scholarly journals Mitochondrial COI Sequence Variations within and among Geographic Samples of the Hemp Pest Psylliodes attenuata from China

Insects ◽  
2020 ◽  
Vol 11 (6) ◽  
pp. 370
Author(s):  
Litao Guo ◽  
Feng Gao ◽  
Yi Cheng ◽  
Chunsheng Gao ◽  
Jia Chen ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Cannabis Sativa ◽  
Flea Beetle ◽  
Dna Barcode ◽  
Coi Gene ◽  
Long Distance ◽  
Mitochondrial Recombination ◽  
Mitochondrial Coi ◽  
Network Analyses ◽  
Industrial Hemp

The hemp flea beetle Psylliodes attenuata (Coleoptera: Chrysomelidae: Psylliodes) is a common pest of Cannabis sativa, including cultivars of both industrial hemp and medicinal marijuana. Both the larval and adult stages of this beetle can cause significant damages to C. sativa, resulting in substantial crop losses. At present, little is known about the populations of this pest, including its genetic diversity. In this study, we obtained 281 P. attenuata samples from nine field sites representing broad industrial hemp productions in China and analyzed their DNA sequences at the mitochondrial COI gene, the insect DNA barcode. Our analyses revealed a total of 48 haplotypes, with 28 being found only in one specimen each while the remaining 20 were shared by two or more specimens each. Of the 20 shared haplotypes, eight were shared among local populations often from far away locations, consistent with recent long-distance dispersals. However, the observed putative long-distance dispersals have not obscured the significant genetic differentiations among the regional populations from northeastern, eastern, central and southwestern China. Interestingly, haplotype network analyses suggest evidence for potential mitochondrial recombination in natural populations of this species. We briefly discuss the implications of our results on its evolution, center of diversity, route of spread, and pest management strategies in hemp fields.

scholarly journals Species detections in environmental DNA using metabarcoding: a useful tool in estuaries monitoring

2015 ◽  
Author(s):  
Adrián Mártinez-Marqués ◽  
Carlos Enrique Carleos ◽  
Eva García-Vazquez ◽  
Yaisel J. Borrell Pichs
Keyword(s):  
Dna Analysis ◽  
Anthropogenic Activities ◽  
Dna Barcode ◽  
Environmental Dna ◽  
Coi Gene ◽  
Universal Primers ◽  
Mitochondrial Coi ◽  
Mitochondrial Coi Gene ◽  
Cantabrian Coast ◽  
Taxonomic Groups

Estuaries are amongst the most productive habitats in Earth, producing more organic materia than forests, meadows or agricultural lands. In addition, estuaries exhibit high, and precious, biodiversity levels. In this study an environmental DNA analysis of the two most important estuaries in Asturias (Cantabrian Coast, north Iberia) in terms of food production (Ría del Eo and Ría de Villaviciosa) was carried out. The objective was to monitor aquatic biodiversity and also to detect alien species that can be associated with anthropogenic activities (e.g.: aquaculture). To achieve these objectives, a metabarcoding methodology based in NGS (next generation sequencing) and the mitochondrial COI gene as a DNA Barcode was used. Results showed that this methodology was useful to detect the presence of three different non-native genera (Crepidula, Lymnaea, Macrobrachium) that are probably parasitating species cultured in these estuaries. It is true that Metabarcoding has still unsolved problems such as the lack of 100% universal primers and paucity of referenced sequences for some taxonomic groups in the databases. However, it represents already a powerful tool to manage the resources of these important ecosystems and to guarantee their long-term sustainailibity.

scholarly journals A finding of a frozen mummy of a lemming (Rodentia, Cricetidae, Lemmus) in the upper pleistocene of Yakutia

2019 ◽  
Vol 489 (1) ◽  
pp. 108-112
Author(s):  
A. V. Lopatin ◽  
N. G. Solomonov ◽  
N. V. Serdyuk ◽  
E. N. Maschenko ◽  
D. V. Mukha ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Coat Color ◽  
Coi Gene ◽  
Lower Incisor ◽  
Upper Pleistocene ◽  
X Ray ◽  
Radiocarbon Age ◽  
Mitochondrial Coi ◽  
Mitochondrial Coi Gene ◽  
Maximum Similarity

