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65 results for “Plant DNA barcoding”
State of biodiversity documentation in the Philippines: Metadata gaps, taxonomic biases, and spatial biases in the DNA barcode data of animal and plant taxa in the context of species occurrence data
<p>These files can be categorized into three groups: (1) raw datasets obtained from public databases (i.e., GBIF, BOLD, and GenBank), (2) manually edited files needed for parsing and analysis, and (3) supplementary files for spatial analysis. All are used in the examination of gaps and biases present in Philippine biodiversity data, which can direct research on the taxa and spatial regions that need more sampling.</p>
Data from: Microfluidic Enrichment Barcoding (MEBarcoding): a new method for high throughput plant DNA barcoding
<p>DNA barcoding has become a valuable tool to support species identification with a broad range of applications in fields such as traditional taxonomy, ecology, forensics, food analysis, and environmental science. We introduce Microfluidics Enrichment Barcoding (MEBarcoding) for plant DNA Barcoding, a cost-effective method for high throughput DNA barcoding. MEBarcoding uses the Fluidigm Access Array™ to simultaneously amplify targeted regions for 48 DNA samples and hundreds of PCR primer pairs (a total of 23,040 PCR products) during a single thermal cycling protocol. A second generation instrument from Fluidigm, called the Juno™, can accommodate 192 DNA samples simultaneously. As a proof of concept, we developed a microfluidic PCR workflow using the Fluidigm Access Array™ and Illumina MiSeq to generate new sequences from 96 samples for each of the four primary DNA barcode loci in plants: rbcL, matK, trnH-psbA, and ITS (384 total sequences). This workflow was used to build a reference library that includes 78 families and 96 genera from all major plant lineages, including bryophytes, ferns and lycophytes, gymnosperms, and all major groups of angiosperms, which are currently lacking in public databases. Our results demonstrate that this technique offers a highly efficient alternative method to traditional PCR and Sanger sequencing by increasing the estimated number of plant DNA barcodes that can be sequenced by a single technician in one week by 800%, at a reduced cost, and by generating a barcode library with a more comprehensive taxonomic coverage.</p>
Data from: Microfluidic Enrichment Barcoding (MEBarcoding): a new method for high throughput plant DNA barcoding
Open the record for dataset details and reuse information.
Data from: Plant DNA barcodes and the influence of gene flow
Success of species assignment using DNA barcodes has been shown to vary among plant lineages due to a wide range of different factors. In this study, we confirm the theoretical prediction that gene flow influences species assignment with simulations and a literature survey. We show that the genome experiencing the highest gene flow is, in the majority of the cases, the best suited for species delimitation. Our results clearly suggest that, for most angiosperm groups, plastid markers will not be the most appropriate for use as DNA barcodes. We therefore advocate shifting the focus from plastid to nuclear markers to achieve an overall higher success using DNA barcodes.
FIGURES 24–28. Wagnerinus frugivorus Yoshitake. 24. Host plant, Weigela middendorffiana. 25 in A new Wagnerinus (Coleoptera: Curculionidae) from northern Japan: Description including a DNA barcode
FIGURES 24–28. Wagnerinus frugivorus Yoshitake. 24. Host plant, Weigela middendorffiana. 25. Habitat in Aizankei, Kamikawa, Hokkaido. 26. Adult on a leaf of W. middendorffiana. 27. Third-instar larva in a seed capsule of W. middendorffiana. 28. Pupa in the soil.
Supplementary material 1 from: Zúñiga JD, Gostel MR, Mulcahy DG, Barker K, Hill A, Sedaghatpour M, Vo SQ, Funk VA, Coddington JA (2017) Data Release: DNA barcodes of plant species collected for the Global Genome Initiative for Gardens Program, National Museum of Natural History, Smithsonian Institution. PhytoKeys 88: 119-122. https://doi.org/10.3897/phytokeys.88.14607
List of samples collected for the Global Genome Initiative for Gardens project selected for DNA barcoding, with GenBank accession numbers and genetic sample identification numbers. All the sequences are included in the GGI-Gardens BioProject. : Explanation note: List of samples collected for the Global Genome Initiative for Gardens project selected for DNA barcoding, with GenBank accession numbers and genetic sample identification numbers.
FIGURE 13 in Exploring species diversity and host plant associations of leaf-mining micromoths (Lepidoptera: Gracillariidae) in the Russian Far East using DNA barcoding
FIGURE 13. Mines of Phyllonorycter spp. from the Russian Far East. (A–B) Ph. ringoniella, host plant Malus mandshurica; (C–D) Ph. sorbicola, Prunus padus and Prunus maackii respectively; (E) Ph. strigulatella, Alnus hirsuta; (F) Phyllonorycter sp. 1, Tilia mandshurica; (G–H) Phyllonorycter sp. 6, Acer pseudosieboldianum. Indications: (m) mine; (t) epidermal tunnel; (b) blotch. Close up: (B–C, F, H) mine. Sampling locations: (A–D, F–H) PK, Gornotaezhnoe, MTS and forest, 22–26.VII.2016; (E) SO, Sakhalin Isl., Yuzhno-Sakhalinsk, 11–20.VII.2017.
