scholarly journals Genome skimming and exploration of DNA barcodes for Taiwan endemic cypresses

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Chung-Shien Wu ◽  
Edi Sudianto ◽  
Yu-Mei Hung ◽  
Bo-Cyun Wang ◽  
Chiun-Jr Huang ◽  
...  
Keyword(s):  
Dna Barcode ◽  
Congeneric Species ◽  
Dna Barcodes ◽  
Illegal Logging ◽  
Chamaecyparis Formosensis ◽  
Genome Skimming ◽  
Forensic Investigations ◽  
Species Specific ◽  
Hypervariable Loci

AbstractCypresses are characterized by their longevity and valuable timber. In Taiwan, two endemic cypress species, Chamaecyparis formosensis and C. obtusa var. formosana, are threatened by prevalent illegal logging. A DNA barcode system is urgently needed for reforestation and conservation of these two cypresses. In this study, both plastomes and 35S rDNAs from 16, 10, and 6 individuals of C. formosensis, C. obtusa var. formosana, and C. obtusa var. obtusa were sequenced, respectively. We show that the loss of plastid trnT-GGU readily distinguishes C. formosensis from its congeneric species. We demonstrate that entire sequences of plastomes or 35S rDNAs are capable of correctly identifying cypress species and varieties, suggesting that they are effective super-barcodes. We also discover three short hypervariable loci (i.e., 3′ETS, ITS1, and trnH-psbA) that are promising barcodes for identifying cypress species and varieties. Moreover, nine species-specific indels of > 100 bp were detected in the cypress plastomes. These indels, together with the three aforementioned short barcodes, constitute an alternative and powerful barcode system crucial for identifying specimens that are fragmentary or contain degraded/poor DNA. Our sequenced data and barcode systems not only enrich the genetic reference for cypresses, but also contribute to future reforestation, conservation, and forensic investigations.

DNA barcodes for two scale insect families, mealybugs (Hemiptera: Pseudococcidae) and armored scales (Hemiptera: Diaspididae)

2011 ◽  
Vol 101 (4) ◽  
pp. 429-434 ◽  
Author(s):  
D.-S. Park ◽  
S.-J. Suh ◽  
P.D.N. Hebert ◽  
H.-W. Oh ◽  
K.-J. Hong
Keyword(s):  
Dna Barcode ◽  
Scale Insect ◽  
Scale Insects ◽  
Congeneric Species ◽  
Dna Barcodes ◽  
Armored Scale ◽  
Effective System

AbstractAlthough DNA barcode coverage has grown rapidly for many insect orders, there are some groups, such as scale insects, where sequence recovery has been difficult. However, using a recently developed primer set, we recovered barcode records from 373 specimens, providing coverage for 75 species from 31 genera in two families. Overall success was >90% for mealybugs and >80% for armored scale species. The G·C content was very low in most species, averaging just 16.3%. Sequence divergences (K2P) between congeneric species averaged 10.7%, while intra-specific divergences averaged 0.97%. However, the latter value was inflated by high intra-specific divergence in nine taxa, cases that may indicate species overlooked by current taxonomic treatments. Our study establishes the feasibility of developing a comprehensive barcode library for scale insects and indicates that its construction will both create an effective system for identifying scale insects and reveal taxonomic situations worthy of deeper analysis.

scholarly journals Assessing Clivia taxonomy using the core DNA barcode regions, matK and rbcLa

Bothalia ◽  
2018 ◽  
Vol 48 (1) ◽  
Author(s):  
Johan J. Spies ◽  
Paula Spies
Keyword(s):  
Dna Barcode ◽  
Taxonomic Revision ◽  
Dna Barcodes ◽  
Eastern Cape ◽  
Base Pairs ◽  
The Core ◽  
The North ◽  
Kwazulu Natal ◽  
North Eastern ◽  
Species Specific

