Comparative application of direct sequencing, PCR-RFLP, and cytogenetic markers in the genetic characterization of Pimelodus (Siluriformes: Pimelodidae) species: Possible implications for fish conservation

Abstract

ABSTRACT. Pimelodus (Pimelodidae) is a genus comprising a group of South American species with complex taxonomic relationships. Cytogenetics, polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP), and sequencing data of mitochondrial genes were analyzed to characterize 4 Pimelodus species: P. fur, P. heraldoi, P. maculatus, and Pimelodus sp. All populations presented 2n = 56 chromosomes and distinct karyotypic formulae. The heterochromatin distribution pattern and the number and location of 5S and 18S rDNA sites are discussed. The application of PCR-RFLP markers and sequencing of mitochondrial DNA genes provided species-specific haplotypes, which allowed us to differentiate the species studied. The mitochondrial gene sequences presented nucleotide mutations in the restriction sites and throughout the sequences, and they were mostly related to synonymous substitutions in the coded proteins; however, they did not affect the protein and its function. Comparing the data obtained using these 3 methodologies, the existence of a species complex in P. maculatus along the basins studied might be inferred, showing that cytogenetics is an important tool in studies focusing on the conservation or management of both natural and captive populations of these fishes.

Contributions to the systematic of Pimelodidae (Osteichthyes, Siluriformes): basic and molecular cytogenetics on seven species of Pimelodus from three Brazilian hydrographic systems

“…These differences in the amount and arrangement of the 5S rDNA sites may indicate the existence of more than one species. According to Ferreira et al (2014), although the populations of the Upper Paraná and São Francisco river basins are not morphologically differentiated, PCR-RFLP data and genetic sequencing indicate the existence of genetically distinct but related groups, which corroborates the hypothesis also suggested by the authors.…”

“…In the Ijuí River, 5S rDNA was located in the terminal position of the long arm of a pair of subtelocentric chromosomes, and for the first time, it was observed syntenic with 18S rDNA in P. maculatus. Populations of the Upper Paraná River studied by Ferreira et al (2014) also show a single pair with 5S rDNA sites. Garcia, Moreira-Filho (2008) performed cytogenetic studies in the P. maculatus population of the São Francisco River and observed 5S rDNA in three pairs of chromosomes.…”

“…Cytogenetic studies in several populations show maintenance of the diploid number with variation in the karyotypic formula. According to Ferreira et al (2014), these variations are subtle and may be related to different patterns of condensation of the chromosomal preparations or due to the fixation of distinct chromosomal rearrangements during the evolutionary process of each population. The population of the Ijuí River studied here presents a karyotypic formula and distribution pattern of heterochromatin similar to the Lake Guaíba population studied by Treco et al (2008), which may indicate close evolutionary history between them.…”

Pimelodus maculatus (Siluriformes, Pimelodidae): complete mtDNA sequence of an economically important fish from the São Francisco river basin

“…Several genetic studies of partial mitochondrial and nuclear regions of P. maculatus have found a high degree of genetic diversity among populations (Garcia & Moreira Filho 2005;Paiva & Kalapothakis 2008;Carvalho et al 2011;Lundberg et al 2011;Pereira et al 2011;Ribolli et al 2012;Ferreira et al 2014;Frantine-Silva et al 2015). Here, we provide the first description of the complete mitochondrial DNA (mtDNA) sequence for P. maculatus, which could support the development of molecular markers studies to aid wildlife forensics, evolutionary approaches, and conservation and management studies.…”