Annals of Botany, Год журнала: 2017, Номер 120(1), С. 51 - 61
Опубликована: Март 14, 2017
The extent to which hybridization leads gene flow between plant species depends on the structure of hybrid populations. However, if this varies locations, barriers might prove permeable in some locations but not others. To assess possible variation population structure, magnitude and direction natural two Chinese endemic species, Rhododendron spiciferum spinuliferum , were evaluated.
Язык: Английский
Journal of Pharmaceutical Analysis, Год журнала: 2023, Номер 13(5), С. 431 - 441
Опубликована: Апрель 5, 2023
DNA barcoding has been widely used for herb identification in recent decades, enabling safety and innovation the field of herbal medicine. In this article, we summarize progress medicine to provide ideas further development application technology. Most importantly, standard barcode extended two ways. First, while conventional barcodes have promoted their versatility fresh or well-preserved samples, super-barcodes based on plastid genomes rapidly developed shown advantages species at low taxonomic levels. Second, mini-barcodes are attractive because they perform better cases degraded from materials. addition, some molecular techniques, such as high-throughput sequencing isothermal amplification, combined with identification, which expanded applications brought about post-DNA-barcoding era. Furthermore, high-species coverage reference libraries constructed sequences increases accuracy credibility discrimination barcodes. summary, should play a key role quality control traditional international trade.
Язык: Английский
Процитировано
49
PLoS ONE, Год журнала: 2015, Номер 10(9), С. e0138993 - e0138993
Опубликована: Сен. 25, 2015
DNA barcoding using a fragment of the mitochondrial cytochrome c oxidase subunit 1 gene (COI) has proven to be successful for species-level identification in many animal groups. However, most studies have been focused on relatively small datasets or large taxonomically high-ranked We explore quality barcodes delimit species diverse chironomid genus Tanytarsus (Diptera: Chironomidae) by different analytical tools. The is species-rich taxon tribe Tanytarsini with more than 400 worldwide, some which can notoriously difficult identify morphology. Our dataset, based sequences generated from own material and publicly available data BOLD, consist 2790 length at least 500 base pairs. A neighbor joining tree this dataset comprises 131 well separated clusters representing 121 morphological Tanytarsus: 77 named, 16 unnamed 28 unidentified theoretical species. For our geographically widespread unambiguously discriminate 94.6% recognized through prior study. Deep intraspecific divergences exist complexes, need further taxonomic appropriate nuclear markers as ecological resolved. cluster into 120-242 molecular operational units (OTUs) depending whether Objective Clustering, Automatic Barcode Gap Discovery (ABGD), Generalized Mixed Yule Coalescent model (GMYC), Poisson Tree Process (PTP), subjective evaluation Index Numbers (BINs) are used. suggest that 4-5% threshold delineate non-biting midges.
Язык: Английский
Процитировано
130
Scientific Reports, Год журнала: 2019, Номер 9(1)
Опубликована: Фев. 26, 2019
Taxus (yew) is both the most species-rich and taxonomically difficult genus in Taxaceae. To date, no study has elucidated complexities of plastid genome (plastome) or examined possibility whole plastomes as super-barcodes across yew species worldwide. In this study, we sequenced from two to three individuals for each 16 recognized (including potential cryptics) Pseudotaxus chienii. Our comparative analyses uncovered several gene loss events that independently occurred yews, resulting a lower number than other Taxaceous genera. Taxus, found isomeric arrangements differ by orientation 35 kb fragment flanked "trnQ-IRs". These exist different ratios within sampled individual, intraspecific shifts major are first reported here Taxus. Moreover, demonstrate entire can be used successfully discriminate all with 100% support, suggesting they useful identification. We also propose accD rrn16-rrn23 promising special barcodes species. newly developed plastomic sequences provide resource conservation genetics endangered yews serve comprehensive data improve models plastome complexity Taxaceae authenticate
Язык: Английский
Процитировано
77
Molecular Biology and Evolution, Год журнала: 2021, Номер 39(1)
Опубликована: Окт. 27, 2021
Abstract Evolutionary radiation is a widely recognized mode of species diversification, but its underlying mechanisms have not been unambiguously resolved for species-rich cosmopolitan plant genera. In particular, it remains largely unknown how biological and environmental factors jointly driven occurrence in specific regions. Here, we use Rhododendron, the largest genus woody plants Northern Hemisphere, to investigate geographic climatic factors, as well functional traits, worked together trigger evolutionary radiations shape global patterns richness based on solid phylogeny. Using 3,437 orthologous nuclear genes, reconstructed first highly supported dated backbone phylogeny Rhododendron comprising 200 that represent all subgenera, sections, nearly multispecies subsections, found most extant originated by when migrated southward from circumboreal areas tropical/subtropical mountains, showing rapid increases both net diversification rate Miocene. We also geographically uneven led much higher diversity Asia than other continents, which was mainly two variables, is, elevation range annual precipitation, were further strengthened adaptation leaf traits. Our study provides good example integrating phylogenomic ecological analyses deciphering radiations, sheds new light intensification Asian monsoon has large genera Himalaya-Hengduan Mountains.
