Applicability of chloroplast DNA barcodes for wood identification between Santalum album and its adulterants

Holzforschung ◽  
2019 ◽  
Vol 73 (2) ◽  
pp. 209-218 ◽  
Author(s):  
Lichao Jiao ◽  
Tuo He ◽  
Eleanor E. Dormontt ◽  
Yonggang Zhang ◽  
Andrew J. Lowe ◽  
...  
Keyword(s):  
Chloroplast Dna ◽  
Dna Barcode ◽  
Species Discrimination ◽  
Santalum Album ◽  
Dna Barcodes ◽  
Neighbor Joining ◽  
Discrimination Ability ◽  
East Indian ◽  
Commercial Market ◽  
Increasing Demand

AbstractThe East Indian sandalwood,Santalum albumL., is known for its fragrant heartwood and extractive oils. The increasing demand for the valuable sandalwood products has led to illegal and excessive logging, and there are otherSantalumspecies in the commercial market as substitutes (adulterants). Improved tools for the identification ofSantalumspecies are needed to control this situation. In this study, four chloroplast DNA (cpDNA) regions were screened (matK,psbA-trnH,trnK andtrnL) on 35 vouchered specimens covering fiveSantalumspecies, i.e.Santalum acuminatum,S. album,Santalum lanceolatum,Santalum murrayanumandSantalum spicatum. The goal of this study was to test the species discrimination ability by means of both the TaxonDNA and neighbor-joining (NJ) methods. The results indicate that the combination ofpsbA-trnH+trnK gave the best performance for discrimination (100%) of the studiedSantalumspecies concerning the discrimination ability and recovery rate. Meanwhile, six unvouchered wood specimens were retrieved and accurately identified at the species level based on the recommended DNA barcodes. The DNA barcode method is now ready for application in the monitoring of the trade of this valuable resource, and provides an effective approach for wood species identification and product authentication.

The Low Copy Nuclear Gene Region, Granule Bound Starch Synthase (GBSS1), as a Novel Mini-DNA Barcode for the Identification of Different Sage (Salvia) Species

Planta Medica ◽  
2021 ◽  
Author(s):  
Iffat Parveen ◽  
Natascha Techen ◽  
Sara M. Handy ◽  
Jing Li ◽  
Charles Wu ◽  
...  
Keyword(s):  
Internal Transcribed Spacer ◽  
Dna Barcode ◽  
Nuclear Genome ◽  
Nuclear Gene ◽  
Starch Synthase ◽  
Species Discrimination ◽  
Success Rates ◽  
Discrimination Ability ◽  
Internal Transcribed Spacer 2 ◽  
Granule Bound Starch Synthase

AbstractMorphological similarity within species makes the identification and authentication of Salvia species challenging, especially in dietary supplements that contain processed root or leaf powder of different sage species. In the present study, the species discriminatory power of 2 potential DNA barcode regions from the nuclear genome was evaluated in 7 medicinally important Salvia species from the family Lamiaceae. The nuclear internal transcribed spacer 2 and the exon 9 – 14 region of low copy nuclear gene WAXY coding for granule-bound starch synthase 1 were tested for their species discrimination ability using distance, phylogenetic, and BLAST-based methods. A novel 2-step PCR method with 2 different annealing temperatures was developed to achieve maximum amplification from genomic DNA. The granule-bound starch synthase 1 region showed higher amplification and sequencing success rates, higher interspecific distances, and a perfect barcode gap for the tested species compared to the nuclear internal transcribed spacer 2. Hence, these novel mini-barcodes generated from low copy nuclear gene regions (granule-bound starch synthase) that were proven to be effective barcodes for identifying 7 Salvia species have potential for identification and authentication of other Salvia species.