FIGURE 15 in Exploring species diversity and host plant associations of leaf-mining micromoths (Lepidoptera: Gracillariidae) in the Russian Far East using DNA barcoding
FIGURE 15. Similarity of gracillariid faunas of the Russian regions and Japan. Gracillariid species number is given in the corresponding bar, number of shared species is in the circles. The similarity Sørensen–Dice coefficient is given in red.
FIGURE 12 in Exploring species diversity and host plant associations of leaf-mining micromoths (Lepidoptera: Gracillariidae) in the Russian Far East using DNA barcoding
FIGURE 12. Mines of Phyllonorycter spp. from the Russian Far East. (A) Ph. cretata, host plant Quercus mongolica; (B) Ph. ermani, B. platyphylla; (C) Ph. issikii, Tilia mandshurica; (D) Ph. japonica, Corylus mandshurica; (E) sampling location of Ph. junoniella; (F) Ph. nigristella, Quercus dentata; (G) Ph. orientalis, Acer pictum; (H) Ph. pastorella, Salix sp. Indications: (m) mine; (t) epidermal tunnel; (l) larva; (p) pupa. Close up: (B) deformation of the leaf due to mines (the view from the upper side); (C, F–H) mine, (E) the bush from that the specimens were collected. Sampling locations: (A–B, F) SO, Sakhalin Isl., Yuzhno- Sakhalinsk, Gagarin's Park, 11–20.VII.2017; (E) SO, Sakhalin Isl., Susunay mountain range, 14.VII.2017; (C–D, G–H) PK, Gornotaezhnoe, MTS and forest, 22–26.VII.2016.
FIGURE 8 in Exploring species diversity and host plant associations of leaf-mining micromoths (Lepidoptera: Gracillariidae) in the Russian Far East using DNA barcoding
FIGURE 8. Male genitalia of Phyllonorycter and Cameraria spp. from the Russian Far East. (A) Ph. reduncata, host plant Lonicera maackii, [23Pr-2016-male]; (B) Ph. ringoniella, Malus mandshurica, [10Prin-2016-male]; (C) Ph. similis, Quercus dentata, [8Psim-2016-male]; (D) Ph. ulmifoliella [15Pu-2016-male]; (E) Cameraria niphonica, Acer pseudosieboldianum, [1Cn-2016-male]. Sampling location: Gornotaezhnoe, Primorskii Krai, 22–26.VII.2016. Scale bars: (A–D) 200, (E) 250 µm.
FIGURE 4 in Exploring species diversity and host plant associations of leaf-mining micromoths (Lepidoptera: Gracillariidae) in the Russian Far East using DNA barcoding
FIGURE 4. Forewing pattern of Phyllonorycter spp. from the Russian Far East. (A) Ph. caraganella, host plant Caragana fruticosa, NK- 184-16-9A; (B) Ph. cavella, Betula dahurica, 111.1; (C) Ph. cretata, Quercus mongolica, NK-85-17-4; (D) Ph. issikii, T. mandshurica, NK596; (E) Ph. japonica, Corylus mandshurica, 36.2; (F) Ph. jozanae, Crataegus sp., 44.1; (G) Ph. kisoensis, Alnus hirsuta, 45.1; (H) Ph. pastorella, Salix sp., 49.1; (I) Ph. reduncata, Lonicera maackii, 55.3; (K) Ph. ringoniella, Malus mandshurica, NK-179-16-1A; (L) Ph. similis, Quercus dentata, 42.1; (M) Ph. ulmifoliella, 37.1. Sampling locations: (A) PK, Rakovka, 27.VII.2016; (B, D–M) ibidem, Gornotaezhnoe, 16.VII.2013 (D), 22-25.VII.2016 (B, E–M); (C) SO, Sakhalin Isl., Yuzhno-Sakhalinsk, 12.VII.2017. Scale bars 1 mm.
