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North African Sharptooth Catfish Clarias Gariepinus: in Silico

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North African Sharptooth Catfish Clarias Gariepinus: in Silico Journal of Bioscience and Applied Research2015, Vol.1, No.4, PP.184-191 pISSN: 2356-9174, eISSN: 2356-9182 184 Journal of Bioscience and Applied Research WWW.JBSAR.com North African sharptooth catfish Clarias gariepinus: In silico analyses for genetic expansion of a peculiarly successful catfish species in and out of its African homelands Khaled Mohammed-Geba Molecular Biology and Genetic Engineering Division, Department of Zoology, Faculty of Sciences, Menoufia University, Shebin El- Kom, Menoufia, Egypt. Tel.: 002-0482235690, fax.: 002-0482235689 (Email: [email protected]) Abstract The African sharptooth catfish Clarias gariepinus 1 Introduction originated from Africa, but its sturdiness and resistance to different environmental conditions enabled it to spread to Africa is the hosting continent for many catfish species, almost all continents of the world. To develop effective belonging to varying siluriform families that inhabit its conservation strategies for C. gariepinus, the connection inland water since very long time, mainly Amphiliidae patterns of its geographically related and isolated strains (loach catfishes), Anchariidae (Malagasy catfishes), Ariidae should be precisely described. For this purpose, 65 (shark catfishes), Austroglanididae (southern rock catfish), sequences for cytochrome oxidase subunit 1 (CO1) Bagridae (naked catfishes), Clariidae (the air-breathing or mitochondrial gene were retrieved from GenBank database. walking catfishes), Claroteidae (giraffe catfishes), Common and unique haplotypes, average numbers of Malapteruridae (electric catfishes), Mochokidae (upside down catfishes), and Schilbeidae (glass catfishes) (Zhang, nucleotide substitutions (Dxy), fixation indices (FST), neutrality and expansion, phylogeny, and haplotype 2011; www.Fishbase.org). However, catfishes are well- network analyses were all identified. 13 different known in all continents on earth; with a fossil record haplotypes were found, most of which are related to an extending back to the late Cretaceous found all around the African haplotype mainly found in Nigeria. Other African, world except Australia (Nilson, 2006). Siluriformes are Asian, and South American haplotypes were detected, with believed to be the second primitive-most group in the taxon the South American and some Asian haplotypes showing Otophysi, newer than Cypriniformes but elder than the greatest diversion from the main African one. The Characiformes and Gymnotiformes. Many evidences point Nigerian population of C. gariepinus seems to be the most to that the origin of siluriformes is the new world, more rapidly expanding one, due to the highest frequency of strictly South America. The oldest siluriform fossil singletone haplotypes among all studied populations. Our discovered so far was in Argentina. Furthermore, the most results agreed with the knowledge about the world-wide apomorphic catfish species that are adapted to sea water are propagation of C. gariepinus recorded in the Food and also found in South America; that are Ariidae and Agriculture Organization introduced aquatic species Plotosidae. This latter finding led to a commonly accepted database and other related reports, what may confirm the hypothesis that the evolution of catfish taxa proceeded in effectiveness of such molecular markers and bioinformatic South America, before the separation from Africa. tools for tracking the origin and movement of the C. Separation of Australia might be earlier than the gariepinus out of Africa. completeness of this catfish evolution event due to the complete absence of siluriformes from there. Moreover, the most primitive families are found in the New World also: Keywords: Africa,Clarias gariepinus, CO1, molecular the extinct Diplomystidae in Argentina and Chile, and the markers, population genetics. Journal of Bioscience and Applied Research2015, Vol.1, No.4, PP.184-191 pISSN: 2356-9174, eISSN: 2356-9182 185 fossil Hypsidoridae in USA (Briggs, 2005). In the modern in the GenBank database were retrieved. These era, world siluriformes are categorized in 478 genera sequences came from 65 C. gariepinus samples that containing 3093 species. Most of them are freshwater were obtained, DNA-extracted, and barcoded by CO1 inhabitants, but only 2 families are marine, as mentioned PCRs in different countries, as follows: 5 from Brazil, before. 