Microsatellite loci development for three catfish species from northwestern South America

Natalia Restrepo-Escobar¹ and Edna J. Márquez¹

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Abstract​

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Introduction​

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Genetic population studies are crucial in the generation of valuable information for different programs of management, conservation, and the genetic-diversity monitoring of several species (Schwartz et al., 2007; Allendorf et al., 2010; Frankham, 2010); particularly, those affected by different anthropogenic activities (Frankham, 2010). Among the different molecular markers utilized in genetic population studies, microsatellite loci are one of the most informative and widely used (Hamilton et al., 1999; Guichoux et al., 2011). However, the first approaches for microsatellite loci development in non-model species were expensive, complex (Hamilton et al., 1999; Castoe et al., 2010; Fernandez-Silva et al., 2013), and produced a low number of useful markers obtained for population studies (Zalapa et al., 2012). Fortunately, next-generation sequencing technologies allowed the fast development of different useful molecular markers to generate population and evolutionary information of species at lower costs (Ekblom, Galindo, 2011; Guichoux et al., 2011; Fernandez-Silva et al., 2013; Miller et al., 2013), although for the vast majority of fish species these markers are still limited or absent (Kumar, Kocour, 2017).

In Siluriformes, one of the richest taxonomic order of freshwater fishes in the Neotropics (Pereira et al., 2013; Reis et al., 2016), microsatellite loci have been developed only for 19 of 2,315 Neotropical valid species. Pimelodidae, the most studied family, includes 12 species belonging to the genera Brachyplatystoma (Rodrigues et al., 2009; Batista et al., 2010); Conorhynchos (Carvalho, Beheregaray, 2011), Phractocephalus (Souza et al., 2012), Pimelodella (Moeser, Bermingham, 2005), Pimelodus (Paiva, Kalapothakis, 2008; see Agostini et al., 2011), Pseudoplatystoma (Revaldaves et al., 2005; Saulo-Machado et al., 2011; Prado et al., 2014), Steindachneridion (see Ojeda et al., 2016), and Zungaro (Carrillo-Ávila et al., 2009). Remaining studies includes three species of Loricariidae (Telles et al., 2010; Pereira et al., 2012; Galindo et al., 2015), two species of Trichomycteridae (Zamudio et al., 2009; Muñoz-Rojas et al., 2012), one species of Heptapteridae (Rodrigues et al., 2015) and one species of Pseudopimelodidae (Souza-Shibatta et al., 2013).

Microsatellite loci are absent for catfishes from the west of the Eastern Cordillera of the Andes excepting Pimelodus grosskopfii (Hernandez-Escobar et al., 2011 in Agostini et al., 2011), limiting the population genetic studies for these species. Some authors have used microsatellite loci developed for close phylogenetically related species (heterologous loci); however, in some cases their use seems to be related to failures in the amplification, low levels of polymorphism, size homoplasy, null-alleles, and the amplification of non-orthologous loci (Primmer et al., 2005; Barbará et al., 2007; Castoe et al., 2010; Yue et al., 2010). This has stimulated the development of new molecular markers suitable for their population genetic studies.

Consequently, based on next-generation sequencing with the 454 GS-FLX technology (Roche Applied Science) and bioinformatics analysis, this study developed species-specific microsatellite loci for the non-model catfish species Ageneiosus pardalis (Lütken, 1874), Pimelodus grosskopfii (Steindachner, 1879), and Sorubim cuspicaudus (Littmann, Burr, Nass, 2000). These three carnivorous and migratory species are important for fisheries and many aspects of their basic biology and population genetics remain unknown, restraining the development of adequate management programs. This issue is important since population densities of these species have been decreased by anthropic activities in all Colombian watersheds (Galvis and Mojica, 2007; Usma-Oviedo et al., 2009; Mojica et al., 2012), which led to their classification as vulnerable in the red list of freshwater fish of Colombia (Mojica et al., 2012). Moreover, P. grosskopfii was also included as a critically endangered species in the Red List of Threatened Species of the International Union for the Conservation of Nature (IUCN; Villa-Navarro et al., 2016). These tools will allow for future population genetic studies that support different proposals focused on the sustainable management and conservation of these species.

