scholarly journals Species discrimination of novel chloroplast DNA barcodes and their application for identification of Panax (Aralioideae, Araliaceae)

PhytoKeys ◽  
2022 ◽  
Vol 188 ◽  
pp. 1-18
Author(s):  
Nguyen Nhat Linh ◽  
Pham Le Bich Hang ◽  
Huynh Thi Thu Hue ◽  
Nguyen Hai Ha ◽  
Ha Hong Hanh ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Molecular Marker ◽  
Species Level ◽  
Species Discrimination ◽  
Dna Barcodes ◽  
Chloroplast Markers ◽  
Chloroplast Genomes ◽  
Outgroup Species ◽  
Unidentified Species ◽  
Level Identification

Certain species within the genus Panax L. (Araliaceae) contain pharmacological precious ginsenosides, also known as ginseng saponins. Species containing these compounds are of high commercial value and are thus of particular urgency for conservation. However, within this genus, identifying the particular species that contain these compounds by morphological means is challenging. DNA barcoding is one method that is considered promising for species level identification. However, in an evolutionarily complex genus such as Panax, commonly used DNA barcodes such as nrITS, matK, psbA-trnH, rbcL do not provide species-level resolution. A recent in silico study proposed a set of novel chloroplast markers, trnQ-rps16, trnS-trnG, petB, and trnE-trnT for species level identification within Panax. In the current study, the discriminatory efficiency of these molecular markers is assessed and validated using 91 reference barcoding sequences and 38 complete chloroplast genomes for seven species, one unidentified species and one sub-species of Panax, and two outgroup species of Aralia L. along with empirical data of Panax taxa present in Vietnam via both distance-based and tree-based methods. The obtained results show that trnQ-rps16 can classify with species level resolution every clade tested here, including the highly valuable Panax vietnamensis Ha et Grushv. We thus propose that this molecular marker to be used for identification of the species within Panax to support both its conservation and commercial trade.

scholarly journals Assessing the reliability of medicinal Dendrobium sequences in GenBank for botanical species identification

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hoi-Yan Wu ◽  
Kwun-Tin Chan ◽  
Grace Wing-Chiu But ◽  
Pang-Chui Shaw
Keyword(s):  
Species Identification ◽  
Dna Sequences ◽  
Species Level ◽  
Research Groups ◽  
Voucher Specimen ◽  
Botanical Species ◽  
Promising Tool ◽  
Chloroplast Genomes ◽  
Level Identification ◽  
Annotation Quality

AbstractDNA-based method is a promising tool in species identification and is widely used in various fields. DNA barcoding method has already been included in different pharmacopoeias for identification of medicinal materials or botanicals. Accuracy and validity of DNA-based methods rely on the accuracy and taxonomic reliability of the DNA sequences in the database to be compared against. Here we evaluated the annotation quality and taxonomic reliability of selected barcode loci (rbcL, matK, psbA-trnH, trnL-trnF and ITS) of 41 medicinal Dendrobium species downloaded from GenBank. Annotations of most accessions are incomplete. Only 53.06% of the 2041 accessions downloaded contain a reference to a voucher specimen. Only 31.60% and 4.8% of the entries are annotated with country of origin and collector or assessor, respectively. Taxonomic reliability of the sequences was evaluated by a Megablast search based on similarity to sequences submitted by other research groups. A small number of sequences (211, 7.14%) was regarded as highly doubted. Moreover, 10 out of 60 complete chloroplast genomes contain highly doubted sequences. Our findings suggest that sequences of GenBank should be used with caution for species-level identification. The scientific community should provide more important information regarding identity and traceability of the sample when they deposit sequences to public databases.

scholarly journals Review of the North American fauna of Drymeia Meigen (Diptera, Muscidae) and evaluation of DNA barcodes for species-level identification in the genus

ZooKeys ◽  
2021 ◽  
Vol 1024 ◽  
pp. 31-89
Author(s):  
Jade Savage ◽  
Vera S. Sorokina
Keyword(s):  
New Species ◽  
Prior Knowledge ◽  
North American ◽  
Interspecific Variation ◽  
Species Level ◽  
Dna Barcodes ◽  
The North ◽  
Species Groups ◽  
Annotated Checklist ◽  
Level Identification

The North American fauna of Drymeia Meigen was studied. Four new species are described (Drymeia huckettisp. nov., Drymeia pontisp. nov., Drymeia vockerothisp. nov., Drymeia woodorumsp. nov.), and three new synonymies are proposed: Drymeia amnicola (Huckett, 1966) (= Drymeia rivalis (Huckett, 1966), syn. nov.); Drymeia glacialis (Rondani, 1866) (= Drymeia alpicola (Rondani, 1871), syn. nov.); and Drymeia spinitarsis (Aldrich, 1918) (= Drymeia longiseta Sorokina & Pont, 2015, syn. nov.). An annotated checklist, DNA barcodes (when available), and keys for each sex of the 24 named species of North American Drymeia are provided. The utility of DNA barcodes for the identification of Drymeia species across a wide geographical range was explored using sequences from five countries. A match between morphology and DNA barcodes was found for 71% (22/31) of species studied (including three unnamed taxa). The remaining nine species clustered into two groups of taxa with very little interspecific variation within clusters (groups of two and seven species). Caution is advised against using DNA barcoding as the only determination tool for Drymeia material without prior knowledge of its limitations for certain species groups.

