DNA barcoding of cyprinids (Labeo rohita, Catla catla and Cirrhinus mrigala), mitochondrial CO1-based study

Abstract

For DNA barcoding, the Cytochrome C Oxidase 1 gene (CO1) is a genetic marker used as uniform, testimonial authentication and reliable evidence for a universal species-level bio-cataloguing system compared with the morphological identification. The barcoding of Catla catla, Cirrhinus mrigala and Labeo rohita of family Cyprinidae was accomplished in the present study. Amplified CO1 gene through PCR was sequenced and figured out using bioinformatic tools. Conspecific and congeneric, K2P nucleotide deviation and nucleotide composition, the number of haplotypes and haplotype diversity were calculated. All three species of studied fish (C. catla, L. rohita and C. mrigala) were G-deficient (17.2, 17.8 and 18.5%) than C (28.3, 27.0, 27.3), A (25.2, 27.3, 26.8) and T (28.0, 28.5, 28.1), respectively. The mean intraspecific and intergeneric K2P genetic distance was .031% and 1.23%, respectively, with a high rate of transitional substitutions. Study revealed that C. catla followed the neutral evolution (R ¼ .5), while C. mrigala (R ¼ 2.01) and L. rohita (R ¼ 2.84) deviated from it and offered very low genetic diversity (<.55).

The native and exotic prey community of two invasive paper wasps (Hymenoptera: Vespidae) in New Zealand as determined by DNA barcoding

“…Selected universal primers are then used in the polymerase chain reaction (PCR) to target the specific gene homologues (Valentini et al 2009). Genes that are conserved across a wide range of species, such as cytochrome c oxidase subunit 1 (COI), are often used in DNA barcoding studies (Hebert et al 2004;Steinke and Hanner 2011;Wirta et al 2015;Cheng and Lin 2016;Turanov et al 2016;Ayesha et al 2019). The COI mitochondrial gene is an ideal candidate gene for DNA barcoding as it has been conserved across many taxonomic groups yet has enough variation to allow for the identification of organisms to the species level (Hebert et al 2003).…”

Identification and determination of phylogenetic relationship amongLabeo rohita, Labeo catlaand their reciprocal hybrids by traditional and molecular tools

“…The total number of haplotypes, haplotypes diversity and nucleotide diversity was somewhat higher than the RR cross‐type but less than reported for L . catla (Ayesha et al, 2019). The observed nucleotide composition of CO1 gene sequence in CC cross‐type was similar to RR cross‐type but slightly variable compared to values reported in the literature.…”

“…However, Ayesha et al (2019) reported somewhat different results of CO1 sequence analysis of rohu, that is 89% invariable or constant characters and about 11% variable polymorphic characters with 28 singletons and 65 parsimony informative sites. Here, the observed total number of haplotypes (4) and haplotypes diversity (Hd, 0.455) was comparatively less than 10 and 0.933, respectively, reported by Ayesha et al (2019). However, the sequence analysis of the nucleotide composition of the CO1 gene was in accord with the literature.…”

CO1-Based DNA barcoding for assessing diversity of Pteropus giganteus from the state of Azad Jammu Kashmir, Pakistan

“…Sequence divergence between the Bat species of AJK (Pakistan) and other international reference species was determined by multiple sequence alignments. A phylogenetic tree was generated using the neighbor-joining method and Kimura 2-parameter supported by 1,000 bootstrap replicates (Akhtar and Ali, 2016;Akhtar et al, 2017;Ayesha et al, 2019) in MEGA 6.06 software. Replicate trees percentage in which all the related taxa are grouped in the bootstrap test (thousand replicates) were shown in the next branches of the MEGA 6.06 software.…”