Material and methods

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Samples were collected from 2011 to 2014 in the lower section of the Cauca River and supplied to the Laboratorio de Biología Molecular y Celular (Universidad Nacional de Colombia), through the scientific cooperation agreement CT-2013-002443; framed in the environmental license # 0155 of January 30, 2009 from Ministerio de Ambiente, Vivienda y Desarrollo Territorial. For each species, we took advantage of nuclear reads from pyrosequenced genomic libraries of one individual collected in the lower section of the Cauca River (Restrepo-Escobar et al., 2016a,b). Identification of microsatellite loci, primer design, and electronic PCR to guarantee the correct alignment of primers were performed using the software and procedures used by Landínez-García, Márquez (2016). About 39 and 43 pairs from the list of primers validated by electronic PCR were selected to evaluate their consistent amplification and polymorphism under standard PCR conditions in 12 individuals from each species. Then, we selected pairs of primers that fulfilled the conditions proposed by Landínez-García, Márquez (2016): (1) specific amplification in all individuals within the sizes that were designed (100 to 350 bp), (2) band resolution, (3) specificity, and (4) ability to detect heterozygotes. The forward primers of these pairs were directly fluorescently labeled or universal markers were added to their 5´-tail to produce their fluorescent label through the three primer PCR method (Blacket et al., 2012) and were further evaluated in 50 individuals of each species.

The PCR amplification was carried out under the conditions proposed by Landínez-García, Márquez (2016) for the directly labeled primers, and by Landínez-García, Marquez (2018) for the primers marked using the three primer method. In both cases, the PCR products were separated in an ABI 3130 automatic sequencer (Applied Biosystems, USA) using GeneScan-500 LIZ (Applied Biosystems, USA) as the size marker; the electropherograms obtained were reviewed using GeneMapper 4.0 (Applied Biosystems, USA). Before the statistical analysis, Micro-Checker 2.2.1 (Van Oosterhout et al., 2004) was used to detect possible genotyping errors.

For each species, the genetic diversity, the allelic frequencies, the observed (Ho) and expected (He) average heterozygosity and the average number of alleles per locus (Na) were determined with the GenAlEx 6.503 (Peakall, Smouse, 2012). Additionally, Arlequin 3.5.2.2 (Excoffier, Lischer, 2010) was used to determine the statistical significance of the allelic frequencies in Hardy-Weinberg and Linkage equilibria. In the case of multiple comparisons, the statistical significance was adjusted by sequential Bonferroni correction (Rice, 1989). Furthermore, the polymorphic information content (PIC) was determined for each loci with CERVUS 3.0.7 (Marshall et al., 1998).

Results​

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Genomic sequencing for A. pardalis generated 176,196 reads, 75,442 (43%) contained microsatellite loci, 19,940 (11%) potentially amplifiable loci (PAL) and 8,906 (5%) were validated by electronic PCR. For P. grosskopfii, the genomic sequencing generated 138,830 reads, 47,438 (34%) containing microsatellite loci, 23,937 (17%) PAL and 12,542 (9%) were validated by electronic PCR. Finally, the genomic sequencing for S. cuspicaudus generated a total of 123,158 reads, 43,302 (35%) contained microsatellite loci; 16,428 (13%) PAL and 8,840 (7%) were validated by electronic PCR.

The three studied species showed higher diversity of microsatellite loci with 2-mer motifs (57%-69%), followed by the 4-mer (15%-23%), 3-mer (10%-12%), 5-mer (4%-5%) and a small portion of 6-mer motifs (2%-3%; Fig. 1). Additionally, the three species showed similar patterns in the abundance of specific repeat motifs. For 2-mer motifs, the most common recurrence pattern was AC, and the less common was CG. Among the 3-mer motifs, the most common was ATT, and the least common was TCG for the three species. Lastly, among the 4-mer, the five most common motifs were AAAT, ATCT, TCTG, AGTG, and AATG.

FIGURE 1| Frequency of identified microsatellite loci and potentially amplifiable loci (PAL) obtained from 454 FLX sequencing for Ageneiosus pardalis, Pimelodus grosskopfii, and Sorubim cuspicaudus.

