The use of dna for oomycete species identification is well established, but dna barcoding with cytochrome c oxidase subunit i coi is a relatively new approach that has yet to be assessed over a significant sample of oomycete genera. We developed a flexible software tool for dna taxonomy, named taxi. Traditionally the cytochrome b cyt b gene was used for species identification, but in 2003 the cytochrome c oxidase subunit 1 co1 gene was introduced under the terminology barcoding. The aligned sequences, 658 base pairs in length, were analyzed for divergence using the kimura2parameter k2p distance model with mega5.
The enzyme cytochrome c oxidase or complex iv, ec 1. In the present study, we examined the suitability of cox 1 as a marker for trypanosoma cruzi identification from other closely related species. The dna barcoding system using the cytochrome c oxidase subunit 1 mitochondrial gene cox1 or coi is highly efficient for discriminating vertebrate and invertebrate species. Cell line identification the applicability of cytochrome. Cytochrome c oxidase subunit i barcodes provide an efficient tool.
The most frequently used bioinformatic software include mothur, uparse, qiime, galaxy, obitools, jamp, barque, and dada2. Pdf exploring the use of cytochrome oxidase c subunit 1. Single nucleotide polymorphism barcoding of cytochrome c. Cytochrome c oxidase subunit i barcodes provide an. Exploring the use of cytochrome oxidase c subunit 1 coi for dna barcoding of freeliving marine nematodes sofie derycke1,2, jan vanaverbeke1, annelien rigaux1,2, thierry backeljau3,4, tom moens1 1marine biology research group, department of biology, ghent university, ghent, belgium, 2centrum for molecular phylogeny and evolution, ghent university. Biomatters, auckland, new zealand and aligned using the. In the present study, we examined the suitability of cox1 as a marker for trypanosoma cruzi identification from other closely related species. Single nucleotide polymorphism barcoding of cytochrome c oxidase. For marine nematodes, coi based dna barcoding is problematic. A gene from mitochondria, called cytochrome c oxidase subunit 1 co1, was selected by the consortium for the barcode of life cbol as the ideal gene for dna barcoding animal species. Other genes suitable for dna barcoding are the internal transcribed spacer its rrna often used for fungi and rubisco used for plants. Cytochrome c oxidase subunit 1 gene as a dna barcode for. Exploring the use of cytochrome oxidase c subunit 1 coi for dna barcoding of freeliving marine nematodes article pdf available in plos one.
Cytochrome oxidase definition of cytochrome oxidase by. Dna barcoding as a tool for robust identification of. With millions of species and their lifestage transformations, the animal kingdom provides a challenging target for taxonomy. To maximize barcoding inferences, hierarchybased sequence classification methods are increasingly common. The dna sequences were manually edited and aligned using the software bioedit and clustal x. A threshold value of 5% k2p genetic divergence marked a clear dna barcoding gap separating intra and interspecific distances. The most commonly used barcode region for animals and some protists is a portion of the cytochrome c oxidase i coi or cox1 gene, found in mitochondrial dna. The use of a pcr and sequencing based cytochrome c oxidase subunit 1 co1 barcode assay for establishing the species level identity of animal cells is discussed below. Exploring the use of cytochrome oxidase c subunit 1 coi for dna barcoding of freeliving marine nematodes article pdf available in plos one 510. The full length of cytochrome oxidase 1 coi sequence is suitable for species identification and phylogenetic inference. Exploring the utility of partial cytochrome c oxidase.
We present methods for the construction and curation of a database designed for hierarchical classification of a 157 bp barcoding region of the arthropod. Sofie derycke, jan vanaverbeke, annelien rigaux, thierry backeljau, tom moens. Molecular evolutionary genetics analysis mega software version 4. The sequences were manually edited using geneious software version 8. Dna barcoding of oomycetes with cytochrome c oxidase. The mitochondrial cytochrome oxidase c subunit 1 coi gene is one of. The aligned sequences, 658 base pairs in length, were analyzed for. Metabarcoding is a popular application which warrants continued methods optimization. Derycke s, vanaverbeke j, rigaux a, backeljau t, moens t 2010 exploring the use of cytochrome oxidase c subunit 1 coi for dna barcoding of freeliving marine nematodes. Testing the utility of mitochondrial cytochrome oxidase. The fiveprime region of cytochrome c oxidase subunit i coi5p is the most. However, the effectiveness of dna barcoding for identifying crane species is unknown. Standard cytochrome c oxidase subunit i coi gene fragments were sequenced for dna barcoding of 39 samples from 9 snake species, including bungarus multicinctus, the officially recognized origin animal by chinese pharmacopoeia, and other 8 adulterate species. Proceedings of the royal society of london series bbiological sciences.
Recent work has suggested that a dnabased identification system, founded on the mitochondrial gene, cytochrome c oxidase subunit 1 coi, can aid the resolution of this diversity. The co1 codes for a that has an essential role in cellular respiration. Software tools that allow for the local or webbased alignment of. An oxidizing enzyme that contains iron and a porphyrin and is found in the mitochondrial membrane, where it catalyzes the transfer of electrons to oxygen as part of the electron transport chain, ultimately leading to the formation of atp. Cytochrome c oxidase the crystal structure of bovine cytochrome c oxidase in a phospholipid bilayer. Exploring the use of cytochrome oxidase c subunit 1 coi for dna barcoding of freeliving marine nematodes. The methodology targets a semiconserved region of the mitochondrial co1 gene for specieslevel identity testing of animal mammalian and insect cells. A reference cytochrome c oxidase subunit i database. Dna barcoding is a method of species identification using a short section of dna from a. Geneious tool and faster than most popular software for barcoding analysis. Exploring the use of cytochrome oxidase c subunit 1 coi. While past work has validated the ability of coi sequences to. Exploring the use of cytochrome oxidase c subunit 1 coi for dna.
892 490 1451 686 1222 678 1270 1527 944 1339 632 1321 1587 1460 631 864 206 401 1478 958 133 535 1390 1106 146 667 1334 521 1461 568 139 798 886 7 581 876 212 355 637 762 1028 1242