DNA barcodes for insect pest identification: a test case with tussock moths (Lepidoptera: Lymantriidae)

2006 ◽  
Vol 36 (2) ◽  
pp. 337-350 ◽  
Author(s):  
Shelley L Ball ◽  
Karen F Armstrong
Keyword(s):  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Sequence Data ◽  
Mitochondrial Gene ◽  
Insect Pest ◽  
Reference Sequence ◽  
Identification System ◽  
Pest Species ◽  
Dna Barcodes ◽  
Data Set

Reliable and rapid identification of exotic pest species is critical to biosecurity. However, identification of morphologically indistinct specimens, such as immature life stages, that are frequently intercepted at borders is often impossible. Several DNA-based methods have been used for species identification; however, a more universal and anticipatory identification system is needed. Consequently, we tested the ability of DNA "barcodes" to identify species of tussock moths (Lymantriidae), a family containing several important pest species. We sequenced a 617 base pair fragment of the mitochondrial gene cytochrome c oxidase 1 for 20 lymantriid species. We used these, together with other Noctuoidea species sequences from GenBank and the Barcoding of Life Database to create a "profile" or reference sequence data set. We then tested the ability of this profile to provide correct species identifications for 93 additional lymantriid specimens from a data set of mock unknowns. Of the unknowns, 100% were correctly identified by the cytochrome c oxidase 1 profile. Mean interspecific sequence (Kimura 2-parameter) divergence was an order of magnitude greater (14%) than mean intraspecific divergence (<1%). Four species showed deeper genetic divergences among populations. We conclude that DNA barcodes provide a highly accurate means of identifying lymantriid species and show considerable promise as a universal approach to DNA-based identification of pest insects.

scholarly journals Using DNA barcodes to assess identity and diversity of Dendropsophus minutus: Failure?

Zootaxa ◽  
2008 ◽  
Vol 1691 (1) ◽  
pp. 67 ◽  
Author(s):  
M. ALEX SMITH
Keyword(s):  
Cytochrome C ◽  
Small Group ◽  
Cytochrome C Oxidase ◽  
Species Identification ◽  
Mitochondrial Gene ◽  
Dna Barcode ◽  
Gene Region ◽  
Dna Barcodes ◽  
Taxonomic Groups

The 5' end (Folmer or Barcode region) of cytochrome c oxidase 1 (CO1) has been proposed as the gene region of choice for a standardized animal DNA barcode (Hebert et al. 2003). Concerns have been raised regarding the decision to utilize this particular mitochondrial gene region as a barcode. Nevertheless, widely divergent taxonomic groups have reported success using CO1 for both species identification and discovery. The utility of CO1 for barcoding amphibians was raised early on (Vences, et al. 2005) and concerns for this group were reported widely (Waugh 2007)—although some considered that the reporting of the concerns outstripped the data that had been analyzed at that point (Smith et al. 2008). Indeed, our analysis of CO1 for a small group of Holarctic amphibians was neither more difficult to generate nor to analyze than for other groups where we have utilized the technique.

Adult and larval associations of the alpine stonefly genus Riekoperla McLellan (Plecoptera:Gripopterygidae) using mitochondrial DNA

2011 ◽  
Vol 25 (1) ◽  
pp. 11 ◽  
Author(s):  
J. H. Mynott ◽  
J. M. Webb ◽  
P. J. Suter
Keyword(s):  
Mitochondrial Dna ◽  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Aquatic Insects ◽  
Sequence Data ◽  
New South ◽  
Mitochondrial Gene ◽  
Life Stage ◽  
Molecular Data ◽  
South Wales

The current taxonomic understanding of the genus Riekoperla McLellan, 1971 (Gripopterygidae) is poor, with 15 of the 28 species and subspecies having unknown or uncertain larval associations. Sequences of a 657 bp fragment from the mitochondrial gene cytochrome c oxidase subunit 1 (CO1) were obtained from 122 specimens of 13 species collected throughout the alpine areas of New South Wales and Victoria, Australia. Of these, sequence data associated adults and larvae for the following 10 species: R. alpina McLellan, 1971, R. cf. intermedia, R. compressa Theischinger, 1985, R. hynesorum Theischinger, 1985, R. karki McLellan, 1971, R. montana Theischinger, 1985, R. reticulata (Kimmins, 1951), R. rugosa (Kimmins, 1951), R. trapeza Theischinger, 1985, and R. tuberculata McLellan, 1971. Adults of R. intermedia Theischinger, 1985, R. triloba triloba McLellan, 1971 and R. williamsi McLellan, 1971 were sequenced but no larvae were associated with them. The 13 species were reciprocally monophyletic and had minimum interspecific sequence divergences ranging from 7.2–19.5%, higher than the maximum intraspecific sequence divergences (0.6–5.8%). The combination of morphology and molecular data enabled rapid life stage association for alpine Riekoperla species and this method should be used more frequently for other environmentally significant aquatic insects.

