Molecular Characterization of Two Catfish Species (Chrysichthys nigrodigitatus and Chrysichthys auratus) from the Cross River, Nigeria, Using Ribosomal RNA and Internal Transcribed Spacers

Abstract

Studies were conducted on Chrysichthys nigrodigitatus and C. auratus from the Cross River, Nigeria. The objective was to document intra- and inter-specific variations in molecular structure among four populations of the genus in the river. DNA was extracted from caudal fin and primers designed for the ribosomal RNA and Internal Transcribed Spacer Region were used for amplification. Molecular characterization yielded a fragment containing partial sequences of 18S rRNA, ITS-1, ITS-2 and 28S rRNA genes and a complete sequence of 5.8S rRNA. The 5.8S rRNA was the only gene amplified consistently in all samples indicating that it is more conserved among the samples studied. The percentage of GC contents fall within the range observed in other catfish species. They were generally higher in C. auratus than in C. nigrodigitatus and also higher than the AT contents in both species. The high GC content could be an adaptation to warmer climates. Alignment of the nucleotide sequences of the two species from the two regions showed that the rRNA and ITS genes are highly conserved with >99% nucleotide identity. However, a total of 284 single nucleotide polymorphisms (SNPs) were observed in these genes in the two species, made up of deletions (0.35%), single base insertions (11.27%), multiple base insertions (14.39%), single base transition substitutions (29.93%), single base transversion substitutions (33.8%) and multiple base substitutions (11.27%). The overall ratio of transition to transversion polymorphisms was approximately 1: 1 indicating a low level of genetic instability in Chrysichthys spp. The indels were responsible for length variations in the sequences. Sequence information for the ITS region of these fishes is reported for the first time. This study has provided an insight into polymorphism patterns of these genes in Chrysichthys spp across the four populations studied which could form the basis for further genomic characterization and mapping of these species.