Background: Clivia is a genus of the family Amaryllidaceae endemic to South Africa and Swaziland. Six species and one natural hybrid have been described. Some morphological traits overlap between some species, thus causing taxonomic confusion.Objectives: The discriminatory power of the core DNA barcodes (matK and rbcLa) was evaluated, and the current taxonomy of Clivia was assessed.Method: Seventy-four two-locus DNA barcodes from 4 to 18 specimens per species were generated.Results: The matK region had a higher mean intraspecific variation of 0.21 compared with the 0.02 of rbcLa. The two-locus barcodes have an aligned length of 1335 base pairs. Three species, Clivia mirabilis, Clivia nobilis and Clivia caulescens, are monophyletic in the Bayesian Inference (BI) cladogram. The remaining Clivia species (Clivia miniata, Clivia gardenii, Clivia robusta and their affinities) are paraphyletic. Clivia is divided into 17 haplogroups with those of C. mirabilis and C. nobilis being unique. Clivia caulescens has three haplotypes. The Clivia species from the north-eastern distribution range of the Eastern Cape and KwaZulu-Natal provinces have 11 haplogroups and no species-specific DNA barcodes. These groups have no correlation with the current taxonomy or geographical distribution.Conclusions: Only 37.33% of the species can be correctly identified with the ‘best match’ option in SpeciesIdentifier. Clivia mirabilis, C. nobilis and C. caulescens have unique DNA barcodes to identify them. Specimens from the Ngome area in KwaZulu-Natal have a unique DNA barcode, separating them from the rest of C. gardenii. A taxonomic revision is suggested.

Development of DNA Barcode and Species-Specific Markers forHelopeltis antoniiSignoret andPachypeltis maesarum(Kirkaldy) (Heteroptera: Miridae), Pests of Cashew in India

2012 ◽  
Vol 122 (2) ◽  
pp. 173-182
Author(s):  
R. Asokan ◽  
K. B. Rebijith ◽  
N. K. Krishna Kumar ◽  
K. K. Srikumar ◽  
P. Shivarama Bhat
Keyword(s):  
Dna Barcode ◽  
Species Specific

DNA barcodes provide evidence for the independent origin of the cultivated silkworms Samia ricini and Samia cynthia

2021 ◽  
pp. 1-8
Author(s):  
J.-C. Huang ◽  
X.-Y. Li ◽  
Y.-P. Li ◽  
R.-S. Zhang ◽  
D.-B. Chen ◽  
...  
Keyword(s):  
Genetic Distance ◽  
Phylogenetic Relationship ◽  
Dna Barcode ◽  
Distinct Species ◽  
Coi Gene ◽  
Molecular Evidence ◽  
Dna Barcodes ◽  
Close Relationship ◽  
Molecular Phylogenetic ◽  
Phylogenetic Framework

Samia ricini (Wm. Jones) and Samia cynthia (Drury) (Lepidoptera: Saturniidae) have been used as traditional sources of food as well as silk-producing insects. However, the phylogenetic relationship between the two silkworms remains to be addressed. In this study, the mitochondrial cytochrome c oxidase subunit 1 (COI) gene sequences corresponding to DNA barcodes from 13 Samia species were analysed, and a DNA barcode-based phylogenetic framework for these Samia species was provided. Phylogenetic analysis showed that multiple individuals of a species could be clustered together. Our analysis revealed a close relationship among Samia yayukae Paukstadt, Peigler and Paukstadt, Samia abrerai Naumann and Peigler, Samia kohlli Naumann and Peigler, Samia naessigi Naumann and Peigler, Samia naumanni Paukstadt, Peigler and Paukstadt, and Samia kalimantanensis Paukstadt and Paukstadt. The mixed clustering relationship and low Kimura-2-parameter (K2P) genetic distance (0.006) between individuals of S. ricini and Samia canningi (Hutton) indicated that the cultivated silkworm S. ricini was derived from the non-cultivated silkworm S. canningi. The remote phylogenetic relationship and high K2P genetic distance (0.039) indicated that S. ricini and S. cynthia are distinct species, thus providing solid molecular evidence that they had entirely independent origins. The relationships between S. kalimantanensis and S. naumanni and between S. cynthia and Samia wangi Naumann and Peigler, as well as the potential cryptic species within S. abrerai were also discussed. This is the first study to assess the DNA barcodes of the genus Samia, which supplements the knowledge of species identification and provides the first molecular phylogenetic framework for Samia species.