scholarly journals Membrane-Based Oligonucleotide Array Developed from Multiple Markers for the Detection of Many Phytophthora Species

2013 ◽  
Vol 103 (1) ◽  
pp. 43-54 ◽  
Author(s):  
Wen Chen ◽  
Zeinab Robleh Djama ◽  
Michael D. Coffey ◽  
Frank N. Martin ◽  
Guillaume J. Bilodeau ◽  
...  
Keyword(s):  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Plant Pathogens ◽  
Sequence Data ◽  
Phytophthora Species ◽  
Phytophthora Ramorum ◽  
Oligonucleotide Array ◽  
Data Set ◽  
Phytophthora Spp ◽  
Field Samples

Most Phytophthora spp. are destructive plant pathogens; therefore, effective monitoring and accurate early detection are important means of preventing potential epidemics and outbreaks of diseases. In the current study, a membrane-based oligonucleotide array was developed that can detect Phytophthora spp. reliably using three DNA regions; namely, the internal transcribed spacer (ITS), the 5′ end of cytochrome c oxidase 1 gene (cox1), and the intergenic region between cytochrome c oxidase 2 gene (cox2) and cox1 (cox2-1 spacer). Each sequence data set contained ≈250 sequences representing 98 described and 15 undescribed species of Phytophthora. The array was validated with 143 pure cultures and 35 field samples. Together, nonrejected oligonucleotides from all three markers have the ability to reliably detect 82 described and 8 undescribed Phytophthora spp., including several quarantine or regulated pathogens such as Phytophthora ramorum. Our results showed that a DNA array containing signature oligonucleotides designed from multiple genomic regions provided robustness and redundancy for the detection and differentiation of closely related taxon groups. This array has the potential to be used as a routine diagnostic tool for Phytophthora spp. from complex environmental samples without the need for extensive growth of cultures.

Molecular and Ultrastructural Analysis of a Porocephalus sp. (Arthropoda: Pentastomida) Removed from a Rattlesnake

2021 ◽  
Vol Vol 66 (1) (January (1)) ◽  
pp. 1-5
Author(s):  
Jerome Goddard ◽  
Gerald Baker ◽  
Petra Jericke ◽  
Lawrence Birchman ◽  
Ethan Woodward ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Adult Female ◽  
Sequence Data ◽  
Molecular Data ◽  
Ultrastructural Analysis ◽  
Oxidase Subunit ◽  
Data Support ◽  
Partial 18S

Ultrastructural and molecular data are provided from a single adult female pentastomid opportunistically collected from a road-killed rattlesnake in Russell, KS. Ultrastructural data consisted of light and SEM microscopy of the pentastomid and its eggs, while molecular data consisted of partial 18S and 28S ribosomal sequences and a partial cytochrome c oxidase subunit 1 sequence from the same specimen used for SEM. Ultrastructural and molecular data support generic identification of the pentastomid as Porocephalus sp. These molecular data were also used with previously published pentastomid sequence data for a concatenated phylogenetic analysis, which support the current, morphology-based taxonomic placement of the genus.

Isostenosmylus ammirabilis sp. nov., a remarkable new species of lance lacewing (Neuroptera: Osmylidae) from the Colombian Andes

Zootaxa ◽  
2020 ◽  
Vol 4803 (3) ◽  
pp. 561-575
Author(s):  
ADRIAN ARDILA-CAMACHO ◽  
CALEB CALIFRE MARTINS ◽  
JORGE ARI NORIEGA
Keyword(s):  
New Species ◽  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Mitochondrial Gene ◽  
Dna Barcode ◽  
Neotropical Region ◽  
Andean Region ◽  
Oxidase Subunit ◽  
Colombian Andes ◽  
South Of Brazil

Isostenosmylus Krüger, 1913 is the richest genus of Osmylidae of the Neotropical region, with 17 described species so far, which are distributed mainly in the Andean region and in the South of Brazil and Paraguay. A new remarkable Colombian species of Isostenosmylus—I. ammirabilis sp. nov.—is herein described and illustrated. DNA barcode of mitochondrial gene cytochrome c oxidase subunit I (COI) for this species is also provided. Taxonomic keys for the genus are updated. 