External morphological, X‑ray and tomographic study of the rodent frozen mummy from the Upper Pleistocene Yedoma deposits on the Tirekhtyakh River (tributary of the Semyulyakh River, Abyi District, Republic of Sakha (Yakutia)) showed its belonging to Lemmus sp. The radiocarbon age of the find is 41 305-41 885 cal BP. This is the first Pleistocene discovery of a frozen mummy of the representative of the genus Lemmus. In terms of body and skull size, coat color, length of the lower incisor and the structure of the molars, the specimen studied is closed to the Recent Lemmus sibiricus (Kerr, 1792). Comparison of the mitochondrial COI gene sequence with the DNA sequences presented in the GenBank database demonstrates maximum similarity with the Recent Siberian brown lemming too.

scholarly journals Species detections in environmental DNA using metabarcoding: a useful tool in estuaries monitoring

2015 ◽  
Author(s):  
Adrián Mártinez-Marqués ◽  
Carlos Enrique Carleos ◽  
Eva García-Vazquez ◽  
Yaisel J. Borrell Pichs
Keyword(s):  
Dna Analysis ◽  
Anthropogenic Activities ◽  
Dna Barcode ◽  
Environmental Dna ◽  
Coi Gene ◽  
Universal Primers ◽  
Mitochondrial Coi ◽  
Mitochondrial Coi Gene ◽  
Cantabrian Coast ◽  
Taxonomic Groups

Estuaries are amongst the most productive habitats in Earth, producing more organic materia than forests, meadows or agricultural lands. In addition, estuaries exhibit high, and precious, biodiversity levels. In this study an environmental DNA analysis of the two most important estuaries in Asturias (Cantabrian Coast, north Iberia) in terms of food production (Ría del Eo and Ría de Villaviciosa) was carried out. The objective was to monitor aquatic biodiversity and also to detect alien species that can be associated with anthropogenic activities (e.g.: aquaculture). To achieve these objectives, a metabarcoding methodology based in NGS (next generation sequencing) and the mitochondrial COI gene as a DNA Barcode was used. Results showed that this methodology was useful to detect the presence of three different non-native genera (Crepidula, Lymnaea, Macrobrachium) that are probably parasitating species cultured in these estuaries. It is true that Metabarcoding has still unsolved problems such as the lack of 100% universal primers and paucity of referenced sequences for some taxonomic groups in the databases. However, it represents already a powerful tool to manage the resources of these important ecosystems and to guarantee their long-term sustainailibity.

scholarly journals The dna barcoding data and genetic distance of leaf beetles (Coleoptera, Chrysomelidae) in Vietnam

2020 ◽  
Vol 42 (4) ◽  
Author(s):  
Nguyen Thi Dinh
Keyword(s):  
Genetic Distance ◽  
Dna Barcoding ◽  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Dna Barcode ◽  
Coi Gene ◽  
Biodiversity Assessment ◽  
Leaf Beetles ◽  
The World ◽  
Living Organisms

DNA barcoding is a useful tool in identifying species, biodiversity assessment, and revealing phylogenetic relationships of living organisms in the world. However, the DNA barcode data for leaf beetles in Vietnam is lacking. In this study, sixteen DNA sequences of 658 bp of COI gene from nine species (five genera; three subfamilies) of Chrysomelidae in Vietnam were (obtained). Intra- and inter-specific diversities, and phylogenetic relationships of these species were analyzed. 

scholarly journals Molecular identification and characterization of medically and veterinary important flies of Bangladesh based on mitochondrial COI gene sequences

2019 ◽  
pp. 69-79
Author(s):  
Faria Farhana Rain ◽  
Abdul Jabber Howlader ◽  
Abu Faiz Md. Aslam
Keyword(s):  
Research Work ◽  
Dna Barcode ◽  
Haplotype Network ◽  
First Record ◽  
Coi Gene ◽  
Gene Sequences ◽  
Accurate Identification ◽  
Haematobia Irritans ◽  
Mitochondrial Coi ◽  
Mitochondrial Coi Gene