More than 68% of the evaluated loci generated fragments in the expected size range (100-350 bp) and were polymorphic in A. pardalis (27 loci), P. grosskopfii (27 loci), and S. cuspicaudus (37 loci). The PIC values for the microsatellite loci developed were 0.601-0.903 for A. pardalis, 0.748-0.946 for P. grosskopfii, and 0.383-0.876 for S. cuspicaudus (Tabs. 1-3). The average number of alleles per locus ranged from 7-15 alleles/locus (average: 11.286 ± 0.574) in A. pardalis; 9-30 alleles/locus (average: 14.944 ± 1.136) in P. grosskopfii; and 5-14 alleles/locus (average: 9.500 ± 0.552 alleles/locus) in S. cuspicaudus. In addition, the expected average heterozygosity ranged from 0.622 to 0.910 in A. pardalis (He: 0.834 ± 0.015), 0.771-0.948 in P. grosskopfii (He: 0.878 ± 0.010), and 0.419-0.887 in S. cuspicaudus (He: 0.757 ± 0.025). The observed average heterozygosity ranged from 0.320-0.920 in A. pardalis (Ho: 0.757 ± 0.035), 0.340-0.920 in P. grosskopfii (Ho: 0.612 ± 0.042), and 0.300-0.940 in S. cuspicaudus (Ho: 0.747 ± 0.031).

For A. pardalis (17 of 21, Tab. 1) and S. cuspicaudus (17 of 24, Tab. 3), all or most of the evaluated loci were shown to be in linkage and Hardy-Weinberg equilibria after the Bonferroni correction. In contrast, P. grosskopfii showed 13 loci with heterozygote deficit, allelic frequencies departures from Hardy-Weinberg equilibrium (Tab. 2), and significant linkage disequilibrium between the pairs of loci Pgrk01-Pgrk02 and Pgrk08-Pgrk20.

TABLE 1 | Primer sequences and characteristics of 21 polymorphic microsatellite loci identified in Ageneiosus pardalis. Ra: Allelic size range; Na: Average number of alleles per locus; Ho and He: observed and expected heterozygosity, respectively; P: Statistical significance for tests of departure of Hardy-Weinberg equilibrium; PIC: Polymorphic information content. Annealing temperature: 56.5 °C, for all primers.

TABLE 2 | Primer sequences and characteristics of 18 polymorphic microsatellite loci identified in Pimelodus grosskopfii. Ra: Allelic size range; Na: Average number of alleles per locus; Ho and He: observed and expected heterozygosity, respectively; P: Statistical significance for tests of departure of Hardy-Weinberg equilibrium; PIC: Polymorphic information content.^1,2,3 Annealing temperatures: 56.5 °C, 59 °C, 60 °C, respectively.

TABLE 3 | Primer sequences and characteristics of 24 polymorphic microsatellite loci identified in Sorubim cuspicaudus. Ra: Allelic size range; Na: Average number of alleles per locus; Ho and He: observed and expected heterozygosity, respectively; P: Statistical significance for tests of departure of Hardy-Weinberg equilibrium; PIC: Polymorphic information content. Annealing temperature: 56.5 °C, for all primers.

Discussion​

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In this work, 63 microsatellite loci were designed for future studies of the genetic diversity of A. pardalis (21), S. cuspicaudus (24), and P. grosskopfii (18). The microsatellite loci of A. pardalis and S. cuspicaudus represent the first species-specific codominant markers for both Neotropical genera. Along with the above, the new 18 microsatellite loci for P. grosskopfii complement the currently available markers (Agostini et al., 2011). Pyrosequencing also allowed us to examine the richness of microsatellite motifs of the species and compare them with the information available for eukaryotic organisms (Meglécz et al., 2012), particularly bony fishes (Osteichthyes) of the order Siluriformes (Somridhivej et al., 2008; Mohindra et al., 2012; Zhang et al., 2014), Characiformes (Villanova et al., 2015; Yazbeck et al., 2018), Cypriniformes (Luo et al., 2012; Jorge et al., 2018), Perciformes (Saarinen, Austin, 2010), and Tetraodontiformes (Edwards et al., 1998).