scholarly journals Mitochondrial Antisense RNA for Cytochrome C Oxidase (MARCO) Can Induce Morphologic Changes and Cell Death in Human Hematopoietic Cell Lines

Blood ◽  
1997 ◽  
Vol 90 (11) ◽  
pp. 4567-4577 ◽  
Author(s):  
Naoki Shirafuji ◽  
Satoshi Takahashi ◽  
Satoru Matsuda ◽  
Shigetaka Asano
Keyword(s):  
Molecular Weight ◽  
Cell Death ◽  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Antisense Rna ◽  
Mitochondrial Gene ◽  
Neutrophilic Granulocytes ◽  
High Molecular Weight Dna ◽  
Tnf Α ◽  
Morphologic Changes

To identify essential molecules capable of inducing terminal morphologic maturation and cell death of myeloid progenitor cells, we isolated cDNA clones by functional expression cloning using a library constructed from all-trans retinoic acid (ATRA)-treated human promyelocytic HL-60 cells. Clones which induced morphologic changes in HL-60 cells from blastic cells to mature neutrophilic granulocytes were selected. The isolated positive cDNA clone was demonstrated to encode an antisense RNA for cytochrome c oxidase/serine tRNA derived from a mitochondrial gene (MARCO). When MARCO was expressed in HL-60 cells with the lac switch system, blastic cell morphology became neutrophilic after 48-hour incubation with IPTG, and cell death was observed after 3 days. Also, high molecular weight DNA fragmentation was observed after 36 hours in culture. Similar results were observed using transformants from human K562 cells and CMK cells. RT-PCR analysis revealed that MARCO was transcribed in both ATRA and TNF-α systems, and also in human blood neutrophilic granulocytes. Following transfection with cytochrome c oxidase expression plasmids, TNF-α–induced high molecular weight DNA fragmentation in U937 cells and HL-60 cells was inhibited in these transformants. These results indicate that maturational changes in hematopoietic cells and the process of cell death may be induced by mitochondrial respiratory insufficiency, and also that the mitochondrial gene MARCO may be used as one of the candidates for gene supplementation therapy for the acute leukemias.

Two new feather mites (Acari: Analgoidea) isolated from the grey-headed woodpecker, Picus canus (Piciformes: Picidae) in Korea

2019 ◽  
Vol 24 (11) ◽  
pp. 2167-2183
Author(s):  
Yeong-deok Han ◽  
Sergey V. Mironov ◽  
Gi-sik Min
Keyword(s):  
New Species ◽  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Coi Gene ◽  
Mitochondrial Cytochrome ◽  
Dna Barcodes ◽  
Feather Mites ◽  
Oxidase Subunit ◽  
Two New Species ◽  
First Time

Two new species of feather mites from the superfamily Analgoidea are described from the grey-headed woodpecker, Picus canus, in Korea: Neopteronyssus koreanus sp. nov. (Pteronyssidae) and Proterothrix picinus sp. nov. (Proctophyllodidae: Pterodectinae). Feather mites of the genera Neopteronyssus Mironov, 2002 and Proterothrix Gaud, 1968 are described for the first time in Korea. Morphological descriptions of both new species are complemented with partial sequences of their mitochondrial cytochrome c oxidase subunit I (COI) gene as DNA barcodes.

scholarly journals coil: an R package for cytochrome c oxidase I (COI) DNA barcode data cleaning, translation, and error evaluation

Genome ◽  
2020 ◽  
Vol 63 (6) ◽  
pp. 291-305 ◽  
Author(s):  
Cameron M. Nugent ◽  
Tyler A. Elliott ◽  
Sujeevan Ratnasingham ◽  
Sarah J. Adamowicz
Keyword(s):  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Sequence Data ◽  
Dna Barcode ◽  
R Package ◽  
Data Generation ◽  
Error Identification ◽  
Reading Frame ◽  
Biological Contaminants ◽  
And Function

Biological conclusions based on DNA barcoding and metabarcoding analyses can be strongly influenced by the methods utilized for data generation and curation, leading to varying levels of success in the separation of biological variation from experimental error. The 5′ region of cytochrome c oxidase subunit I (COI-5P) is the most common barcode gene for animals, with conserved structure and function that allows for biologically informed error identification. Here, we present coil ( https://CRAN.R-project.org/package=coil ), an R package for the pre-processing and frameshift error assessment of COI-5P animal barcode and metabarcode sequence data. The package contains functions for placement of barcodes into a common reading frame, accurate translation of sequences to amino acids, and highlighting insertion and deletion errors. The analysis of 10 000 barcode sequences of varying quality demonstrated how coil can place barcode sequences in reading frame and distinguish sequences containing indel errors from error-free sequences with greater than 97.5% accuracy. Package limitations were tested through the analysis of COI-5P sequences from the plant and fungal kingdoms as well as the analysis of potential contaminants: nuclear mitochondrial pseudogenes and Wolbachia COI-5P sequences. Results demonstrated that coil is a strong technical error identification method but is not reliable for detecting all biological contaminants.

