scholarly journals Cytochrome c oxidase barcodes for aquatic oligochaete identification: development of a Swiss reference database

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e4122 ◽  
Author(s):  
Régis Vivien ◽  
Maria Holzmann ◽  
Inge Werner ◽  
Jan Pawlowski ◽  
Michel Lafont ◽  
...  
Keyword(s):  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Morphological Data ◽  
Reference Database ◽  
Its2 Region ◽  
Aquatic Oligochaete ◽  
Aquatic Oligochaetes ◽  
Morphological Criteria ◽  
Unidentified Species ◽  
Coi Sequences

Introduction Aquatic oligochaetes represent valuable indicators of the quality of sediments of watercourses and lakes, but their difficult identification based on morphological criteria compromises their more common use for eco-diagnostic analyses. This issue could be overcome by using DNA barcodes for species identification. A 10% threshold of cytochrome c oxidase (COI) divergence was proposed for differentiating between oligochaete species based on molecular and morphological data. A Swiss database of COI sequences of aquatic oligochaetes was initiated in 2012. The aim of this study is to complement the Swiss oligochaete database of COI sequences and to confirm the relevance of this threshold for species delimitation. Methods We sequenced the COI sequence of 216 specimens collected in different regions of Switzerland and ITS2 region of some lineages whose delimitation with COI data was doubtful. Results We distinguished 53 lineages, among which 34 were new for Switzerland and 17 sequenced for the first time. All the lineages were separated by more than 10% of COI variation, with the exception of some species within Nais and Uncinais. In these two genera, the threshold was lowered to 8% to be congruent with the morphological analysis. The total number of lineages reported so far for Switzerland is 75, including 59 morphospecies or unidentified species and 16 cryptic species. Discussion Our study shows that the threshold of 10% of COI divergence is generally appropriate to distinguish aquatic oligochaete lineages, but that it must be adjusted for some species. The database reported here will be complemented in the future in parallel to the development of genetic oligochaete indices.

scholarly journals DNA barcoding of Naididae (Annelida, Oligochaeta), based on cytochrome C oxidase gene and ITS2 region in China

2021 ◽  
Vol 9 ◽  
Author(s):  
Tingting Zhou ◽  
Wei Jiang ◽  
Hongzhu Wang ◽  
Yongde Cui
Keyword(s):  
Cytochrome C ◽  
Dna Barcoding ◽  
Cytochrome C Oxidase ◽  
Species Identification ◽  
Genetic Distances ◽  
Coi Gene ◽  
Tubifex Tubifex ◽  
Its2 Region ◽  
Aquatic Oligochaetes ◽  
Barcode Gap

Exploring the effectiveness of DNA barcoding in species identification is a prerequisite for biodiversity conservation and environmental monitoring. Aquatic oligochaetes could serve as excellent indicators in aquatic monitoring programmes. However, few studies have examined the effectiveness of DNA barcoding in these specific organisms. The mitochondrial cytochrome C oxidase (COI) gene of 83 specimens belonging to 40 species of 18 genera were sequenced in this study. The results showed that there was a barcode gap between species of Naididae and the intraspecific genetic distances of each species were smaller than interspecific genetic distances. The classification results of ABGD (Automatic Barcode Gap Discovery) were consistent with those of morphological identification, except for Tubifex tubifex and Lumbriculus variegatus. All species were successfully distinguished in the phylogenetic tree, based on the ITS2 region, which was coincident with the morphological result. Our results provided evidence that DNA barcoding can be used as an effective and convenient tool for species identification of the family Naididae and even for other aquatic oligochaetes.

scholarly journals First results of Central Asiatic Euchalcia DNA-studies: comparison of nucleotide sequence differences in COI between Euchalcia herrichi and Euchalcia gyulai (Lepidoptera: Noctuidae)

2020 ◽  
Vol 6 ◽  
pp. 1-4
Author(s):  
Stanislav K Korb
Keyword(s):  
Nucleotide Sequence ◽  
Cytochrome C ◽  
Dna Barcoding ◽  
Cytochrome C Oxidase ◽  
Coi Gene ◽  
First Results ◽  
The Difference ◽  
Coi Sequences ◽  
Lepidoptera Noctuidae ◽  
Two Populations

We submitted first results of the DNA studies of the Central Asiatic owlet moths of the genus Euchalcia. Standard cytochrome C oxidase subunit I (COI) gene fragments were sequenced for DNA barcoding of six specimens belonging to Euchalcia herrichi and Euchalcia gyulai. We compared the received sequences between discussed species and with two European Euchalcia species (E. variabilis and E. consona). We found no variability within the COI sequences of the samples collected in the same locality (Alai Mts., Kyrgyzstan), whereas the difference in COI sequences between two populations (Ketmen Mts., Kazakhstan and Alai Mts., Kyrgyzstan) was 0.005.