The phylogenetic analysis of Dalbergia (Fabaceae: Papilionaceae) based on different DNA barcodes

Holzforschung ◽  
2017 ◽  
Vol 71 (12) ◽  
pp. 939-949 ◽  
Author(s):  
Qiwei Li ◽  
Jihong Wu ◽  
Yesheng Wang ◽  
Xiaoming Lian ◽  
Feilong Wu ◽  
...  
Keyword(s):  
Internal Transcribed Spacer ◽  
Reliable Method ◽  
Dna Barcodes ◽  
Illegal Logging ◽  
Good Discrimination ◽  
Close Match ◽  
Discrimination Ability ◽  
Overall Performance ◽  
Resources Conservation ◽  
Barcode Gap

AbstractThe genusDalbergiacontains approximately 250 species with many valuable trees being destroyed by targeted and illegal logging. DNA barcoding is a reliable method for the molecular identification of different species and resources conservation. In the present study, the specimen discrimination ability of internal transcribed spacer (ITS),matK,rbcL andpsbA-trnH barcoding were tested onDalbergiasequences, downloaded from the National Center for Biotechnology Information (NCBI), and the combined barcoding ITS+matK+rbcL was used to identify unknown specimens. It was found that ITS+matK+rbcL have good discrimination rates based on the analysis methods best match (BM) and best close match (BCM). These barcodes also have the best performance concerning barcode gap distribution, and are able to discriminate unknown specimens from South-China. Furthermore, it was demonstrated thatD. tamarindifoliaandD. rubiginosaare also relatively close to sister-speciesD. pinnataandD. candenatensiswithin the phylogeneticDalbergiatree. Considering the overall performance of these barcodes, we suggest that the ITS+matK+rbcL region is a suitable barcode for identifyingDalbergiaspecies.

scholarly journals A Systematic Study on DNA Barcoding of Medicinally Important Genus Epimedium L. (Berberidaceae)

Genes ◽  
2018 ◽  
Vol 9 (12) ◽  
pp. 637 ◽  
Author(s):  
Mengyue Guo ◽  
Yanqin Xu ◽  
Li Ren ◽  
Shunzhi He ◽  
and Xiaohui Pang
Keyword(s):  
Dna Barcode ◽  
Morphological Characteristics ◽  
Identification Accuracy ◽  
Dna Barcodes ◽  
Success Rates ◽  
Data Set ◽  
Herba Epimedii ◽  
Potential Risks ◽  
Medicinal Properties ◽  
Species Being

Genus Epimedium consists of approximately 50 species in China, and more than half of them possess medicinal properties. The high similarity of species’ morphological characteristics complicates the identification accuracy, leading to potential risks in herbal efficacy and medical safety. In this study, we tested the applicability of four single loci, namely, rbcL, psbA-trnH, internal transcribed spacer (ITS), and ITS2, and their combinations as DNA barcodes to identify 37 Epimedium species on the basis of the analyses, including the success rates of PCR amplifications and sequencing, specific genetic divergence, distance-based method, and character-based method. Among them, character-based method showed the best applicability for identifying Epimedium species. As for the DNA barcodes, psbA-trnH showed the best performance among the four single loci with nine species being correctly differentiated. Moreover, psbA-trnH + ITS and psbA-trnH + ITS + rbcL exhibited the highest identification ability among all the multilocus combinations, and 17 species, of which 12 are medicinally used, could be efficiently discriminated. The DNA barcode data set developed in our study contributes valuable information to Chinese resources of Epimedium. It provides a new means for discrimination of the species within this medicinally important genus, thus guaranteeing correct and safe usage of Herba Epimedii.

