Abstract
ABSTRACT The Neotropical catfish species Ageneiosus pardalis, Pimelodus grosskopfii, and Sorubim cuspicaudus are important fishery resources in Colombia that show historical declines in their capture. This study used next-generation sequencing with 454 FLX technology (Roche Applied Science) and bioinformatics analysis to develop between 18 and 24 microsatellite loci for these species. The novel microsatellite loci showed high values of polymorphic information content -PIC (A. pardalis: 0.601-0.903, P. grosskopfii: 0.748-0.946 and S. cuspicaudus: 0.383-0.876), and the average number of alleles/locus ranged from 7-15 for A. pardalis, 9-30 for P. grosskopfii and 5-14 for S. cuspicaudus. The average observed and expected heterozygosities were respectively, 0.757 ± 0.035 and 0.834 ± 0.015 for A. pardalis; 0.596 ± 0.040 and 0.881 ± 0.009 for P. grosskopfii; and 0.747 ± 0.031 and 0.757 ± 0.025 for S. cuspicaudus. For future studies, these loci can be useful to estimate the genetic diversity and population structure in these three Neotropical catfishes.
Highlights
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); those affected by different anthropogenic activities (Frankham, 2010)
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)
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
Summary
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); 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). 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). Nextgeneration 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), for the vast majority of fish species these markers are still limited or absent (Kumar, Kocour, 2017). 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
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