scholarly journals OLICH: A reference library of DNA barcodes for Nordic lichens

2019 ◽  
Vol 7 ◽  
Author(s):  
Gunnhild Marthinsen ◽  
Siri Rui ◽  
Einar Timdal
Keyword(s):  
Species Identification ◽  
Dna Barcode ◽  
Its Sequences ◽  
New Combination ◽  
Dna Barcodes ◽  
Reference Library ◽  
Additional Species ◽  
First Time ◽  
Barcode Gap

DNA barcodes are increasingly being used for species identification amongst the lichenised fungi. This paper presents a dataset aiming to provide an authoritative DNA barcode sequence library for a wide array of Nordic lichens. We present 1324 DNA barcode sequences (nrITS) for 507 species in 175 genera and 25 orders. Thirty-eight species are new to GenBank and, for 25 additional species, ITS sequences are here presented for the first time. The dataset covers 20–21% of the Nordic lichenised species. Barcode gap analyses are given and discussed for the three genera Cladonia, Ramalina and Umbilicaria. The new combination Bryobilimbia fissuriseda (Poelt) Timdal, Marthinsen & Rui is proposed for Mycobilimbia fissuriseda and Nordic material of the species, currently referred to as Pseudocyphellaria crocata and Psoroma tenue ssp. boreale, are shown to belong in Pseudocyphellaria citrina and Psoroma cinnamomeum, respectively.

scholarly journals A new species of Litarachna Walter, 1925 (Acari: Hydrachnidia: Pontarachnidae) from Corozal Bay (Belize), described based upon morphology and DNA barcodes

Acarologia ◽  
2021 ◽  
Vol 61 (3) ◽  
pp. 602-613
Author(s):  
Lucia Montes-Ortiz ◽  
Tom Goldschmidt ◽  
Lourdes Vásquez-Yeomans ◽  
Manuel Elías-Gutiérrez
Keyword(s):  
Dna Barcode ◽  
Morphological Description ◽  
Estuarine System ◽  
Dna Barcodes ◽  
Sem Images ◽  
The Family ◽  
Coi Sequences ◽  
First Time ◽  
A New Species ◽  
Electronic Microscope

A new planktonic species of the marine water mites of the family Pontarachnidae Koenike, 1910 is described from Corozal Bay, an estuarine system in Belize. The morphological description includes Scanning Electronic Microscope (SEM) images and is augmented by an analysis of DNA cytochrome c oxidase I (COI) sequences, the DNA barcode, used for the first time for a species description in this group.

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.

scholarly journals DNA barcodes identify medically important tick species in Canada

Genome ◽  
2017 ◽  
Vol 60 (1) ◽  
pp. 74-84 ◽  
Author(s):  
Danielle A. Ondrejicka ◽  
Kevin C. Morey ◽  
Robert H. Hanner
Keyword(s):  
Dna Barcode ◽  
Nearest Neighbour ◽  
Cryptic Diversity ◽  
Dna Barcodes ◽  
Genetic Cluster ◽  
Potential Health ◽  
Intraspecific Divergence ◽  
Coi Sequences ◽  
I Gene ◽  
Barcode Gap

Medically important ticks (Acari: Ixodidae) are often difficult to identify morphologically. A standardized, molecular approach using a 658 base pair DNA barcode sequence (from the 5′ region of the mitochondrial cytochrome c oxidase subunit I gene) was evaluated for its effectiveness in discriminating ticks in North America, with an emphasis on Canadian ticks. DNA barcodes were generated for 96 of 154 specimens representing 26 ixodid species. A genetic cluster analysis was performed on the barcode sequences, which separated specimens into haplogroups closely corresponding with morphologically identified species. The tree topology was further supported by a BIN analysis. COI sequences generated were found to have a mean maximum intraspecific divergence of 1.59% and a mean nearest neighbour divergence of 12.8%, indicating a significant “barcode gap”. This study also revealed possible cryptic diversity among specimens morphologically identified as Ixodes soricis and Ixodes texanus. A PCR-based test for Borrelia burgdorferi determined that 18.1% of Lyme-competent ticks in this study were positive. This study is also the first to record a B. burgdorferi-positive exoskeleton. In conclusion, DNA barcoding is a powerful tool that clinicians can use to determine the identification of tick specimens which can help them to suggest whether an attached tick is a potential health risk.