scholarly journals Current limitations and future prospects of detection and biomonitoring of NIS in the Mediterranean Sea through environmental DNA

NeoBiota ◽  
2021 ◽  
Vol 70 ◽  
pp. 151-165
Author(s):  
Francesco Zangaro ◽  
Benedetta Saccomanno ◽  
Eftychia Tzafesta ◽  
Fabio Bozzeda ◽  
Valeria Specchia ◽  
...  
Keyword(s):  
Mediterranean Sea ◽  
Dna Barcode ◽  
Environmental Dna ◽  
Special Focus ◽  
Indigenous Species ◽  
Dna Barcodes ◽  
Identification Of Species ◽  
The Mediterranean ◽  
Taxonomic Groups ◽  
Non Indigenous Species

The biodiversity of the Mediterranean Sea is currently threatened by the introduction of Non-Indigenous Species (NIS). Therefore, monitoring the distribution of NIS is of utmost importance to preserve the ecosystems. A promising approach for the identification of species and the assessment of biodiversity is the use of DNA barcoding, as well as DNA and eDNA metabarcoding. Currently, the main limitation in the use of genomic data for species identification is the incompleteness of the DNA barcode databases. In this research, we assessed the availability of DNA barcodes in the main reference libraries for the most updated inventory of 665 confirmed NIS in the Mediterranean Sea, with a special focus on the cytochrome oxidase I (COI) barcode and primers. The results of this study show that there are no barcodes for 33.18% of the species in question, and that 45.30% of the 382 species with COI barcode, have no primers publicly available. This highlights the importance of directing scientific efforts to fill the barcode gap of specific taxonomic groups in order to help in the effective application of the eDNA technique for investigating the occurrence and the distribution of NIS in the Mediterranean Sea.

scholarly journals DNA barcodes and morphology of P. krempfi, P. mekongensis, and P. elongatus

2016 ◽  
Vol 14 (1) ◽  
pp. 29-37 ◽  
Author(s):  
Dương Thúy Yên ◽  
Nguyễn Kiệt ◽  
Bùi Sơn Nên ◽  
Nguyễn Văn Thường ◽  
Nguyễn Bạch Loan ◽  
...  
Keyword(s):  
Dna Barcode ◽  
Morphological Characteristics ◽  
Mekong Delta ◽  
Genetic Distances ◽  
Dna Barcodes ◽  
Gill Rakers ◽  
Coi Sequences ◽  
Relationship Of ◽  
Metric Traits ◽  
I Gene

Three Pangasius species including P. krempfi, P. elongatus and P. mekongensis, are economically important. They can be mis-identified due to similar external appreance at small sizes. This study aimed to distinguish these species based on their differences in DNA barcode, COI (cytochrome c oxidase subunit I) gene, and morphological characteristics. Fish with various sizes (>90 samples/species) were sampled at the lower Mekong delta region. Kimura-2 parameter genetic distances based on COI sequences of three species (15 samples, in which, 4 unique sequences were assigned Genbank accession numbers from KT289877 to KT289880) are relatively high, ranging 9.33 – 12.10 %. Morphological measurements show that coutanble traits including numbers of fin rays and the first gill rakers vary in similar ranges but ratios of metric traits are significantly different among three species (P<0.01). Principle component analysis using metric traits sets three species apart. P. elongatus is characterized by elongated body, long caudal preduncle, large eyes, and retangle palatine tooth plates. P. krempfi differs from P. mekongesis in characteristics on their head. The number of sections, shape and length of barbel are different among three species. Phylogenetic relationship of three species based on morphology and COI sequences indicate that P. krempfi is closer to P. mekongenis rather than P. elongatus, and that the distance between P. mekongenis and P. elongatus is the largest.

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.

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