Superficial sequencing on A. pardalis, P. grosskopfii, and S. cuspicaudus, showed a higher frequency of 2-mer motifs; a characteristic previously described for several eukaryotic organisms (Meglécz et al., 2012). Additionally, in this study, 4-mer are the second most frequent motif for the three species studied, a similar outcome to others fishes such as Megaleporinus obtusidens (=Leporinus obtusidens in Villanova et al., 2015); Craterocephalus fluviatilis, Galaxias fuscus, Henicorhynchus lobatus, Henicorhynchus siamensis, Alticus arnoldorum, Amphiprion sandaracinos and Amphiprion mccullochi (Meglécz et al., 2012). This result is in contrast however, to others species of fishes such as Ictalurus punctatus (Somridhivej et al., 2008), Clarias batrachus (Mohindra et al., 2012), Tachysurus fulvidraco (=Pelteobagrus fulvidraco in Zhang et al., 2014), Brycon orbignyanus (Yazbeck et al., 2018) and Schizothorax biddulphi (Luo et al., 2012), which exhibit 3-mer as the second most frequent motif.

The high frequency of the AC repeat motif is concordant with that described for all the Chordata phylum species, especially for the species of the Actinopterygii class (Meglécz et al., 2012). Similarly, the low frequency of the CG repeat motif found in this work is consistent with that described for most eukaryotic species (Meglécz et al., 2012). The most common repeat motifs found in this work, AC and ATT, have been described in bony fishes such as Rhamdia sp. (Rodrigues et al., 2015), I. punctatus (Somridhivej et al., 2008), C. batrachus (Mohindra et al., 2012), T. fulvidraco (Zhang et al., 2014), M. obtusidens (Villanova et al., 2015), S. biddulphi (Luo et al., 2012), and Etheostoma okaloosae (Saarinen, Austin, 2010). However, the frequency of the ATT motif differs from that found in Piaractus brachypomus (AGC, Jorge et al., 2018) and Takifugu rubripes (AGG; Edwards et al., 1998). The most frequent 4-mer motifs repeat found for the three studied catfish species (AAAT, ATCT, TCTG, AGTG, and AATG) are also among the most frequent for other catfishes, such as I. punctatus (Somridhivej et al., 2008), C. batrachus (Mohindra et al., 2012) and T. fulvidraco (Zhang et al., 2014), as well as other Neotropical fishes such as P. brachypomus (Jorge et al., 2018) and M. obtusidens (Villanova et al., 2015).

All the microsatellite loci developed in this work (except Scus11) have PIC values that allow them to be considered highly informative according to the classification proposed by Botstein et al. (1980), and also are higher than those described for Brachyplatystoma rousseauxii (PIC: 0.207-0.910; Batista et al., 2010), Microglanis cottoides (PIC: 0.115-0.927, Souza-Shibatta et al., 2013), Steindachneridion parahybae (PIC: 0.429; Fonseca et al., 2016), Hypostomus ancistroides (PIC: 0.089-0.880; Galindo et al., 2015), and Pterygoplichthys pardalis (PIC: 0.294-0.880; Pereira et al., 2012). Moreover, the loci designed for A. pardalis and S. cuspicaudus showed evidence of linkage equilibrium and most of their allelic frequencies are in Hardy-Weinberg equilibrium, which make them highly informative for determining the diversity and structure of populations of these species. In contrast, most of the loci of P. grosskopfii showed allelic frequencies deviated from the Hardy-Weinberg equilibrium and two pairs of loci showed signals of linkage disequilibrium. It remains to be explored if these characteristics are technical problems or a consequence of the high levels of exploitation of P. grosskopfii. The linkage disequilibrium has been described in some pairs of loci for the exploited species B. rousseauxii (Batista et al., 2010), S. parahybae (Fonseca et al., 2016), and Pimelodus maculatus (Paiva, Kalapothakis, 2008).