scholarly journals A contribution to the earthworm diversity (Clitellata, Moniligastridae) of Kerala, a component of the Western Ghats biodiversity hotspot, India, using integrated taxonom

2021 ◽  
pp. 117-137
Author(s):  
S. S. Thakur ◽  
A. R. Lone ◽  
S. K. Tiwari ◽  
S. K. Jain ◽  
S. W. James ◽  
...  
Keyword(s):  
Western Ghats ◽  
National Park ◽  
Gap Analysis ◽  
Mitochondrial Gene ◽  
Dna Barcode ◽  
Wildlife Sanctuary ◽  
Tiger Reserve ◽  
First Time ◽  
Barcode Gap

Earthworms (Clitellata, Moniligastridae) of Chaliyar River Malappuram, Eravikulam National Park, Neyyar Wildlife Sanctuary, Parambikulam Tiger Reserve, Peppara Wildlife Sanctuary, Periyar National Park, Shendurney Wildlife Sanctuary and Wayanad Forest, Kerala, a component of the hotspot of Western Ghats, India, were studied by the standard method of taxonomy, and their DNA barcode signatures using the mitochondrial gene cytochrome c oxidase I (COI) were generated for the first time. This study represents eleven species of earthworms of the family Moniligastridae: Drawida brunnea Stephenson, Drawida circumpapillata Aiyer, Drawida ghatensis Michaelsen, Drawida impertusa Stephenson, Drawida nilamburensis (Bourne), Drawida robusta (Bourne), Drawida scandens Rao, Drawida travancorense Michaelsen, Moniligaster aiyeri Gates, Moniligaster deshayesi Perrier, and Moniligaster gravelyi (Stephenson). In the phylogenetic analysis all the species were recovered in both neighbour–joining (NJ) and maximum likelihood (ML) trees with high clade support. The average K2P distance within and between species was 1.2 % and 22 %, whereas the clear barcode gap of 2–5 % was suggested by barcode gap analysis (BGA) of studied species, reflecting the accuracy of characterization. The study presents the first step in the molecular characterization of the native earthworm family Moniligastridae of India. Data published through GBIF (Doi: 10.15470/l2nlhz)

scholarly journals Revision of the Afrotropical species of the hover fly genus Mesembrius Rondani (Diptera, Syrphidae) using morphological and molecular data

ZooKeys ◽  
2021 ◽  
Vol 1046 ◽  
pp. 1-141
Author(s):  
Kurt Jordaens ◽  
Georg Goergen ◽  
Jeffrey H. Skevington ◽  
Scott Kelso ◽  
Marc De Meyer
Keyword(s):  
Dna Barcode ◽  
Molecular Data ◽  
Junior Synonym ◽  
Dna Barcodes ◽  
Identification Keys ◽  
Males And Females ◽  
Morphological And Molecular Data ◽  
First Time

The Afrotropical representatives of the hover fly genus Mesembrius Rondani, 1857 (Diptera) are divided into two subgenera, namely Mesembrius s.s. and Vadonimyia Séguy, 1951 and, in this present work, the subgenus Mesembrius s.s. is revised. A total of 23 Mesembrius s.s. species are recognised for the Afrotropics. Known species are re-described and six species new to science are described: Mesembrius arcuatussp. nov., M. copelandisp. nov., M. longipilosussp. nov., M. sulcussp. nov., M. tibialissp. nov. and M. vockerothisp. nov. Mesembrius africanus (Verrall, 1898) is considered a junior synonym of M. senegalensis (Macquart, 1842), M. ctenifer Hull, 1941 a junior synonym of M. caffer (Loew, 1858), M. lagopus (Loew, 1869) a junior synonym of M. capensis (Macquart, 1842) and M. platytarsis Curran, 1929 a junior synonym of M. simplicipes Curran, 1929. The females of Mesembrius chapini Curran, 1939, M. rex Curran, 1927 and M. regulus (Hull, 1937) are described for the first time. Lectotypes are designated for Mesembrius caffer, M. capensis, M. cyanipennis (Bezzi, 1915), M. minor (Bezzi, 1915), M. senegalensis, M. strigilatus (Bezzi, 1912) and M. tarsatus (Bigot, 1883). Separate identification keys for males and females are presented. We obtained 236 DNA barcodes for 18 species. The relationships amongst the different Mesembrius species are briefly discussed, based on morphological and DNA barcode data.