2 from Indonesia, 17 from Nigeria, 11 from Thailand, In terms of modern ecological states and economies, catfishes are among the relatively low-value species, yet 21 from Turkey, 7 from India, 1 from Syria and 1 contribute well to the international aquaculture products from Ethiopia. The sequences were uploaded to the trade (FAO, 2014). The North African catfish Clarias program MEGA6 (Tamura et al. 2013) and aligned gariepinus gains special popularity in Africa and other areas using ClustalW (Thompson et al. 1994). The where it is cultivated due to its tolerance to extreme sequences were then trimmed to obtain a final environmental conditions, capability of air breathing under common zone of a 513 base-long gene fragment. Best dry conditions and omnivorousity (FAO, 2010). Since the DNA substitution model was determined by start of the millennia, its production increased more than 30 ModelTest procedure integrated in MEGA 6 folds. Nigeria dominates the production of North African Software. Based on this, a neighbor-joining catfish in the world. Netherlands, Italy, Hungary, Kenya, phylogenetic tree was constructed. 1,000 bootstraps Syria, Brazil, Cameroon, Mali and South Africa account also for significant productions. The fish was also were used to enhance the quality of the test. introduced to Jordan, Turkey, Lebanon, and other Asian and The alignment was then uploaded to DNAsp 5.0 South American countries (FAO, 2010). Software (Rozas et al. 2003) in order to determine the To develop effective conservation strategies for the North haplotypes existing in common and separately withtin African catfish and obtain a better understanding for its the selected CO1 fragment, together with haplotype physiological responses under different rearing conditions, (h) and nucleotide (π) diversity indices. Also, recent the connections of its different, geographically related and population expansions as detected by the increasing isolated strains should be precisely described by detailed diversity of haplotypes in a given population and the genealogical studies based on DNA markers. The homogenous patterns of pairwise differences among mitochondrial enzyme cytochrome C oxidase subunit 1 them were inferred from calculating the index of (CO1) gene has been particularly popular for estimating relationships among closely allied taxa and efficient raggedness, r (Harpending, 1994) and R2 parameter elucidation of biological diversity. (Ramos-Onsins and Rozas, 2002). DNA barcode technology, using short CO1 sequences, has The haplotypes determined through DNAsp 5.0 been proposed as a method for enabling rapid, accurate Software were then uploaded to the program Network detection and identification of species. This method is 4.6.1.2 (Bandelt et al. 1999) in order to draw median- accepted as a standard for characterization of life forms in joining haplotype network and further demonstrate numerous groups of living organisms, i.e. DNA- the interrelationships among different haplotypes. fingerprinting of these organisms. It is now being proposed Average number of nucleotide substitutions per site as a method for cataloguing life and developing a between populations, pairwise genetic differences comprehensive species-specific sequence library for all between samples using the F-statistics, based on eukaryotes (Marshall, 2005; Hajibabaei et al. 2007; Yu et al, 2011). This approach will significantly broaden the haplotypes frequencies, and the Fst value, based on application of DNA barcoding in biodiversity studies. DNA haplotypes frequencies and sequence divergences barcoding is increasingly used in studies with the North between them-were all estimated using the software African Catfish, for example, in order to detect species ARLEQUIN 3.5.1.1 (Excoffier and Lischer 2010). substitution for market control and combating the Components of variability among samples were unsustainable commercial use of vulnerable species (Wong partitioned using the analysis of molecular variance et al. 2011), to identify commercially important species in (AMOVA, Excoffier et al. 1992), integrated to the fish market (Keskin and Atar, 2013), and to infer the ARLEQUIN 3.5.1.1, after merging the sequences phylogenetic relationships with other siluriform species according to the results of the phylogenetic tree. (Indu et al. 2012). The aim of this work is to use the CO1 Moreover, neutrality analysis was performed by partial gene sequences to understand the spread of C. gariepinus in and out of Africa, and the relationship determining the D test statistic of Tajima (1989), and between its different world-wide populations and their the Fs statistic of Fu (Fu, 1997), whose negative possible genetic interactions, using several in silico values arise due to the excess of low-frequency bioinformatic analyses. haplotypes that arise from selection or rapid population growth (Tajima, 1989; Borrell et al. 2012). 2 Materials and Methods 3 Results Sixty five (65) Clarias gariepinus cytochrome A phylogenetic, neighbor-joining tree was calculated oxidase 1 gene (CO1) nucleotide sequences available by progressive aligning the 65 CO1 nucleotide Journal of Bioscience and Applied Research2015,
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