Comparative efficacy of four candidate DNA barcode regions for identification of Vicia species

2015 ◽  
Vol 15 (4) ◽  
pp. 286-295 ◽  
Author(s):  
Sebastin Raveendar ◽  
Jung-Ro Lee ◽  
Donghwan Shim ◽  
Gi-An Lee ◽  
Young-Ah Jeon ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Dna Barcode ◽  
Resolving Power ◽  
Conservation Strategies ◽  
Species Discrimination ◽  
Dna Barcodes ◽  
Additional Tool ◽  
Germplasm Collections ◽  
Classification Tool ◽  
Individual Locus

AbstractThe genus Vicia L., one of the earliest domesticated plant genera, is a member of the legume tribe Fabeae of the subfamily Papilionoideae (Fabaceae). The taxonomic history of this genus is extensive and controversial, which has hindered the development of taxonomic procedures and made it difficult to identify and share these economically important crop resources. Species identification through DNA barcoding is a valuable taxonomic classification tool. In this study, four DNA barcodes (ITS2, matK, rbcL and psbA-trnH) were evaluated on 110 samples that represented 34 taxonomically best-known species in the Vicia genus. Topologies of the phylogenetic trees based on an individual locus were similar. Individual locus-based analyses could not discriminate closely related Vicia species. We proposed a concatenated data approach to increase the resolving power of ITS2. The DNA barcodes matK, psbA-trnH and rbcL were used as an additional tool for phylogenetic analysis. Among the four barcodes, three-barcode combinations that included psbA-trnH with any two of the other barcodes (ITS2, matK or rbcL) provided the best discrimination among Vicia species. Species discrimination was assessed with bootstrap values and considered successful only when all the conspecific individuals formed a single clade. Through sequencing of these barcodes from additional Vicia accessions, 17 of the 34 known Vicia species could be identified with varying levels of confidence. From our analyses, the combined barcoding markers are useful in the early diagnosis of targeted Vicia species and can provide essential baseline data for conservation strategies, as well as guidance in assembling germplasm collections.

scholarly journals New or little-known Boreoheptagyia (Diptera, Chironomidae) in China inferred from morphology and DNA barcodes

ZooKeys ◽  
2021 ◽  
Vol 1040 ◽  
pp. 187-200
Author(s):  
Xiao-Long Lin ◽  
Hai-Jun Yu ◽  
Xin-Hua Wang ◽  
Wen-Jun Bu ◽  
Chun-Cai Yan ◽  
...  
Keyword(s):  
Dna Barcode ◽  
Morphological Characteristics ◽  
Dna Barcodes ◽  
Neighbor Joining ◽  
Male Adult ◽  
Male And Female ◽  
Associated Data

The male adult of Boreoheptagyia zhengi Lin & Liu, sp. nov. is described and illustrated based on material collected in China. Associated morphological characteristics and reference to its DNA barcode are provided. Boreoheptagyia kurobebrevis (Sasa & Okazawa, 1992) is newly recorded from China based on both a male and female, with additional associated data on the DNA barcode of the male adult. A neighbor-joining tree based on available Boreoheptagyia DNA barcodes and a key to the adults of Boreoheptagyia from China are given.

scholarly journals A DNA barcode database for the woody plants of Japan

2021 ◽  
Author(s):  
Suzuki SETSUKO ◽  
Kensuke YOSHIMURA ◽  
Saneyoshi UENO ◽  
James Raymond Peter WORTH ◽  
Tokuko UJINO-IHARA ◽  
...  
Keyword(s):  
Chloroplast Dna ◽  
Woody Plants ◽  
Dna Barcode ◽  
Species Level ◽  
Dna Barcodes ◽  
Genus Level ◽  
Chloroplast Dna Regions ◽  
Total Species ◽  
Level Identification