Taxonomy of the genus Craspedomerus Bernhauer, 1911 (Coleoptera: Staphylinidae: Philonthina) from China

Zootaxa ◽  
2010 ◽  
Vol 2506 (1) ◽  
pp. 1 ◽  
Author(s):  
LIANG LI ◽  
HONG-ZHANG ZHOU
Keyword(s):  
Electron Microscopy ◽  
Scanning Electron Microscopy ◽  
New Species ◽  
Species Identification ◽  
Geographical Distribution ◽  
Additional Species ◽  
Three New Species ◽  
First Time ◽  
Scanning Electron

Three new species of the genus Craspedomerus from China are described and illustrated: C. giganteus Li & Zhou sp. n. from Sichuan, C. gongshanus Li & Zhou sp. n. from Yunnan and C. zhangi Li & Zhou sp. n. from Tibet. Four species are reported for the first time from China: C. sinetuber (Coiffait, 1977a) from Tibet, C. cyanipennis Scheerpeltz, 1976b, C. ganeshensis Coiffait, 1983 and C. glenoides (Schubert, 1908) from Yunnan. These four and two additional species previously recorded from China (C. beckeri Bernhauer, 1934 and C. violaceipennis Cameron, 1928 are redescribed and illustrated. Sensory peg setae located on the underside of the paramere of the aedeagus of all nine Chinese species are compared using scanning electron microscopy (SEM) and the result shows that this character is useful for species identification. A key to the Chinese species of Craspedomerus is presented and geographical distribution of all sixteen species of Craspedomerus is mapped.

scholarly journals Calibrating the taxonomy of a megadiverse insect family: 3000 DNA barcodes from geometrid type specimens (Lepidoptera, Geometridae)

Genome ◽  
2016 ◽  
Vol 59 (9) ◽  
pp. 671-684 ◽  
Author(s):  
Axel Hausmann ◽  
Scott E. Miller ◽  
Jeremy D. Holloway ◽  
Jeremy R. deWaard ◽  
David Pollock ◽  
...  
Keyword(s):  
18Th Century ◽  
Dna Barcode ◽  
Data Systems ◽  
Dna Barcodes ◽  
Reference Library ◽  
Type Specimens ◽  
Voucher Specimen ◽  
Tropical Regions ◽  
Taxonomic Assignments ◽  
Insect Family

It is essential that any DNA barcode reference library be based upon correctly identified specimens. The Barcode of Life Data Systems (BOLD) requires information such as images, geo-referencing, and details on the museum holding the voucher specimen for each barcode record to aid recognition of potential misidentifications. Nevertheless, there are misidentifications and incomplete identifications (e.g., to a genus or family) on BOLD, mainly for species from tropical regions. Unfortunately, experts are often unavailable to correct taxonomic assignments due to time constraints and the lack of specialists for many groups and regions. However, considerable progress could be made if barcode records were available for all type specimens. As a result of recent improvements in analytical protocols, it is now possible to recover barcode sequences from museum specimens that date to the start of taxonomic work in the 18th century. The present study discusses success in the recovery of DNA barcode sequences from 2805 type specimens of geometrid moths which represent 1965 species, corresponding to about 9% of the 23 000 described species in this family worldwide and including 1875 taxa represented by name-bearing types. Sequencing success was high (73% of specimens), even for specimens that were more than a century old. Several case studies are discussed to show the efficiency, reliability, and sustainability of this approach.

scholarly journals Identification of species and materia medica withinSaussureasubg.Amphilaenabased on DNA barcodes

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6357 ◽  
Author(s):  
Jie Chen ◽  
Yong-Bao Zhao ◽  
Yu-Jin Wang ◽  
Xiao-Gang Li
Keyword(s):  
Internal Transcribed Spacer ◽  
Evolutionary History ◽  
Dna Barcode ◽  
Dna Barcodes ◽  
Additional Species ◽  
Plant Materials ◽  
Materia Medica ◽  
The Family ◽  
Identification Of Species ◽  
Medical Plants

