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.

Morphological and Genetic Diversity Studies of Chrysichthys nigrodigitatus from the Cross River, Nigeria, Using Microsatellite Markers

“…Similar to our findings, [25] concluded that the observed morphometric differences in C. nigrodigitatus samples from Lagos Lekki and Badagry Lagoon were related to environmental and climatic differences and were therefore phenotypic rather than genetic. This argument by [25] is concurred by [26] who reported that there is greater than 99 per cent homology between specimens of Chrysichthys nigrodigitatus from the Cross River in both lower and middle Cross River which constitute the sampling area of the present study. Cluster analysis of morphometric data of C. nigrodigitatus in this study also showed good differentiation between sampling locations.…”

“…Such reduction in the size of a population can reduce variations in a gene pool, leaving a limited number of species to pass on genes to offspring through sexual reproduction. Earlier studies of C. nigrodigitatus from Cross River region of the Niger Delta using mtDNA and AFLP analyses reached similar conclusions of low genetic diversity [9,10,26].…”

“…It is worth noting that different methods applied by different authors, AFLP [9], mt DNA [10], Microsatellite [12,14] and ribosomal RNA and Internal transcribed spacers [26] all revealed the low genetic diversity of Chrysichthys nigrodigitatus of the Cross River. This therefore lends credence to the reliability of this study and its findings.…”

Ecology and population dynamics of silver catfish, <I>Chrysichthys nigrodigitatus</I> (Siluriformes: Claroteidae), of the Cross River, Nigeria

“…This may also be the reason the species are less in abundance in the dry season with high temperatures. Moreover, Uyoh et al (2020) and Adelieje, et al;(2020) reported that Chrysichthys nigrodigitatus population of the Cross River has very low genetic diversity. Such low genetic variation could lead to spontaneous wipe out of populations in the face of environmental variability and may likely contribute to the increase in natural mortality observed here.…”

“…Moses (2001) reported that flood regime was important in recruitment and abundance in succeeding years of spawning, as a result of climatic phenomena, including rainfall and flooding. Uyoh et al (2020) reported that Chrysichthys nigrodigitatus of the Cross River has very low genetic diversity and that such low genetic diversity can lead to population eradication in the face of environmental variability. The linkage of the species to climatic phenomena, the enlisting of it in the IUCN Red list of endangered species and the reported low genetic diversity underscore the need for regular assessment of its population to provide proactive management measures in the face of climate change and environmental variability.…”