scholarly journals First known larva of omicrine genus Psalitrus d’Orchymont (Coleoptera, Hydrophilidae)

2019 ◽  
Vol 66 (1) ◽  
pp. 107-118 ◽  
Author(s):  
Yûsuke N. Minoshima
Keyword(s):  
Molecular Marker ◽  
Cytochrome Oxidase ◽  
Dna Barcoding ◽  
Head Capsule ◽  
Species Level ◽  
Mitochondrial Cytochrome ◽  
Larval Morphology ◽  
Fukuoka Prefecture ◽  
Mitochondrial Cytochrome Oxidase ◽  
Level Identification

The larval morphology of the water scavenger beetlePsalitrusyamatensisHoshina & Satô, 2005 is described based on a specimen collected from Fukuoka Prefecture, Kyushu, Japan. This is the first description of the larval morphology of the hydrophilid genusPsalitrusd’Orchymont, 1919, as well as the first description of larval chaetotaxy of the tribe Omicrini. Species-level identification of the larva was performed using DNA barcoding of a molecular marker: a 658 bp fragment of the mitochondrial cytochrome oxidase I. A description including chaetotaxy of head capsule and head appendages, diagnosis, and illustrations of the larva is provided.Psalitruslarvae can be distinguished from other known larvae of the tribe Omicrini by the morphology of the head and legs. The larva shares characters with other known larvae of Omicrini; potential plesiomorphies are shared with Cylominae and aquatic hydrophilids; some characters are also shared with larvae of Megasternini and Sphaeridiini.

scholarly journals Terrestrial planarians (Platyhelminthes, Tricladida, Terricola) from the Iberian peninsula: first records of the family Rhynchodemidae, with the description of a new Microplana species

1998 ◽  
Vol 67 (4) ◽  
pp. 267-276 ◽  
Author(s):  
Eduardo Mateos ◽  
Gonzalo Giribet ◽  
Salvador Carranza
Keyword(s):  
Molecular Markers ◽  
Molecular Marker ◽  
Iberian Peninsula ◽  
Species Level ◽  
Bursa Copulatrix ◽  
The Family ◽  
Spanish Pyrenees ◽  
Characteristic Features ◽  
First Time ◽  
Land Planarian

The first records of terrestrial planarians belonging to the family Rhynchodemidae are reported for the Iberian Peninsula. A new endemic species from the Spanish Pyrenees, Microplana Nana sp. nov., is described. The characteristic features of this species are: i) small size (8-10 mm) in adult individuals, ii) very long conical penis papilla and iii) absence of seminal vesicle, bursa copulatrix, genito-intestinal duct, and well-developed penial bulb. Moreover, the widespread common European land planarian Microplana terrestris (Müller, 1774) is reported for the first time from the Iberian Peninsula. The two species, M. nana sp. nov. and M. terrestris, are described by means of external morphology using histological sections, and have been characterized by the ITS-1 molecular marker. The study of molecular markers such as ITS-1 is proposed as a powerful technique for identification at the species level in terrestrial planarians.

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.

scholarly journals Uncovering dynamic evolution in the plastid genome of seven Ligusticum species provides insights into species discrimination and phylogenetic implications

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Can Yuan ◽  
Xiufen Sha ◽  
Miao Xiong ◽  
Wenjuan Zhong ◽  
Yu Wei ◽  
...  
Keyword(s):  
Plastid Genome ◽  
Species Discrimination ◽  
Chloroplast Genomes ◽  
Genomic Arrangement ◽  
Phylogenetic Implications ◽  
Solid Foundation ◽  
Conserved Gene ◽  
Fine Resolution ◽  
Genome Scale ◽  
First Time

AbstractLigusticum L., one of the largest members in Apiaceae, encompasses medicinally important plants, the taxonomic statuses of which have been proved to be difficult to resolve. In the current study, the complete chloroplast genomes of seven crucial plants of the best-known herbs in Ligusticum were presented. The seven genomes ranged from 148,275 to 148,564 bp in length with a highly conserved gene content, gene order and genomic arrangement. A shared dramatic decrease in genome size resulted from a lineage-specific inverted repeat (IR) contraction, which could potentially be a promising diagnostic character for taxonomic investigation of Ligusticum, was discovered, without affecting the synonymous rate. Although a higher variability was uncovered in hotspot divergence regions that were unevenly distributed across the chloroplast genome, a concatenated strategy for rapid species identification was proposed because separate fragments inadequately provided variation for fine resolution. Phylogenetic inference using plastid genome-scale data produced a concordant topology receiving a robust support value, which revealed that L. chuanxiong had a closer relationship with L. jeholense than L. sinense, and L. sinense cv. Fuxiong had a closer relationship to L. sinense than L. chuanxiong, for the first time. Our results not only furnish concrete evidence for clarifying Ligusticum taxonomy but also provide a solid foundation for further pharmaphylogenetic investigation.