Язык: Английский
Процитировано
76
Molecular Ecology Resources, Год журнала: 2021, Номер 22(1), С. 404 - 414
Опубликована: Июль 26, 2021
Standard plant DNA barcodes based on 2-3 plastid regions, and nrDNA ITS show variable levels of resolution, fail to discriminate among species in many groups. Genome skimming recover complete genome sequences arrays has been proposed as a solution address these resolution limitations. However, few studies have empirically tested what gains are achieved practice. Of particular interest is whether adding substantially more characters will lead an increase discriminatory power, or the limitations standard fundamentally due genomes not tracking boundaries. To this, we used near-complete nuclear ribosomal from Rhododendron compared discrimination success with barcodes. We sampled 218 individuals representing 145 this species-rich taxonomically difficult genus, focusing global biodiversity hotspots Himalaya-Hengduan Mountains. Only 33% were distinguished using ITS+matK+rbcL+trnH-psbA. In contrast, 55% sequences. The vast majority additional characters. Thus, despite previous showing asymptote beyond 3-4 results that demonstrable power possible extensive data. gains, remain unresolved, also reinforce need access multiple unlinked loci obtain transformative plants.
Язык: Английский
Процитировано
61
Molecular Ecology Resources, Год журнала: 2022, Номер 23(2), С. 424 - 439
Опубликована: Окт. 11, 2022
Cymbidium is an orchid genus that has undergone rapid radiation and high ornamental, economic, ecological cultural importance, but its classification based on morphology controversial. The plastid genome (plastome), as extension of plant standard DNA barcodes, been widely used a potential molecular marker for identifying recently diverged species or complicated groups. In this study, we newly generated 237 plastomes 50 (at least two individuals per species) by skimming, covering 71.4% members the Cymbidium. Sequence-based analyses (barcoding gaps automatic barcode gap discovery) tree-based (maximum likelihood, Bayesian inference multirate Poisson tree processes model) were conducted identification Our work provides comprehensive reference library identification. results show compared with barcodes (rbcL + matK) well trnH-psbA, rate plastome increased moderately from 58% to 68%. At same time, propose optimized strategy species. cannot completely resolve Cymbidium, main reasons being incomplete lineage sorting, artificial cultivation, natural hybridization chloroplast capture. To further explore use nuclear data in species, Skmer method was adopted 72%. It appears have vital role are expected be next-generation barcodes.
Язык: Английский
Процитировано
41
Frontiers in Plant Science, Год журнала: 2017, Номер 8
Опубликована: Май 19, 2017
Chloroplast DNA (cpDNA) is frequently used for species demography, evolution, and discrimination of plants. However, the lack efficient universal markers often brings particular challenges genetic studies across different plant groups. In this study, chloroplast genomes from two closely related (Quercus rubra Castanea mollissima) in Fagaceae were compared to explore cpDNA Chinese oak Quercus subgenus Quercus, a diverse group without sufficient molecular differentiation. With comparison, nine 14 plastid selected as barcoding phylogeographic candidates oaks. Five (psbA-trnH, matK-trnK, ycf3-trnS, matK ycf1) candidate barcodes, with addition newly designed ITS single-copy nuclear gene (SAP), then tested on 35 employing four approaches (genetic distance-, BLAST-, character- tree-based methods). The methods showed identification powers character-based method performing best. Of seven barcodes tested, gap was absent all them oaks, while psbA-trnH provided highest resolution (30.30%) BLAST-based methods, respectively. six-marker combination (psbA-trnH + matK-trnK ycf1 SAP) best (84.85%) using results additional implications taxonomy oaks subg. basically identifying three major infrageneric clades among (corresponding Groups Cerris Ilex) referenced previous phylogenetic classification Quercus. While morphology-based allocations proposed challenged. A low variation rate genome, complex speciation patterns involving incomplete lineage sorting, interspecific hybridization introgression, possibly have negative impacts assignment phylogeny species.
