97 - 125 0.958 0.681 0.428 0.156 0.627 -0.388 KF134922
Mcot10 (ATGA)6 F: GTGGGATCCGGATTAACCTC 48 7 118 - 138 0.667 0.666 0.409 0.170 0.607 0.019 KF134923
Mcot11 (GT)5 F: TCATTTGGAACCAGGACTCTG 54 4 165 - 188 0.417 0.386 0.215 0.400 0.363 -0.057 KF134924
Mcot12 (ATGA)6 F: GTGGGATCCGGATTAACCTC 60 5 166 - 182 0.375 0.641 0.393 0.180 0.589 **0.432 KF134925
Mcot13 (TGT)8 F: GAAGGTGTGGATTGAGAGCAG 60 3 125- 131 0.125 0.119 0.0598 0.780 0.115 -0.029 KF134926
All loci 108 8.3 0.580 0.579 0.999 2.16x10-6 0.538 0.021

The individuals were genotyped with the GeneMarker 1.85 software (SoftGenetics, State College, PA) followed by manual checking. Tests for Hardy-Weinberg Equilibrium (HWE) and the presence of linkage disequilibrium among the pairs of loci were calculated using GENEPOP 4.0.10 (Raymond & Rousset, 1995; Rousset, 2008); P values were subsequently adjusted applying the sequential Bonferroni correction (Rice, 1989). The software GenAlEx v.6.41 (Peakall & Smouse, 2006) was used to estimate the observed (Ho ) and expected (He ) heterozygosities and the average number of alleles per locus. The paternity exclusion probability (Q) (Weir, 1996), and the genetic identity probabilities (I) (Paetkau et al., 1995) were estimated using Identity 1.0 (Wagner & Sefc, 1999). Estimates of the polymorphic information content (PIC) and potential null alleles were obtained through Cervus v.3.0 (Marshall et al., 1998) and Micro-Checker v.2.2.3 (Van Oosterhout et al., 2004) software, respectively. Default settings were used for all tests.


Of 96 clones sequenced, 25 contained microsatellite repeats but only 18 were suitable for primer design and PCR reactions. After testing the different amplification conditions, 13 loci were successfully amplified. From these, two were monomorphic and 11 were polymorphic (Table 1).

The eleven polymorphic loci produced a total of 108 different alleles, with high levels of variability, ranging from 2 to 20, with an average of 8.3 alleles per locus. The observed and expected heterozygosity ranged from 0.125 to 0.958 and from 0.119 to 0.931, respectively. After Bonferroni correction for multiple comparisons, no evidence of linkage disequilibrium between any pair of loci examined was observed. Only the locus Mcot09 showed significant deviation from Hardy-Weinberg equilibrium (P < 0.05). This locus showed the presence of null alleles, inferred from excess homozygous genotypes which could explain the observed deviation from HWE. Additionally, the locus Mcot08 revealed an excess of homozygotes and the possible presence of null alleles, but did not show any significant deviation from the HWE. It was also observed that the loci Mcot08 and Mcot12 were the only ones showing significant values of endogamic coefficient (FIS ) (Table 1).


A high combined probability of paternity exclusion value (0.999) and a low combined probability of genetic identity value (2.16 x 10-6) were obtained, showing that the set of loci described herein, exhibits good applicability for studies of parentage and population differentiation of M. cottoides.

The average PIC was 0.528, ranging from 0.115 to 0.927. According to Botstein et al. (1980), PIC values above 0.5 indicate highly informative markers; from 0.25 to 0.50, moderately informative; and below 0.25, slightly informative. Of the 13 loci obtained, eight proved to be highly informative (Mcot02, Mcot03, Mcot04, Mcot07, Mcot08, Mcot09, Mcot10 and Mcott12) with PIC values equal to or higher than 0.589; two were moderately informative (Mcot05 and Mcot11) presenting PIC values equal to or higher than 0.337. Only one locus (Mcot13) was slightly informative, exhibiting a PIC value equal to 0.115.

All 13 microsatellite primers developed for M. cottoides were successfully cross-amplified in two from four Pseudopimelodidae species (Table 2). Only two loci (Mcot04 and Mcot09) failed to amplify in P. pulcher and M. garavelloi, respectively. From the set of loci tested, Microglanis garavelloi and M. parahybae exhibited 10 polymorphic loci, while M. cibelae and P. pulcher showed, respectively, 11 and 12 polymorphic loci each.

Table 2 Cross-amplification of 13 loci in four species of Pseudopimelodidae. Amplifications and polymorphisms were tested in five individuals of each species. - indicates no amplification. k = the number of alleles per locus. 

Mcot01 Mcot02 Mcot03 Mcot04 Mcot05 Mcot06 Mcot07 Mcot08 Mcot09 Mcot10 Mcot11 Mcot12 Mcot13
Species Allele size range (bp) and the number of alleles per locus observed (k)
Microglanis cibelae 244-246 114-122 104-218 180-196 114-132 148-168 244-246 168-214 113-125 122-132 165 166-174 128
k= 2 k= 4 k= 2 k= 5 k= 3 k= 5 k= 2 k= 5 k= 3 k= 4 k= 1 k= 3 k= 1
Microglanis garavelloi 232 114-124 195-197 181-191 112-132 155-161 232-256 152-172 - 116-130 184 168-172 126-129
k= 1 k= 3 k= 1 k= 3 k= 3 k= 3 k= 2 k= 3 - k= 3 k= 1 k= 3 k= 2
Microglanis parahybae 251 116-126 202-208 207-221 114-132 145-155 244-252 162-176 114-124 122-126 184 170-178 122
k= 1 k= 5 k= 3 k= 4 k= 2 k= 4 k= 1 k= 5 k= 4 k= 3 k= 1 k= 3 k= 1
Pseudopimelodus pulcher 238-258 100-134 182-214 - 110-156 145-153 245-247 158-170 115-197 122-126 186-192 170-174 101-128
k= 4 k= 5 k= 6 - k= 2 k= 4 k= 2 k= 5 k= 5 k= 2 k= 2 k= 2 k= 5

The successful cross-species amplification of microsatellite loci described herein can be attributed to the high conservatism of the flanking microsatellite regions, which is expected among close related species, as reported elsewhere (Barbará et al., 2007). Thus, the set of primers presented in the current study appear as promising tools for future population genetic studies involving these five species of Neotropical fish.


The authors are grateful to "Coordenação de Aperfeiçoamento de Pessoal de Nível Superior" (CAPES) for the scholarship granted to L. Souza-Shibatta, and Fundação Araucária for their financial support to this research (Programa Universal 05/2011, protocol 22.633); Lúcia Giuliano Caetano (Universidade Estadual de Londrina) for donating samples of M. cottoides; Claudete F. Ruas, for helping build the library; and IBAMA/SISBIO, for providing permission to collect fish (License nº 12120-1). The authors also thank to the anonymous referees, who contributed with valuable comments and suggestions.

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Received: July 03, 2013; Accepted: August 26, 2013

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