dna barcoding gene cytochrome c oxidase subunit i of channa species in the mekong delta

CAN THO UNIVERSITY COLLEGE OF AQUACULTURE AND FISHERIES DNA BARCODING GENE CYTOCHROME C OXIDASE SUBUNIT I OF CHANNA SPECIES IN THE MEKONG DELTA By NGUYEN THI NGOC TRAN A thesis submitted in partial fulfillment of the requirements for the degree of Bachelor of Aquaculture Science Can Tho, December 2014 CAN THO UNIVERSITY COLLEGE OF AQUACULTURE AND FISHERIES DNA BARCODING GENE CYTOCHROME C OXIDASE SUBUNIT I OF CHANNA SPECIES IN THE MEKONG DELTA By NGUYEN THI NGOC TRAN A thesis submitted in partial fulfillment of the requirements for the degree of Bachelor of Aquaculture Science Supervisor Dr. DUONG THUY YEN Can Tho, December 2014 DNA BARCODING GENE CYTOCHROME C OXIDASE SUBUNIT I OF CHANNA SPECIES IN THE MEKONG DELTA Nguyen Thi Ngoc Tran 1 and Duong Thuy Yen 2 1 Advanced Aquaculture Course 36 2 Department of Freshwater Aquaculture College of Aquaculture and Fisheries, Can Tho University Email: tran108566@student.ctu.edu.vn ABSTRACT Channa species are indigenous freshwater fish that are important for aquaculture in Vietnam. This genus shows a variety of variation in morphology, resulting in 7 different local names while only 4 speices, including Channa striata, Channa micropeltes, Channa lucius, and Channa gachua were scientifically classified. The taxonomic systems of Channa species, especially three newly-observed phenotypes including Projected lip Channa, Triangle head Channa and Square head Channa are still controversial. This study aimed to investigate the taxonomic classification of different phenotypes of Channa species and understand phylogeny relationship of Channa species based on morphological characteristics and DNA barcoding (Cytochrome C oxidase subunit I, COI). Thirty individuals of each phenotype were measured morphological characteristics, and five of these were sequenced COI gene. Morphological results showed that Triangle head Channa and Square head Channa had similar ranges of countable parameters, but were different in the shape of their head. The phylogeny tree based on 684 base-pair region of COI gene showed that 6 Channa species formed 2 large branches with C. striata (and 2 Channa phenotypes) – C. gachua and C. micropeltes – C. lucius. COI gene sequences of 2 undefined species (Triangle head Channa and Square head Channa) were 99% identity with C. striata. Based on countable traits and COI gene, it can be concluded that Triangle head Channa and Square head Channa are the same species with C. striata. Keywords: Channidae, species classification, DNA barcoding, species diversity, morphology 1. INTRODUCTION Channa species are among the most popular species in Viet Nam. There are four species of Channa found in the Mekong Delta of Viet Nam, including Channa striata, Channa micropeltes, Channa lucius, Channa gachua (Truong Thu Khoa and Tran Thi Thu Huong, 1993). Beside these common species there are some new phenotypes that have not been taxonomically classified. They are “triangle head (TH) Channa”, “projected lip (PL) Channa”, “square head (SH) Channa”, which have been cultured popularly in the Mekong Delta and are favorite food for local consumers. Thanks to their high flesh quality and price, culturing them has brought a lot of benefits and improved income for fish farmers in many provinces in Viet Nam such as An Giang, Dong Thap, Ca Mau and Can Tho (Nguyen Bach Loan et al., 2003). In previous studies, Channa species were classified by morphological methods. Channa species had similarities in elongated body and cylinder shape (Truong Thu Khoa and Tran Thi Thu Huong, 1993). Head was broad and flattened with large mouth, strong teeth and projecting lower jaw (Tran Dac Dinh et al., 2013). The dorsal fin was longer than anal fin and beginning the pectoral fin (Rainboth, 1996). C. micropletes was distinguished by the completed lateral line and many black spots 1 in body. C. gachua was recognized by orange edge in the dorsal, anal and caudal fin. The lateral line that broke suddenly in one point and fell into 2 slides of scales belonged to the group of C. lucius and C. striata. However, C. lucius was different from C. striata in the dorsal profile of head concaved (Tran Dac Dinh et al., 2013). Moreover, the appearance of camie tooth of C. lucius helped recognize it from C. striata (Truong Thu Khoa and Tran Thi Thu Huong, 1993). Besides four morphologically distinct species, TH Channa, SH Channa and PL Channa were still on research. A previous study comparing morphological characteristics between PL Channa and C. striata showed that 18 of 20 measurable parameters were significantly different (p[...]