Язык: Английский
Процитировано
86
Scientific Reports, Год журнала: 2018, Номер 8(1)
Опубликована: Янв. 25, 2018
DNA barcoding has been proposed as a useful tool for forensic wood identification and development of reliable reference library is an essential first step. Xylaria (wood collections) are potentially enormous data repositories if information could be extracted from specimens. In this study, 31 xylarium specimens 8 leaf six important commercial species Pterocarpus were selected to investigate the reliability barcodes authentication at level determine feasibility building barcode libraries Four (ITS2, matK, ndhF-rpl32 rbcL) their combination tested evaluate discrimination ability with both TaxonDNA tree-based analytical methods. The results indicated that matK + ITS2 yielded best studied. mini-barcode (167-173 bps) performed well distinguishing P. santalinus its anatomically inseparable tinctorius. Results study verified not only using specimens, but importance rather than leaves source tissue, when botanical material identified.
Язык: Английский
Процитировано
72
Frontiers in Ecology and Evolution, Год журнала: 2020, Номер 8
Опубликована: Май 15, 2020
The Qinghai-Tibet Plateau sensu lato (QTP s.l.) harbors an exceptionally high biodiversity, especially at its southeastern margin: this area encompasses the Hengduan Mountains and eastern Himalayas, which have been listed as biodiversity hotspots. To contrary, plateau interior (namely stricto, QTP s.s.) is relatively species-poor because of particularly harsh climate. With contrasting geological histories environmental conditions Mountains, Himalayas s.s., it would be expected that floristic compositions diversity patterns these three regions differ between each other. compare regions, we assembled data on seed plant's distribution in based county-level mapping from published monographs online databases, then analyzed their features species (horizontal elevational). We found hosted most plant (8,439), expected. highest percentage shrub (22.88%) tree (9.80%) were whereas herbaceous (81.50%) more prominent s.s.. also had species-rich genera (10) with than 50% total China. Also, temperate dominated across a (77.61%) within Across s.l., gradually decreased part to northwest, plants distributed southern margin East Himalayas. Along elevational gradients, richness all demonstrated hump-shape curve, but elevation zone differed for type life-form regions. Our study sets base exploring origin evolution mountain taxa, well provides snapshot current distribution, will certainly modified by climate change.
Язык: Английский
Процитировано
60
Frontiers in Plant Science, Год журнала: 2022, Номер 13
Опубликована: Фев. 25, 2022
The Fritillaria is an extremely complicated genus in taxonomy and phylogeny, which contains numerous medicinal species China. Both traditional characteristic-based universal DNA barcodes (ITS, trnH - psbA , rbcL ) are difficult to effectively identify the species. Here, we generated a large dataset of chloroplast genomes from multiple accessions per evaluate their effectiveness discrimination. Moreover, phylogeny China was explored based on complete genomes, then divergence times each node were estimated. results showed that all 21 here (including two suspicious species) could be correctly discriminated using cpDNA except F. cirrhosa suggested super-barcode greatly enhance discriminatory resolution for genera. Furthermore, four regions ( ycf1 matK trnG-GCC rpoC1 gained remarkably higher than other plastid regions, but only might suitable consideration its lengths. Phylogenomic analysis subgenus divided into major clades with obvious geographic structure. Among them, Clade I, mainly distributed southwest China, young group. according analysis, taxonomic treatments species, namely “ omeiensis ” hupehensis Flora (2000) questionable need further revision. Molecular dating revealed both origin as well clades, significantly associated geological climatic fluctuations during Middle Late Miocene. This study would enrich case studies provide new insights speciation, lineage diversification, biogeography
Язык: Английский
Процитировано
36