Despite the high frequency of the 2-mer motifs, the microsatellite loci selected in this work were preferentially perfect repeats of 3-mer, 4-mer, and 5-mer motifs; because these type of motifs (uninterrupted and longer monomer) are most recommended in practice, due to their ease in genotyping and classifying the alleles (Gusmão et al., 2006; Castoe et al., 2010, ²⁰¹²; Guichoux et al., 2011). Contrary to the expectation for longer repeat motifs, the average number of alleles/locus found for A. pardalis, P. grosskopfii, and S. cuspicaudus is higher than those 2-mer microsatellite loci found in other Neotropical catfishes (Revaldaves et al., 2005; Moeser, Bermingham, 2005; Paiva, Kalapothakis, 2008; Rodrigues et al., 2009, 2015; Carrillo-Ávila et al., 2009; Zamudio et al., 2009; Batista et al., 2010; Telles et al., 2010; Agostini et al., 2011; Carvalho, Beheregaray, 2011; Saulo-Machado et al., 2011; Muñoz-Rojas et al., 2012; Pereira et al., 2012; Souza et al., 2012; Souza-Shibatta et al., 2013; Prado et al., 2014; Galindo et al., 2015; Ojeda et al., 2016).

Levels of observed and expected heterozygosity for A. pardalis and S. cuspicaudus are higher than those reported in microsatellite loci developed for other Neotropical catfishes (Moeser, Bermingham, 2005; Revaldaves et al., 2005; Paiva and Kalapothakis, 2008; Rodrigues et al., 2009, 2015; Carrillo-Ávila et al., 2009; Zamudio et al., 2009; Batista et al., 2010; Telles et al., 2010; Agostini et al., 2011; Carvalho, Beheregaray, 2011; Saulo-Machado et al., 2011; Souza et al., 2012; Muñoz-Rojas et al., 2012; Pereira et al., 2012; Souza-Shibatta et al., 2013; Prado et al., 2014; Ojeda et al., 2016). Additionally, the microsatellite loci identified in this work for P. grosskopfii showed average values of alleles/locus and expected heterozygosity greater than those previously designed for this species by Hernandez-Escobar et al. (2011). Thus, we recommend the loci developed in this work for future population genetic studies and monitoring of populations and stocks of A. pardalis, P. grosskopfii, and S. cuspicaudus required in different conservation measures for these species.

Acknowledgments​

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This work was funded by the Universidad Nacional de Colombia, Sede Medellín and Empresas Públicas de Medellín, Grant CT-2013-002443 “Variación genotípica y fenotípica de poblaciones de especies reófilas presentes en el área de influencia del proyecto hidroeléctrico Ituango”. We thank the engineering consulting company Integral S.A., for providing the field samples used in this work.

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Authors

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Natalia Restrepo-Escobar¹ and Edna J. Márquez¹

^[1]    Facultad de Ciencias, Escuela de Biociencias, Laboratorio de Biología Molecular y Celular, Universidad Nacional de Colombia -Sede Medellín. Carrera 65 Nro. 59A – 110 Bloque 19 A Laboratorio 310, 050034 Medellín, Colombia. (NRE) nrestree@unal.edu.co, (EJM) ejmarque@unal.edu.co

Authors’ Contribution

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Natalia Restrepo-Escobar: Conceptualization, Data curation, Formal Analysis, Funding acquisition, Investigation, Methodology, Validation, Visualization, Writing (original draft), Writing (review & editing).

Edna J. Márquez: Conceptualization, Data curation, Formal Analysis, Funding acquisition, Investigation, Methodology, Project administration, Resources, Supervision, Validation, Visualization, Writing (original draft), Writing (review & editing).

Ethical Statement​

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Samples were collected under the environmental license # 0155 of January 30, 2009 from Ministerio de Ambiente, Vivienda y Desarrollo Territorial.

Competing Interests

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Not applicable.

How to cite this article

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Restrepo-Escobar N, Márquez EJ. Microsatellite loci development for three catfish species from northwestern South America. Neotrop Ichthyol. 2020; 18(1):e190079. https://doi. org/10.1590/1982-0224-2019-0079

Copyright​

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This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

Distributed under

Creative Commons CC-BY 4.0

© 2020 The Authors.

Diversity and Distributions Published by SBI

Accepted December 19, 2019 by Guillermo Orti

Submitted July 24, 2019

Epub April 20, 2020