The use of DNA barcode evidence for inferring species of Chlorophthalmus (Aulopiformes, Chlorophthalmidae) in the Indo-West Pacific

2014 ◽  
Vol 65 (11) ◽  
pp. 1027 ◽  
Author(s):  
Martin F. Gomon ◽  
Robert D. Ward ◽  
Stephanie Chapple ◽  
Joshua M. Hale
Keyword(s):  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Dna Barcode ◽  
Morphological Evidence ◽  
Undescribed Species ◽  
West Pacific ◽  
Oxidase Subunit ◽  
Variable Nature ◽  
Gene Coi ◽  
Coi Sequences

Recent studies have revealed evidence that the identities and distributions of several Indo-West Pacific species of Chlorophthalmus, as redefined by Sato and Nakabo (2002a), are inaccurately understood and reported in the literature. The current confusion is mostly attributable to the meristic conservatism of the genus and the individually variable nature of the morphology in those species. An analysis of the DNA barcode region of cytochrome c oxidase subunit I sequences was employed to independently group specimens into natural species assemblages, providing evidence for verifying or correcting species concepts and identities. A re-examination of the morphology of vouchers in the resultant 12 groupings identified features corroborating the distinctiveness of 10 of the 12 groups at the species level. Each of the other two groups comprised two presumed species on the basis of morphological evidence that do not appear to be separable by cytochrome c oxidase subunit I gene (COI) sequences. Two undescribed species of Chloropthalmus are now known to inhabit slope waters of Australia, and a further two undescribed species were identified elsewhere.

Can DNA barcoding be used to identify closely related Clunio Haliday, 1855 species (Diptera: Chironomidae, Orthocladiinae)?

Zootaxa ◽  
2021 ◽  
Vol 4927 (1) ◽  
pp. 1-8
Author(s):  
PARASKEVA MICHALOVA ◽  
VALERIA LENCIONI ◽  
MOMCHIL NENOV ◽  
SVETOSLAV NIKOLOV
Keyword(s):  
Cytochrome C ◽  
Dna Barcoding ◽  
Cytochrome C Oxidase ◽  
Methodological Approach ◽  
Dna Barcode ◽  
Mitochondrial Cytochrome ◽  
Base Pairs ◽  
Oxidase Subunit ◽  
Gene Coi ◽  
Mitochondrial Cytochrome C

DNA barcoding based on a fragment of mitochondrial Cytochrome C Oxidase subunit 1 gene (COI) was applied to the two chironomids Clunio balticus Heimbach (690 base pairs) and C. ponticus Michailova (691 base pairs). The two species differed by one deletion in the nucleotide sequence Adenine. However, the 658-nucleotide long sequences of DNA from the mitochondrial Cytochrome C Oxidase subunit 1 gene (COI) of C. balticus and C. ponticus were identical upon comparison. Further, they compared with homologous sequences for C. marinus Holiday and C. tsushimensis Tokunaga from the Barcode of Life (BOLD) database and the results plotted as a weighted graph, where C. tsushimensis, C. marinus and C. balticus C. ponticus formed three almost equidistant groups. From this, we established that the genetic distance between the respective COI sequences of C. balticus and C. ponticus is minimal, indicating a close relationship between the species indicative of recent common origin. However, the comparative analysis between C. tsushimensis, C. marinus, C. balticus and C. ponticus showed a wider divergence in their respective nucleotide sequences. Overall, our results emphasized that the COI region does not work well as a DNA barcode to identify species within the Clunio genus. Either longer sequences or a multifaceted methodological approach, including morphology, cytogenetic and ecology is needed to distinguish some members of Clunio genus.  

Four new species of the primitively segmented spider genus Songthela (Mesothelae, Liphistiidae) from Chongqing Municipality, China

Zootaxa ◽  
2022 ◽  
Vol 5091 (4) ◽  
pp. 546-558
Author(s):  
ZHAOYANG CHEN ◽  
FENGXIANG LIU ◽  
DAIQIN LI ◽  
XIN XU
Keyword(s):  
Mitochondrial Dna ◽  
New Species ◽  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Dna Barcode ◽  
Morphological Characters ◽  
Oxidase Subunit ◽  
Chongqing Municipality ◽  
Males And Females

This paper reports four new species of the primitively segmented spider genus Songthela from Chongqing Municipality, China, based on morphological characters of both males and females: S. jinyun sp. nov., S. longbao sp. nov., S. serriformis sp. nov. and S. wangerbao sp. nov. We also provide the GenBank accession codes of mitochondrial DNA barcode gene, cytochrome c oxidase subunit I (COI), for the holotype of four new species for future identification.  