DNA barcode databases are increasingly available for a range of organisms facilitating the wide application of DNA barcode –based pursuits. Here we announce the development of a comprehensive DNA barcode database of the Japanese woody flora representing 43 orders, 99 families, 303 genera and 834 species and comprising 77.3% of genera and 72.2% of species of woody plants in Japan. A total of 6,216 plant specimens were collected from 223 sites (municipalities, i.e. city, town, village) across the subtropical, temperate, boreal and alpine biomes in Japan with most species represented by multiple accessions. This database utilised three chloroplast DNA regions (rbcL, trnH –psbA and matK) and consists of 14,404 barcode sequences. Individual regions varied in their identification rates with species-level and genus-level rates for rbcL, trnH –psbA and matK being 57.4%/ 96.2%, 78.5%/ 99.1 % and 67.8%/ 98%, respectively. Identification rates were higher using region combinations with total species level rates for two region combinations (rbcL & trnH, rbcL & matK, and trnH –psbA & matK) ranging between 90.6 —95.8%, and for all three regions equal to 98.6%. Genus level identification rates were even higher ranging between 99.7 —100% for two region combinations and being 100% for the three regions. These results indicate that this DNA barcode database is an effective resource for investigations of woody plants in Japan using DNA barcodes and provides a useful template for development of libraries for other components of the Japanese flora.

scholarly journals DNA barcode library for European Gelechiidae (Lepidoptera) suggests greatly underestimated species diversity

ZooKeys ◽  
2020 ◽  
Vol 921 ◽  
pp. 141-157 ◽  
Author(s):  
Peter Huemer ◽  
Ole Karsholt ◽  
Leif Aarvik ◽  
Kai Berggren ◽  
Oleksiy Bidzilya ◽  
...  
Keyword(s):  
Species Diversity ◽  
Dna Barcode ◽  
Species Level ◽  
Coi Gene ◽  
Species Discrimination ◽  
Nominal Species ◽  
Nearest Neighbour ◽  
Cryptic Diversity ◽  
Dna Barcodes ◽  
First Time

For the first time, a nearly complete barcode library for European Gelechiidae is provided. DNA barcode sequences (COI gene – cytochrome c oxidase 1) from 751 out of 865 nominal species, belonging to 105 genera, were successfully recovered. A total of 741 species represented by specimens with sequences ≥ 500bp and an additional ten species represented by specimens with shorter sequences were used to produce 53 NJ trees. Intraspecific barcode divergence averaged only 0.54% whereas distance to the Nearest-Neighbour species averaged 5.58%. Of these, 710 species possessed unique DNA barcodes, but 31 species could not be reliably discriminated because of barcode sharing or partial barcode overlap. Species discrimination based on the Barcode Index System (BIN) was successful for 668 out of 723 species which clustered from minimum one to maximum 22 unique BINs. Fifty-five species shared a BIN with up to four species and identification from DNA barcode data is uncertain. Finally, 65 clusters with a unique BIN remained unidentified to species level. These putative taxa, as well as 114 nominal species with more than one BIN, suggest the presence of considerable cryptic diversity, cases which should be examined in future revisionary studies.

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.

Phyllocnistis podocarpa sp. nov. (Lepidoptera, Gracillariidae), a buddhist pine leaf-miner from Japan: taxonomy, DNA barcodes, damage and parasitoids

Zootaxa ◽  
2018 ◽  
Vol 4422 (4) ◽  
pp. 558 ◽  
Author(s):  
TENGTENG LIU ◽  
JIE SUN ◽  
BO CAI ◽  
YING WU
Keyword(s):  
Economic Value ◽  
Iucn Red List ◽  
Red List ◽  
Leaf Miner ◽  
Dna Barcodes ◽  
Neighbor Joining ◽  
Parasitoid Species ◽  
Frontal Process ◽  
Podocarpus Macrophyllus ◽  
Garden Plant

Phyllocnistis podocarpa sp. nov., is described from mines in Podocarpus macrophyllus (Family Podocarpaceae). The host plant P. macrophyllus, also known as buddhist pine on the IUCN Red List, is a noticeable garden plant and thus of high economic value. Buddhist pine has been introduced to many other countries from its native habitat in southern Japan. Special attention has been paid for it during the overseas import in China. The morphology of the pupae of P. podocarpa, particularly the frontal process of the head and the spine clusters on terga, ones of the most useful diagnostic characters for species identification of Phyllocnistis on morphology, is demonstrated using SEM. Two parasitoid species of Eulophidae (Hymenoptera) are identified and illustrated. COI barcode sequences are provided along with a Neighbor Joining Tree covering related species for aiding identification. 

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