scholarly journals First Report of a Gall Midge Species (Diptera: Cecidomyiidae) Associated With Pistachios

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Farshid O Sirjani ◽  
Edwin E Lewis
Keyword(s):  
Gall Midge ◽  
Species Level ◽  
Plant Tissues ◽  
First Report ◽  
Branch Dieback ◽  
First Time ◽  
Level Identification

Abstract A new dipterous pest is reported, for the first time, on commercial pistachios from Sirjan, Kerman province, Iran. The genus of the insect was determined to be Resseliella Seitner (Diptera: Cecidomyiidae). Adults are light brown to brown in color and 0.8–1.5 mm in length with females, generally, slightly larger than males. Females have an elongated ovipositor, which is characteristic of the genus. Larvae are orange in color, 2–3 mm in length in the later instars, feed under bark without inducing galls, and cause branch dieback on trees of various ages. Brown to black discolorations are observed on plant tissues under bark where the larvae feed. Infestations observed on current and the previous—year’s growths, ranged from 0.5 to 1.2 cm in diameter, and all located in outer branches. Dry leaves and fruit clusters on infested branches remain attached, which may be used to recognize infestation by the gall midge. Dark-colored, sunken spots with splits on the bark located at the base of the wilted sections of the shoots also are symptoms of Resseliella sp. larval activity. Species-level identification of the gall midge is currently underway.

scholarly journals Comparative analysis of chloroplast genomes of cultivars and wild species of sweetpotato (Ipomoea batatas [L.] Lam)

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Shizhuo Xiao ◽  
Pan Xu ◽  
Yitong Deng ◽  
Xibin Dai ◽  
Lukuan Zhao ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Genetic Structure ◽  
Chloroplast Genome ◽  
Wild Species ◽  
Ipomoea Batatas ◽  
Nuclear Genome ◽  
Ipomoea Trifida ◽  
Chloroplast Markers ◽  
Chloroplast Genomes ◽  
Chloroplast Dna Markers

Abstract Background Sweetpotato (Ipomoea batatas [L.] Lam.) is an important food crop. However, the genetic information of the nuclear genome of this species is difficult to determine accurately because of its large genome and complex genetic background. This drawback has limited studies on the origin, evolution, genetic diversity and other relevant studies on sweetpotato. Results The chloroplast genomes of 107 sweetpotato cultivars were sequenced, assembled and annotated. The resulting chloroplast genomes were comparatively analysed with the published chloroplast genomes of wild species of sweetpotato. High similarity and certain specificity were found among the chloroplast genomes of Ipomoea spp. Phylogenetic analysis could clearly distinguish wild species from cultivars. Ipomoea trifida and Ipomoea tabascana showed the closest relationship with the cultivars, and different haplotypes of ycf1 could be used to distinguish the cultivars from their wild relatives. The genetic structure was analyzed using variations in the chloroplast genome. Compared with traditional nuclear markers, the chloroplast markers designed based on the InDels on the chloroplast genome showed significant advantages. Conclusions Comparative analysis of chloroplast genomes of 107 cultivars and several wild species of sweetpotato was performed to help analyze the evolution, genetic structure and the development of chloroplast DNA markers of sweetpotato.

scholarly journals Comparative analysis and phylogenetic investigation of Hong Kong Ilex chloroplast genomes

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Bobby Lim-Ho Kong ◽  
Hyun-Seung Park ◽  
Tai-Wai David Lau ◽  
Zhixiu Lin ◽  
Tae-Jin Yang ◽  
...  
Keyword(s):  
Hong Kong ◽  
Comparative Analysis ◽  
Phylogenetic Relationships ◽  
Species Level ◽  
The Other ◽  
Trna Genes ◽  
Protein Coding ◽  
Chloroplast Genomes ◽  
Plant Group ◽  
Ilex Rotunda

AbstractIlex is a monogeneric plant group (containing approximately 600 species) in the Aquifoliaceae family and one of the most commonly used medicinal herbs. However, its taxonomy and phylogenetic relationships at the species level are debatable. Herein, we obtained the complete chloroplast genomes of all 19 Ilex types that are native to Hong Kong. The genomes are conserved in structure, gene content and arrangement. The chloroplast genomes range in size from 157,119 bp in Ilex graciliflora to 158,020 bp in Ilex kwangtungensis. All these genomes contain 125 genes, of which 88 are protein-coding and 37 are tRNA genes. Four highly varied sequences (rps16-trnQ, rpl32-trnL, ndhD-psaC and ycf1) were found. The number of repeats in the Ilex genomes is mostly conserved, but the number of repeating motifs varies. The phylogenetic relationship among the 19 Ilex genomes, together with eight other available genomes in other studies, was investigated. Most of the species could be correctly assigned to the section or even series level, consistent with previous taxonomy, except Ilex rotunda var. microcarpa, Ilex asprella var. tapuensis and Ilex chapaensis. These species were reclassified; I. rotunda was placed in the section Micrococca, while the other two were grouped with the section Pseudoaquifolium. These studies provide a better understanding of Ilex phylogeny and refine its classification.

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