The Rhyacophila fasciata Group in Greece: Rhyacophila kykladica Malicky & Sipahiler 1993 (stat. prom.) (Trichoptera: Rhyacophilidae). Morphological description, genetic and ecological features

Zootaxa ◽  
2019 ◽  
Vol 4657 (3) ◽  
pp. 503-522
Author(s):  
MARIA VALLADOLID ◽  
IOANNIS KARAOUZAS ◽  
MERCEDES ARAUZO ◽  
BEATRIZ A. DORDA ◽  
ISABEL REY
Keyword(s):  
New Species ◽  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Molecular Analysis ◽  
Taxonomic Status ◽  
Morphological Data ◽  
Morphological Description ◽  
Mitochondrial Cytochrome ◽  
Male And Female ◽  
Ecological Features

The morphology of the different stages (larva, pupa, male, and female) of Rhyacophila fasciata kykladica Malicky & Sipahiler 1993 was examined as a basis for the description of the taxon. Morphological data were supplemented by molecular analysis of mitochondrial cytochrome C oxidase subunit I (mtCOI), which were compared with samples of the nominate subspecies Rhyacophila fasciata fasciata Hagen 1859, as well as with other new species in this group, Rhyacophila denticulata McLachlan 1879 and Rhyacophila sociata Navás 1916. Our results revealed genetic differences between all the taxa; therefore, a change of taxonomic status of R. fasciata kykladica to R. kykladica (stat. prom.) is proposed.

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.

scholarly journals First results of Central Asiatic Euchalcia DNA-studies: comparison of nucleotide sequence differences in COI between Euchalcia herrichi and Euchalcia gyulai (Lepidoptera: Noctuidae)

2020 ◽  
Vol 6 ◽  
pp. 1-4
Author(s):  
Stanislav Korb
Keyword(s):  
Nucleotide Sequence ◽  
Cytochrome C ◽  
Dna Barcoding ◽  
Cytochrome C Oxidase ◽  
Coi Gene ◽  
First Results ◽  
The Difference ◽  
Coi Sequences ◽  
Lepidoptera Noctuidae ◽  
Two Populations

We submitted first results of the DNA studies of the Central Asiatic owlet moths of the genus Euchalcia. Standard cytochrome C oxidase subunit I (COI) gene fragments were sequenced for DNA barcoding of six specimens belonging to Euchalcia herrichi and Euchalcia gyulai. We compared the received sequences between discussed species and with two European Euchalcia species (E. variabilis and E. consona). We found no variability within the COI sequences of the samples collected in the same locality (Alai Mts., Kyrgyzstan), whereas the difference in COI sequences between two populations (Ketmen Mts., Kazakhstan and Alai Mts., Kyrgyzstan) was 0.005.

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.

scholarly journals DNA barcode of the Lanzones scale insect, Unaspis mabilis Lit & Barbecho (Hemiptera: Diaspididae)

2020 ◽  
Vol 14 (3) ◽  
Keyword(s):  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Phylogenetic Analyses ◽  
Dna Barcode ◽  
Scale Insect ◽  
Coi Gene ◽  
Species Identity ◽  
Management Options ◽  
Nucleotide Sequence Alignment ◽  
Coi Sequences

The mitochondrial cytochrome c oxidase subunit 1 (COI) nucleotide sequences of Unaspis mabilis Lit & Barbecho (Hemiptera: Diaspididae), are provided for the first time. The total genomic DNA of each scale insect was extracted from individuals infesting lanzones leaves from three selected sites in Los Baños, Laguna. A partial COI gene amplicon with approximately 750 bp was obtained using the primer pair PcoF1 and LepR1. Nucleotide sequence alignment showed no variation among the COI sequences from all the samples. BLASTn search yielded no significant match with any of the available sequences for Unaspis species. The closest hit was Aulacaspis tubercularis Newstead (GenBank Accession No. HM474091) with 87.4% nucleotide similarity. Nonetheless, phylogenetic analyses revealed that generated COI sequences from U. mabilis form a monophyletic clade with U. yanonensis and U. euonymi, with closer proximity to the former. These findings also strengthen the species status of U. mabilis under the genus Unaspis. The DNA barcodes generated from this study (GenBank Acc. Nos. MN114099, MN14101, and MN114102), could, therefore, be used to verify the species identity of other lanzones scale accessions, as well as monitor the distribution and spread of U. mabilis, which would greatly influence possible pest management options. KEYWORDS: cytochrome C oxidase I, COI, Lansium domesticum Correa, lanzones

scholarly journals Molecular identification and phylogenetic relationships of seven Satyrinae butterflies in Bangladesh using Cytochrome c oxidase subunit I gene