Flies are considered serious pests which cause health problems of human and animal, transmitting many pathogenic microbes. Pest management programs depend on proper identification of pests. The present research work is an initiative to identify the medically and veterinary important flies based on mitochondrial COI gene sequences. Eleven species of the fly pests were identified. Among them, four fly species were the first record from Bangladesh. The phylogenetic analysis of retrieved sequences confirmed that the evolution of these species occurred from a common ancestor. Highest AT percentage (69.9%) was found in Haematobia irritans exigua and lowest GC percentage (30.4%) was found in Haematobia irritans exigua. The substitution rate of codon was found 1.88 in 1st position, 0.73 in 2nd position and 1.22 in 3rd position, respectively. Interspecific genetic divergence range of flies sequences was 5-20%. Haplotype network showed that Atylotus agrestis was mostly diverged from its common ancestors by 37 mutational steps. This research is the first molecular approach to identify the medically and veterinary important flies based on MT-COI gene sequences along with the establishment of first DNA barcode dataset for accurate identification in Bangladesh.

scholarly journals Evidence for Persistent Heteroplasmy and Ancient Recombination in the Mitochondrial Genomes of the Edible Yellow Chanterelles From Southwestern China and Europe

2021 ◽  
Vol 12 ◽  
Author(s):  
Ying Zhang ◽  
Shaojuan Wang ◽  
Haixia Li ◽  
Chunli Liu ◽  
Fei Mi ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Related Species ◽  
Dna Barcode ◽  
Nuclear Genome ◽  
Nuclear Gene ◽  
Southwestern China ◽  
Mitochondrial Genomes ◽  
Mitochondrial Recombination ◽  
Geographic Locations ◽  
Mitochondrial Atp Synthase

Mitochondrial genes and genomes have patterns of inheritance that are distinctly different from those of nuclear genes and genomes. In nature, the mitochondrial genomes in eukaryotes are generally considered non-recombining and homoplasmic. If heteroplasmy and recombination exist, they are typically very limited in both space and time. Here we show that mitochondrial heteroplasmy and recombination may not be limited to a specific population nor exit only transiently in the basidiomycete Cantharellus cibarius and related species. These edible yellow chanterelles are an ecologically very important group of fungi and among the most prominent wild edible mushrooms in the Northern Hemisphere. At present, very little is known about the genetics and population biology of these fungia cross large geographical distances. Our study here analyzed a total of 363 specimens of edible yellow chanterelles from 24 geographic locations in Yunnan in southwestern China and six geographic locations in five countries in Europe. For each mushroom sample, we obtained the DNA sequences at two genes, one in the nuclear genome and one in the mitochondrial genome. Our analyses of the nuclear gene, translation elongation factor 1-alpha (tef-1) and the DNA barcode of C. cibarius and related species, suggested these samples belong to four known species and five potential new species. Interestingly, analyses of the mitochondrial ATP synthase subunit 6 (atp6) gene fragment revealed evidence of heteroplasmy in two geographic samples in Yunnan and recombination within the two new putative species in Yunnan. Specifically, all four possible haplotypes at two polymorphic nucleotide sites within the mitochondrial atp6 gene were found distributed across several geographic locations in Yunnan. Furthermore, these four haplotypes were broadly distributed across multiple phylogenetic clades constructed based on nuclear tef-1 sequences. Our results suggest that heteroplasmy and mitochondrial recombination might have happened repeatedly during the evolution of the yellow chanterelles. Together, our results suggest that the edible yellow chanterelles represent an excellent system from which to study the evolution of mitochondrial-nuclear genome relationships.

