DNA barcoding of freshwater fishes from Brahmaputra River in Eastern Himalaya biodiversity hotspot

Abstract

The genetic diversity of freshwater fishes is still anonymous in several drainage systems in northeast India. Moreover, the comparative genetic analysis is largely sporadic to judge their actual diversity and true status. We generated 89 DNA barcodes of 40 morphologically identified fishes collected from two major tributaries of Brahmaputra River. The comparative study revealed that most of the species were clearly discriminated by their estimated genetic distances and monophyletic clustering in Bayesian (BA) tree. Considering the genetic divergence (2%) for species discrimination boundary, the high genetic diversity (2.36–10.73%) was detected in 11 species ( Macrognathus pancalus , Channa punctata , Puntius terio , Bangana ariza , Garra arupi , Badis badis , Mystus vittatus , Rita rita , Gagata cenia , Mastacembelus armatus , and Danio dangila ), which signified the occurrence of concealed genetic diversity in this ecozone. However, the insignificant genetic distances were also noticed in few reportedly valid species: Channa stiktos and C. ornatipinnis (1.43%); Mystus ngasep , M. rufescens , and M. carcio (0.4%); Glyptothorax trilineatus , G. churamanii , and G. verrucosus (0.4%); Botia almorhae , B. histrionica , B. lohachata , and B. rostrata (0–0.4%); Barilius barilia and B. vagra (0.4%); Batasio merianiensis and B. tengana (1.2%); Puntius chola and P. fraseri (0%), Schistura beavani and S. paucireticulata (0%); hence to validate this species, generation of more barcode data was required from their types or topotypes. The present study would help to develop conservation schemes for the native species and collegiate ecosystem, which associated with the livelihoods of millions of ethnic communities in this region.

DNA barcoding of a lesser-known catfish, Clupisoma bastari (Actinopterygii: Ailiidae) from Deccan Peninsula, India

“…Besides traditional taxonomy, the molecular data is effectively evidenced to identify and distinguish freshwater fishes around the world (Hubert et al 2008;Ward et al 2009;Steinke et al 2009;April et al 2011;Collins et al 2012). Several small to large-scale attempts have been endeavored to build-up the DNA barcode reference library of freshwater fishes from India and neighboring countries, aiming to quick and reliable species identification and to illuminate species diversity from different biogeographic zones (Khedkar et al 2014;Chen et al 2015;Barman et al 2018;Laskar et al 2018;Kundu et al 2019;Rahman et al 2019). Although, the GenBank database holds several publicly available DNA barcode sequences of Clupisoma species, the genetic information on C. bastari was lacking.…”

DNA barcoding identification of Perciform fishes of the Arabian Gulf commercially harvested in Qatar

“…Since it was developed by Hebert et al (2003) the DNA, barcoding technique has been used for the identification of both marine and freshwater fish species in many countries and regions across the world (Ardura et al, 2010;Zhang, 2011;Mabragana et al, 2011;Abbas et al, 2017;Popa et al, 2017;Bingpeng et al, 2018;Wang et al, 2018;Kundu et al, 2019;Panpromminet al, 2019). The success of identifying fishes with mtDNA CO1 gene barcode ranged from 93 to 100% (Ivanova et al, 2007;Hubert et al, 2008;Steinke et al, 2009).…”

DNA barcoding of commercially relevant marine fish species in Tunisian waters

“…DNA barcoding has been applied not only for the identification of fish species and products (Smith et al ., 2008; Lakra et al ., 2011; Triantafyllidis et al ., 2011; Malakar et al ., 2012; Di Pinto et al ., 2015) but also for fish product examination such as fillets, fins, fragments, canned fish, dried fish and mixtures, conservation of threatened and endangered species, identification of fish eggs and larvae, identification of prey items in stomach contents (Soininen et al ., 2009; Barman et al ., 2012), identification of new species, population structure assessment, phylogenetics and biodiversity assessment (Bingpeng et al ., 2018; Rabaoui et al ., 2019; Ghouri et al ., 2020). To date, DNA barcoding has been applied for the identification of more than 6000 species of marine and freshwater fish in many countries and regions around the world (Ward et al ., 2009; Ardura et al ., 2010; Zhang, 2011; Mabragana et al ., 2011; Keskin & Atar, 2013; Abbas et al ., 2017; Paracchini et al ., 2017; Kundu et al ., 2019; Ghouri et al ., 2020). Their COI sequences have been deposited in the Barcode of Life Data Systems (BOLD) and GenBank nucleotide database (NCBI; Ward et al ., 2005; Ratnasingham & Hebert, 2007; Lakra et al ., 2011).…”