2019 ◽  
Vol 8 (1) ◽  
pp. 67-74
Author(s):  
Ananna Ghosh ◽  
Muhammad Sohel Abedin ◽  
Abdul Jabber Howlader ◽  
Md Monwar Hossain
Keyword(s):  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Molecular Identification ◽  
Phylogenetic Trees ◽  
Coi Gene ◽  
Neighbor Joining ◽  
Oxidase Subunit ◽  
Traditional Classification ◽  
Nymphalid Butterfly ◽  
Coi Sequences

The Satyrinae is a subfamily of Nymphalid butterfly, which is morphologically and ecologically the most diverse group, occurring in all habitats. In the present study, Cytochrome c oxidase subunit I (COI) gene of seven species of Satyrinae was sequenced, aligned, and used to construct phylogenetic trees. The molecular identification of these Satyrinae species was confirmed by comparing the related sequences in the National Center for Biotechnology Information (NCBI) GenBank. The base compositions of the COI sequences were 39.07% T, 16.44% C, 29.83% A, and 14.64% G, revealing a strong AT bias (68.9%). The sequence distance among Satyrinae species ranged from 0.09% to 0.18%. Phylogenetic trees were constructed by the neighbor-joining (NJ) and maximum likelihood (ML) methods, using Orthetrum sabina as an outgroup. Both trees had almost identical topologies. The sampled species in Satyrinae exhibited the following relationships: Melanitis leda + [(Mycalesis mineus+(Mycalesis gotama+Mycalesis anaxias)) + (Ypthima baldus + (Lethe chandica+Elymnias hypermnestra))], suggesting that M. leda might be distantly related with the rest of the Satyrinae species. This clustering result is almost identical to current traditional classification. This study confirms that the COI based DNA barcoding is an efficient method for the identification of butterflies including Satyrinae species and, as such, may further contribute effectively to biodiversity and evolutionary research. Jahangirnagar University J. Biol. Sci. 8(1): 67-74, 2019 (June)

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

2018 ◽  
Author(s):  
Rodney 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, 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 characterized 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.

Morphological and molecular identification of cryptic species in the Sergentomyia bailyi (Sinton, 1931) complex in Sri Lanka

2016 ◽  
Vol 107 (1) ◽  
pp. 58-65 ◽  
Author(s):  
T. Tharmatha ◽  
K. Gajapathy ◽  
R. Ramasamy ◽  
S.N. Surendran
Keyword(s):  
Sri Lanka ◽  
Cytochrome C ◽  
Cryptic Species ◽  
Cytochrome C Oxidase ◽  
Dna Sequences ◽  
Morphological Characteristics ◽  
Relative Length ◽  
Sand Fly ◽  
Correct Identification ◽  
Morphological Criteria

AbstractThe correct identification of sand fly vectors of leishmaniasis is important for controlling the disease. Genetic, particularly DNA sequence data, has lately become an important adjunct to the use of morphological criteria for this purpose. A recent DNA sequencing study revealed the presence of two cryptic species in the Sergentomyia bailyi species complex in India. The present study was undertaken to ascertain the presence of cryptic species in the Se. bailyi complex in Sri Lanka using morphological characteristics and DNA sequences from cytochrome c oxidase subunits. Sand flies were collected from leishmaniasis endemic and non-endemic dry zone districts of Sri Lanka. A total of 175 Se. bailyi specimens were initially screened for morphological variations and the identified samples formed two groups, tentatively termed as Se. bailyi species A and B, based on the relative length of the sensilla chaeticum and antennal flagellomere. DNA sequences from the mitochondrial cytochrome c oxidase subunit I (COI) and subunit II (COII) genes of morphologically identified Se. bailyi species A and B were subsequently analyzed. The two species showed differences in the COI and COII gene sequences and were placed in two separate clades by phylogenetic analysis. An allele specific polymerase chain reaction assay based on sequence variation in the COI gene accurately differentiated species A and B. The study therefore describes the first morphological and genetic evidence for the presence of two cryptic species within the Se. bailyi complex in Sri Lanka and a DNA-based laboratory technique for differentiating them.

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