Pairing of two highly sexually dimorphic species within the genus Lophocampa Harris, 1841 (Lepidoptera: Erebidae: Arctiini)

Zootaxa ◽  
2021 ◽  
Vol 4927 (1) ◽  
pp. 104-112
Author(s):  
MICHEL LAGUERRE ◽  
BENOIT VINCENTCENT
Keyword(s):  
Dna Barcode ◽  
Original Description ◽  
Coi Gene ◽  
Sexually Dimorphic ◽  
Mitochondrial Coi ◽  
Mitochondrial Coi Gene ◽  
First Time ◽  
Dimorphic Species

Two Lophocampa species previously known only by females are paired with morphologically highly different male specimens. This pairing was initiated after the discovery of a mosaic gynandromorph specimen and then confirmed using the mitochondrial COI gene (the so-called DNA barcode). Following the discovery of a labeling error by Rothschild during the original description of two species, two recombinations are proposed. Pairs for each species are illustrated and the male specimens are described for the first time. 

Identification of Neoceratitis asiatica (Becker) (Diptera: Tephritidae) based on morphological characteristics and DNA barcode

Zootaxa ◽  
2017 ◽  
Vol 4363 (4) ◽  
pp. 553
Author(s):  
SHAOKUN GUO ◽  
JIA HE ◽  
ZIHUA ZHAO ◽  
LIJUN LIU ◽  
LIYUAN GAO ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Trees ◽  
Gap Analysis ◽  
Dna Barcode ◽  
Morphological Characteristics ◽  
Coi Gene ◽  
Economic Losses ◽  
Morphological Identification ◽  
Lycium Barbarum ◽  
Accurate Identification

Neoceratitis asiatica (Becker), which especially infests wolfberry (Lycium barbarum L.), could cause serious economic losses every year in China, especially to organic wolfberry production. In some important wolfberry plantings, it is difficult and time-consuming to rear the larvae or pupae to adults for morphological identification. Molecular identification based on DNA barcode is a solution to the problem. In this study, 15 samples were collected from Ningxia, China. Among them, five adults were identified according to their morphological characteristics. The utility of mitochondrial DNA (mtDNA) cytochrome c oxidase I (COI) gene sequence as DNA barcode in distinguishing N. asiatica was evaluated by analysing Kimura 2-parameter distances and phylogenetic trees. There were significant differences between intra-specific and inter-specific genetic distances according to the barcoding gap analysis. The uncertain larval and pupal samples were within the same cluster as N. asiatica adults and formed sister cluster to N. cyanescens. A combination of morphological and molecular methods enabled accurate identification of N. asiatica. This is the first study using DNA barcode to identify N. asiatica and the obtained DNA sequences will be added to the DNA barcode database. 

DNA barcoding unravels three new species and a subspecies of Olepa Watson, 1980 (Lepidoptera, Erebidae, Arctiinae) from India, with morphotypes

2020 ◽  
Vol 19 (2) ◽  
pp. 44-60
Author(s):  
APARNA SURESHCHANDRA KALAWATE ◽  
K. P. DINESH ◽  
A. SHABNAM
Keyword(s):  
New Species ◽  
Dna Barcoding ◽  
Dna Sequences ◽  
Dna Barcode ◽  
Coi Gene ◽  
Male And Female ◽  
Morphological Variations ◽  
Three New Species ◽  
First Time ◽  
Respective Species

The genus Olepa is distributed in Palearctic and Oriental regions with more species in India and Sri Lanka. In the recent studies, morphological variations within the group were well established, with couple of first set of mt COI DNA barcodes for at least three species. In the present account, three new species and a new subspecies are described from the northern Western Ghats region of Maharashtra based on mt COI DNA barcode studies. Due to high morphological divergence and complete genetic homogeneity on the mt COI DNA, four morphotypes under two species are reported. Morphological and genital characters of male and female are provided along with their respective species morphotypes for the first time under this genus from India. The genitalia and the habitus of male and female are illustrated. Preliminary phylogenetic tree based on the mt COI DNA sequences available in the GenBank for the genus with the sequences for the new species also provided and discussed. Key words: new taxa, morphotype, Maharashtra, DNA barcoding, mt COI gene

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