Saussureais one of the most species-rich genera in the family Asteraceae, where some have a complex evolutionary history, including radiation and convergent evolution, and the identification of these species is notoriously difficult. This genus contains many plants with medical uses, and thus an objective identification method is urgently needed.Saussureasubg.Amphilaenais one of the four subgenera ofSaussureaand it is particularly rich in medical resources, where 15/39 species are used in medicine. To test the application of DNA barcodes in this subgenus, five candidates were sequenced and analyzed using 131 individuals representing 15 medical plants and four additional species from this subgenus. Our results suggested that internal transcribed spacer (ITS) +rbcL or ITS +rbcL +psbA-trnH could distinguish all of the species, while the ITS alone could identify all of the 15 medical plants. However, the species identification rates based on plastid barcodes were low, i.e., 0% to 36% when analyzed individually, and 63% when all four loci were combined. Thus, we recommend using ITS +rbcL as the DNA barcode forS.subg.Amphilaenaor the ITS alone for medical plants. Possible taxonomic problems and substitutes for medicinal plant materials are also discussed.

scholarly journals Identification of Nepeta olgae Regel and phylogenetic status of some genera in subtribe Nepetinae (Lamiaceae) using DNA markers

2021 ◽  
Vol 38 ◽  
pp. 00087
Author(s):  
Elena Nikitina ◽  
Abdurashid Rakhmatov
Keyword(s):  
Dna Barcoding ◽  
Large Scale ◽  
Dna Barcode ◽  
Dna Barcodes ◽  
Biodiversity Monitoring ◽  
Reference Library ◽  
Accurate Identification ◽  
Unknown Species ◽  
Phylogenetic Status ◽  
Nuclear Its

The species level diversity is the reference unit for biodiversity accounting, should be systematized and include full information about the species. Reliable identification of any species is critical for a large-scale biodiversity monitoring and conservation. A DNA barcode is a DNA sequence that identifies a species by comparing the sequence of an unknown species with barcodes of a known species sequence database. Accurate identification of important plants is essential for their conservation, inventory. The species diversity assessing exampled on the subtribe Nepetinae (Lamiaceae) representatives, growing in Uzbekistan is given, using DNA barcoding method. The study was aimed to identify indigenous important plants with the nuclear (ITS) and plastid (matK, rbcL, trnL-F) genomes. This work demonstrates the phylogenetic relationships of some genera within the subtribe Nepetinae Coss. & Germ. (Lamiaceae), based on ITS locus gene. All results indicate that the DNA barcoding tool can be successfully used to reliably identify important plants, to inventory the botanical resources of Uzbekistan and to create a reference library of DNA barcodes. So, the combination of three-four locus gene is a good candidate for this approach.

scholarly journals Unravelling the plant diversity of the Amazonian canga through DNA barcoding

2021 ◽  
Author(s):  
Santelmo Vasconcelos ◽  
Gisele Nunes ◽  
Mariana Dias ◽  
Jamily Lorena ◽  
Renato Oliveira ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Plant Diversity ◽  
Vascular Plants ◽  
Dna Barcode ◽  
Brazilian Amazon ◽  
Dna Barcodes ◽  
Dna Metabarcoding ◽  
Industrial Mining ◽  
First Time ◽  
Species Being

The canga of the Serra dos Carajás, in Eastern Amazon, is home to a unique open plant community, harbouring several endemic and rare species. Although a complete flora survey has been recently published, scarce to no genetic information is available for most plant species of the ironstone outcrops of the Serra dos Carajás. In this scenario, DNA barcoding appears as a fast and effective approach to assess the genetic diversity of the Serra dos Carajás flora, considering the growing need for robust biodiversity conservation planning in such an area with industrial mining activities. Thus, after testing eight different DNA barcode markers (matK, rbcL, rpoB, rpoC1, atpF-atpH, psbK-psbI, trnH-psbA and ITS2), we chose rbcL and ITS2 as the most suitable markers for a broad application in the regional flora. Here we describe DNA barcodes for 1,130 specimens of 538 species, 323 genera and 115 families of vascular plants, with a total of 344 species being barcoded for the first time. In addition, we assessed the potential of using DNA metabarcoding of bulk samples for surveying plant diversity in the canga. Upon achieving the first comprehensive DNA barcoding effort directed to a complete flora in the Brazilian Amazon, we discuss the relevance of our results to guide future conservation measures in the Serra dos Carajás.

Sign in / Sign up

Export Citation Format

Share Document