Genomic organization of repetitive DNAs highlights chromosomal evolution in the genus Clarias (Clariidae, Siluriformes)

Abstract

BackgroundThe genus Clarias (Clariidae, Siluriformes) contains at least 61 species naturally spread over vast regions of Asia, India and Africa. However, Clarias species have also been introduced in many different countries and represent the most widespread catfishes in the world. These fishes are also known as “walking catfishes” due to their ability to move over land. A large degree of chromosomal variation has been previously found in this family, mainly using conventional cytogenetic investigations, with diploid chromosome numbers ranging between 48 and 100. In this study, we analyzed the karyotype structure and distribution of four repetitive DNA sequences (5S and 18S rDNAs and (CA)15 and (GA)15 microsatellites) in three Clarias species (C. batrachus, C. gariepinus, C. macrocephalus), as well as in a probable natural hybrid of the two latter species from different Thailand river basins.ResultsClarias gariepinus and C. macrocephalus had 2n = 56 and 2n = 54, respectively, as well as karyotypes composed mainly by metacentric and submetacentric chromosomes. Their karyotypes differed in the number and location of 5S and 18S rDNA sites and in the degree of microsatellite accumulation. An intermediate chromosomal pattern incorporating those of the parental species was found in the probable hybrid, confirming its interspecific origin. Clarias batrachus had 2n = 104 chromosomes and its karyotype was dominated by mainly acrocentric elements, indicating that unusual multiple centric fissions were involved in its karyotype differentiation. The karyotype of this species presented an unexpected dispersion of ribosomal DNAs, possessing 54 and 12 sites of 5S and 18S rDNAs, respectively, as well as a high accumulation and differential distribution of both microsatellite repeats, representing ‘hot spots’ for chromosomal rearrangement.ConclusionBoth conventional and molecular cytogenetic markers were useful tools for demonstrating remarkable evolutionary dynamism and highlighting multiple chromosomal rearrangements and hybridization events correlated with the notable karyotypic diversity of these walking catfishes.

First chromosome analysis of Thai pufferfish Pao cochinchinensis (Steindachner, 1866)

“…Comparisons with other families revealed that the d(CA)15 microsatellite repeats mapping are similar to the nine species of the Bagridae family including Hemibagrus filamentus, H. spilopterus, H. wyckii, H. wyckioides, Mystus atrifasciatus, M. multiradiatus, M. mysticetus, M. bocourti, andPseudomystus siamensis (Supiwong et al 2013a, 2014b), Clarias batrachus and C. macrocephalus (Maneechot et al 2016), Toxotes chatareus (Supiwong et al 2017). This pattern can be found in non-Thai fish species.…”

“…However, this kind of study is scarcely applied in Thai freshwater fish. Exceptions are studies in Bagrid catfishes (Supiwong et al 2013(Supiwong et al , 2014a, Channids (Cioffi et al 2015), three Clarias species (Maneechot et al 2016), Toxotes chatareus (Hamilton, 1822) (Supiwong et al 2017), two cyprinid fishes (Saenjundaeng et al 2018), Asian swamp eel, Monopterus albus (Zuiew, 1793) (Supiwong et al 2019) and silulid catfishes (Ditcharoen et al 2019). The present study is the first report on chromosomal characteristics in P. cochinchinensis using conventional staining, Ag-NOR banding, and FISH technique, being the basis for further study by advanced genetics and for future comparative approaches concerning systematics and evolutionary relationships of buffer-fishes.…”

Dietary supplementation with low molecular weight sodium alginate improves growth, haematology, immune reactions and resistance againstAeromonas hydrophilainClarias gariepinus

“…In the last few years, demand has increased for low cost animal protein sources to close the gap between production and the growing population. Thus, most countries have turned to cultured Clarias species for their high reproductive capacity under natural and controlled conditions, high growth rate, tolerance of bad water conditions and high nutritional value (Ikpi & Offem, ; Khan & Abidi, ; Maneechot et al, ). Several trials using herbal and alternative medicine in fish culture (Hoseinifar et al, ) have been performed to overcome the side effects of using antibiotics for controlling different diseases that cause severe issues in humans, especially drug resistance and antibiotic residues (Chafer‐Pericas et al, ; Obaidat, Salman, & Lafi, ; Park, Jung, & Lee, ).…”

“…Clarias species for their high reproductive capacity under natural and controlled conditions, high growth rate, tolerance of bad water conditions and high nutritional value (Ikpi & Offem, 2011;Khan & Abidi, 2011;Maneechot et al, 2016). Several trials using herbal and alternative medicine in fish culture (Hoseinifar et al, 2015) have been performed to overcome the side effects of using antibiotics for controlling different diseases that cause severe issues in humans, especially drug resistance and antibiotic residues (Valente et al, 2006).…”

Dynamics of tandemly repeated DNA sequences during evolution of diploid and tetraploid botiid loaches (Teleostei: Cobitoidea: Botiidae)

“…lecontei . Over the last decade, many studies have provided evidence of rapidly amplified loci for both major and minor rDNA class in fishes ([ 106 , 107 ] and references therein) including both nascent and ancient polyploids [ 28 , 31 , 33 , 98 ]. Several mechanisms have been put forward to explain this phenomenon including i) unequal crossing-over and ectopic recombination ii) activity of transposable elements (TEs), iii) extrachromosomal replication and reintegration via extrachromosomal circles of rDNA or combined effect of the three (for comprehensive discussion, see: [ 115 , 116 ]).…”