... one includes C lucius and C micropeltes, and the other branch consists of C gachua, C striata and two Channa phenotypes Because of no genetic distance within each group of C lucius, C micropeltes, and C gachua and high genetic distance between groups, probability of clustering 5 individuals of each species into the same group was 100% Figure 7 The phylogeny tree of Channa species Specifically, C striata,... position of the eyes than individuals inhabiting streams Those findings indicate that physical characteristics of the reservoirs changed the morphology of fish living in it The shape of head can be one of the most divergent morphological characteristics, as observed in six populations of Clarias gariepinus collected from different rivers systems in Turkey The reasons of those divergences came from differential... species with 2 new phenotypes that are different in morphological characteristics but similar in DNA barcoding 9 Figure 8 The phylogeny tree of Channa striata, square head Channa and triangle head Channa 4 DISCUSSION The important finding of this study shows that the 2 undefined of Channa species (SH Channa and TH Channa) are different in morphology but similar in COI barcoding gene with C striata This... (Figure 9) Figure 9 The phylogeny tree of Channa striata by regions C striata in Vietnam is in the same branch with C striata in Thailand It is also genetically closer to the same species in the Philippines compared to in Malaysia and Indonesia This can be explained by the countries that Mekong River flows through Vietnam and Thailand are in The Indochinese Peninsula This is the first part of Southeast... sequence of each Channa species that had the highest percentage of identity with the aligned species was chosen to compute the genetic distance and the phylogeny tree The result does not change, indicating it is robust This study also has similar in the ranges of genetic divergence with a study about cytochrome b of phylogeny of Channa species in Malaysia (Bui Minh Tam et al., 2007) The intra -species. .. external characteristics Moreover, the genetic distance between species is higher than within species, so it is easy to distinguish among species in Channa genus A study on Cuban freshwater fishes also used DNA barcoding (COI) to have a general view about fish species to help protect species and ecosystem in Cuba Similar to our 11 result, the genetic distance between species of Gambusia genus found in Cuba... Channa, TH Channa locate in the same branch with 2 smaller but more complicated branches (Figure 8) Combining the genetic distance within and between groups of 2 undefined species of Channa and C striata, into the data of Genbank alignment and phylogeny tree, it can be concluded that SH Channa and TH Channa are the same species with C striata These results indicate that C striata is a diversified species. .. Cuba is from 0.016 to 0.181, with at least 4 cryptic species (Ariagna et al., 2009) 5 CONCLUSION AND RECOMMENDATION 5.1 Conclusion TH Channa and SH Channa are the same species with C striata evidenced by similar countable traits and high identity of COI sequence, although they are different in the shape of head Therefore, C striata is more within -species diversified compared to the other species of Channa. .. genus Four Channa species in the Mekong Delta create 2 large branches (C striata – C gachua and C micropeltes – C lucius) in the phylogenetic tree based on COI sequences Genetic distance between species is large (0.1836 – 0.2449), therefore, COI sequence can be used to easily classify Channa species 5.2 Recommendation − Further studies on the reasons leading to the differences in morphology of these phenotypes... while the inter-specific variation ranged 19.7 – 27.5% depending on each species pair The difference of the study in Malaysia was the appearance of 2 species (C melasoma and C marulioides) that have not been found in Viet Nam This study provides more evidence that COI barcoding gene is a powerful tool to complement to traditional taxonomic method Especially, 2 new species of Channa are hard to classify