Mitochondrial DNA replication and transcription are dissociated during embryonic cardiac hypertrophy

1991 ◽  
Vol 261 (6) ◽  
pp. C1091-C1098 ◽  
Author(s):  
J. M. Kennedy ◽  
S. R. Lobacz ◽  
S. W. Kelley
Keyword(s):  
Mitochondrial Dna ◽  
Cytochrome C ◽  
Cardiac Hypertrophy ◽  
Cytochrome C Oxidase ◽  
Oxidase Activity ◽  
Citrate Synthase ◽  
Incubation Temperature ◽  
Mitochondrial Gene ◽  
Gene Replication ◽  
Mitochondrial Dna Copy Number

Cardiac hypertrophy was produced in embryonic chicks by decreasing the incubation temperature from 38 degrees C to 32 degrees C on day 11. Increases in ventricular protein, RNA, and DNA support the cardiac enlargement. Cytochrome-c oxidase activity and citrate synthase activity were depressed in hypothermic ventricles by 63% and 56%, respectively. No significant differences were seen in enzyme activities in pectoralis muscles. The involvement of mitochondrial gene replication and transcription was evaluated using a cDNA clone for the mitochondrially encoded subunit III of cytochrome-c oxidase (CO III). Quantitative slot-blot analysis demonstrated that the relative CO III mRNA concentration was reduced in hypothermic ventricles. In contrast, the relative mitochondrial DNA concentration was increased in hypothermic ventricles. Taken together, these data indicate that a hypothermia-induced decrease in cytochrome-c oxidase activity is associated with a decrease in CO III mRNA, which is not coupled to a decrease in the mitochondrial DNA copy number. This dissociation of mitochondrial gene replication and transcription may provide a useful model for examining the regulation of mitochondrial biogenesis.

scholarly journals Cytochrome c oxidase III as a mechanism for apoptosis in heart failure following myocardial infarction

2009 ◽  
Vol 297 (4) ◽  
pp. C928-C934 ◽  
Author(s):  
Changgong Wu ◽  
Lin Yan ◽  
Christophe Depre ◽  
Sunil K. Dhar ◽  
You-Tang Shen ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Myocardial Infarction ◽  
Heart Failure ◽  
Cytochrome C ◽  
Protein Expression ◽  
Cell Viability ◽  
Cytochrome C Oxidase ◽  
Mitochondrial Gene

Cytochrome c oxidase (COX) is composed of 13 subunits, of which COX I, II, and III are encoded by a mitochondrial gene. COX I and II function as the main catalytic components, but the function of COX III is unclear. Because myocardial ischemia affects mitochondrial oxidative metabolism, we hypothesized that COX activity and expression would be affected during postischemic cardiomyopathy. This hypothesis was tested in a monkey model following myocardial infarction (MI) and subsequent pacing-induced heart failure (HF). In this model, COX I protein expression was decreased threefold after MI and fourfold after HF ( P < 0.05 vs. sham), whereas COX II expression remained unchanged. COX III protein expression increased 5-fold after MI and further increased 10-fold after HF compared with sham ( P < 0.05 vs. sham). The physiological impact of COX III regulation was examined in vitro. Overexpression of COX III in mitochondria of HL-1 cells resulted in an 80% decrease in COX I, 60% decrease in global COX activity, 60% decrease in cell viability, and threefold increase in apoptosis ( P < 0.05). Oxidative stress induced by H2O2 significantly ( P < 0.05) increased COX III expression. H2O2 decreased cell viability by 47 ± 3% upon overexpression of COX III, but only by 12 ± 5% in control conditions ( P < 0.05). We conclude that ischemic stress in vivo and oxidative stress in vitro lead to upregulation of COX III, followed by downregulation of COX I expression, impaired COX oxidative activity, and increased apoptosis. Therefore, upregulation of COX III may contribute to the increased susceptibility to apoptosis following MI and subsequent HF.

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