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 Three new species of the primitively segmented spider genus Songthela (Araneae, Mesothelae) from Guizhou Province, China

ZooKeys ◽  
2021 ◽  
Vol 1037 ◽  
pp. 57-71
Author(s):  
Zhaoyang Chen ◽  
Dengqing Li ◽  
Daiqin Li ◽  
Xin Xu
Keyword(s):  
New Species ◽  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Dna Barcode ◽  
Morphological Characters ◽  
Molecular Data ◽  
Genetic Distances ◽  
Guizhou Province ◽  
Oxidase Subunit ◽  
Three New Species

We diagnose and describe three new species of the primitively segmented spider genus Songthela from Guizhou Province, China, based on morphological characters and molecular data: S. liuisp. nov. (♂♀), S. tianzhusp. nov. (♂♀), and S. yupingsp. nov. (♂♀). We provide the genetic distances within and among the three new species based on the DNA barcode gene, cytochrome c oxidase subunit I (COI) to support our descriptions. We also provide the COI GenBank accession codes for the three new species for future identification.

scholarly journals Three new species of the segmented spider genus Qiongthela (Mesothelae, Liphistiidae) from Hainan Island, China

ZooKeys ◽  
2021 ◽  
Vol 1009 ◽  
pp. 123-138
Author(s):  
Li Yu ◽  
Fengxiang Liu ◽  
Zengtao Zhang ◽  
Daiqin Li ◽  
Xin Xu
Keyword(s):  
New Species ◽  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Dna Barcode ◽  
Hainan Island ◽  
Morphological Characters ◽  
Type Specimens ◽  
Oxidase Subunit ◽  
Three New Species

We report three new species of the segmented trapdoor spider genus Qiongthela Xu & Kuntner, 2015 collected from Hainan Island, China based on morphological characters: Q. dongfangsp. nov. (♂♀), Q. nankaisp. nov. (♂♀), Q. yalinsp. nov. (♂♀). We also provide the GenBank accession codes of the DNA barcode gene, cytochrome c oxidase subunit I (COI), of the type specimens of all three new species to aid future identification.

scholarly journals Coi Gene as a Molecular Marker of Elachista Species (Lepidoptera: Elachistidae: Elachistinae) from Different Lithuanian Populations

2009 ◽  
Vol 63 (1-2) ◽  
pp. 21-24
Author(s):  
Virginijus Sruoga ◽  
Virmantas Stunžėnas ◽  
Brigita Paulavičiūtė
Keyword(s):  
Cytochrome C ◽  
Molecular Marker ◽  
Cytochrome C Oxidase ◽  
Dna Sequences ◽  
Coi Gene ◽  
Oxidase Subunit ◽  
Gene Coi ◽  
I Gene

Coi Gene as a Molecular Marker of Elachista Species (Lepidoptera: Elachistidae: Elachistinae) from Different Lithuanian Populations We compared COI DNA sequences of three Elachista species occurring in Lithuania: Elachista maculicerusella, E. argentella, and E. pollinariella (Gelechioidea: Elachistidae: Elachistinae). Also, intraspecific differences in COI DNA between moth populations were tested. A 705 bp fragment of the 3'-end of cytochrome c oxidase subunit I gene (COI) was used. This mtDNA fragment was significantly different between all studied species. Intraspecific differences were detected only for E. maculicerusella from different Lithuanian populations. Our results support using the COI gene for identification of Elachista species and as a tool for exploring intraspecific differences between populations.

scholarly journals A reference cytochrome c oxidase subunit I database curated for hierarchical classification of arthropod metabarcoding data

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5126 ◽  
Author(s):  
Rodney T. Richardson ◽  
Johan Bengtsson-Palme ◽  
Mary M. Gardiner ◽  
Reed M. Johnson
Keyword(s):  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Input Data ◽  
Hierarchical Classification ◽  
Classification Error ◽  
Sequence Classification ◽  
Oxidase Subunit ◽  
Reliability Score ◽  
Coi Sequences

Metabarcoding is a popular application which warrants continued methods optimization. To maximize barcoding inferences, hierarchy-based sequence classification methods are increasingly common. We present methods for the construction and curation of a database designed for hierarchical classification of a 157 bp barcoding region of the arthropod cytochrome c oxidase subunit I (COI) locus. We produced a comprehensive arthropod COI amplicon dataset including annotated arthropod COI sequences and COI sequences extracted from arthropod whole mitochondrion genomes, the latter of which provided the only source of representation for Zoraptera, Callipodida and Holothyrida. The database contains extracted sequences of the target amplicon from all major arthropod clades, including all insect orders, all arthropod classes and Onychophora, Tardigrada and Mollusca outgroups. During curation, we extracted the COI region of interest from approximately 81 percent of the input sequences, corresponding to 73 percent of the genus-level diversity found in the input data. Further, our analysis revealed a high degree of sequence redundancy within the NCBI nucleotide database, with a mean of approximately 11 sequence entries per species in the input data. The curated, low-redundancy database is included in the Metaxa2 sequence classification software (http://microbiology.se/software/metaxa2/). Using this database with the Metaxa2 classifier, we performed a cross-validation analysis to characterize the relationship between the Metaxa2 reliability score, an estimate of classification confidence, and classification error probability. We used this analysis to select a reliability score threshold which minimized error. We then estimated classification sensitivity, false discovery rate and overclassification, the propensity to classify sequences from taxa not represented in the reference database. Our work will help researchers design and evaluate classification databases and conduct metabarcoding on arthropods and alternate taxa.

Redescription of Triplectides misakianus (Matsumura 1931) (Trichoptera, Leptoceridae) in Japan with notes on its habitat

Zoosymposia ◽  
2016 ◽  
Vol 10 (1) ◽  
pp. 234-242
Author(s):  
NOBUYUKI KATSUMA ◽  
RYOICHI B. KURANISHI
Keyword(s):  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Dna Barcode ◽  
Coi Gene ◽  
Mitochondrial Cytochrome ◽  
Oxidase Subunit ◽  
First Time ◽  
Mitochondrial Cytochrome C

Triplectides misakianus (Matsumura 1931) is redescribed on the basis of adults, larvae, and pupae collected in Japan. This report describes the pupal morphology of this species for the first time. A 658-bp fragment of the mitochondrial cytochrome c oxidase subunit I (COI) gene as a potential “DNA barcode” is provided. The habitat and conservation of the species are discussed.

scholarly journals New Species-Specific Primers for Molecular Diagnosis of Bactrocera minax and Bactrocera tsuneonis (Diptera: Tephritidae) in China Based on DNA Barcodes

Insects ◽  
2019 ◽  
Vol 10 (12) ◽  
pp. 447 ◽  
Author(s):  
Linyu Zheng ◽  
Yue Zhang ◽  
Wenzhao Yang ◽  
Yiying Zeng ◽  
Fan Jiang ◽  
...  
Keyword(s):  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Dna Barcode ◽  
Diagnostic Methods ◽  
Molecular Diagnostic ◽  
Specific Primers ◽  
Oxidase Subunit ◽  
Preimaginal Stages ◽  
Specific Fragment ◽  
Species Specific

Tephritidae fruit flies (Diptera: Tephritidae) are regarded as important damage-causing species due to their ability to cause great economic losses in fruit and vegetable crops. Bactrocera minax and Bactrocera tsuneonis are two sibling species of the subgenus Tetradacus of Bactrocera that are distributed across a limited area of China, but have caused serious impacts. They share similar morphological characteristics. These characteristics can only be observed in the female adult individuals. The differences between them cannot be observed in preimaginal stages. Thus, it is difficult to distinguish them in preimaginal stages morphologically. In this study, we used molecular diagnostic methods based on cytochrome c oxidase subunit I and species-specific markers to identify these two species and improve upon the false-positive results of previous species-detection primers. DNA barcode sequences were obtained from 900 individuals of B. minax and 63 individuals of B. tsuneonis. Based on these 658 bp DNA barcode sequences of the cytochrome c oxidase subunit I gene, we successfully designed the species-specific primers for B. minax and B. tsuneonis. The size of the B. minax specific fragment was 422 bp and the size of the B. tsuneonis specific fragment was 456 bp. A series of PCR trials ensured the specificity of these two pairs of primers. Sensitivity assay results demonstrated that the detection limit for the DNA template concentration was 0.1~1 ng/μL for these two species. In this study, we established a more reliable, rapid, and low-cost molecular identification method for all life stages of B. minax and B. tsuneonis. Species-specific PCR can be applied in plant quarantine, monitoring and control of B. minax and B. tsuneonis.

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