FIGURE 3 in Exploring species diversity and host plant associations of leaf-mining micromoths (Lepidoptera: Gracillariidae) in the Russian Far East using DNA barcoding
FIGURE 3. COI Neighbor-Joining tree of Gracillariidae species sampled in the Russian Far East. Each specimen is accompanied by its sequence number (BOLD "process ID"), species name, sampling location and host plant. Sampling locations are given between two vertical lines, i.e. |Skov.| Skovorodino; |Blag.| Blagoveshchensk; |MTS| Komarov Mountain-Taiga Station FEB RAS and the forest around; |Rakovka|, |Glukhovka| forest around the villages Rakovka and Glukhovka respectively; |Vlad.| Vladivostok; |Sikhote-Alin| Sikhote-Alin Mountains, national park "Zov tigra", |Y-S| Yuzhno-Sakhalinsk and the area around including Susunay mountain range (see Fig. 1 for details). Host plants: A. pseudosieb.—Acer pseudosieboldianum; * sampling done by sweep netting from the bush, whereas all other gracillariids were collected/ reared directly from their mines. Each leafminer species is supplied with its BIN number retrieved from BOLD; blue BINs correspond to known species, red—new BINs.
FIGURE 1 in Exploring species diversity and host plant associations of leaf-mining micromoths (Lepidoptera: Gracillariidae) in the Russian Far East using DNA barcoding
FIGURE 1. The area of study in the Russian Far East, June–July 2010–2017. Black circles indicate cities, yellow circles with the numbers 1–12 are the sampling locations: (1) AO, Skovorodino, tree plantation nearby train station; (2) AO, Blagoveshchensk, Friendship park; (3) KK, Komsomolsk-na-Amure, tree lines along the road; (4) PK, Gornotaezhnoe, MTS; (5) ibidem, forest; (6) PK, Glukhovka, forest; (7) PK, Rakovka, forest; (8) PK, Vladivostok, suburb, tree plantation; (9) PK, Sikhote-Alin Mountains, national park "Zov tigra"; (10) SO, Sakhalin Isl., Yuzhno-Sakhalinsk, Botanical garden FEB RAS Sakhalin Branch; (11) ibidem, Gagarin park; (12) SO, Sakhalin Isl., Susunay mountain range, pass "Verblyud". In the left corner, on the map of Russia the sampled area is shaded in gray. Regions: (ChAO) Chukotsky Autonomous Okrug, (KamK) Kamchatskii Krai, (MA) Magadanskaya Oblast, (AO) Amurskaya Oblast, (KK) Khabarovskii Krai, (JAO) Jewish Autonomous Oblast, (AO) Amurskaya Oblast, (PK) Primorskii Krai, (SO) Sakhalinskaya Oblast (includes Sakhalin Island and Kuril Islands).
FIGURE 7 in Exploring species diversity and host plant associations of leaf-mining micromoths (Lepidoptera: Gracillariidae) in the Russian Far East using DNA barcoding
FIGURE 7. Male genitalia of Phyllonorycter spp. from the Russian Far East. (A) Phyllonorycter junoniella, genitalia slide [21-male]; (B) Ph. pastorella, host plant Salix sp., [12Pp-2016-male]; (C) Ph. populifoliella, Populus balsamifera, [NK-561- 1-male]; (D) Ph. pseudojezoniella, Acer saccharum, [20Pps-2016-male]; (E) Ph. kisoensis, Alnus hirsuta, [5Pk-2016-male]. Sampling location: (A) SO, Sakhalin Isl., 14.VII.2017; (B, D) PK, Gornotaezhnoe, MTS, 22–26.VII.2016; (C) AO, Blagoveshchensk, 27.VI.2016. Scale bars 200µm.
FIGURE 11 in Exploring species diversity and host plant associations of leaf-mining micromoths (Lepidoptera: Gracillariidae) in the Russian Far East using DNA barcoding
FIGURE 11. Mines and leaf shelters of Gracillaria, Callisto, Parornix and Phyllonorycter spp. from the Russian Far East. (A) Gracillaria sp., host plant Syringa amurensis; (B–C) Callisto sp. on Malus sp.; (D) Parornix ermolaevi, Corylus sieboldiana; (E–F) Ph. caraganella, Caragana fruticosa; (G–H) Ph. cavella, Betula platyphylla, (H) "green island" and the mine. Indications: (m) mine; (b) blotch part of the mine; (t) epidermal tunnel; (e) exit hole; (f–f2) folded leaf margin or leaf tip (the indexes 1 and 2 indicate the order of construction appearance); (g.i.) green island region. Close up: (B, E–G) mine. Sampling locations: (A–D, G–H) PK, Gornotaezhnoe, MTS and forest, 22–27.VII.2016; (E–F) ibidem, Glukhovka, forest, 27.VII.2016.
FIGURE 2 in Exploring species diversity and host plant associations of leaf-mining micromoths (Lepidoptera: Gracillariidae) in the Russian Far East using DNA barcoding
FIGURE 2. Sampling localities in the Russian Far East. (A–C) PK, Gornotaezhnoe, MTS: (A) European woody plant species zone, (B) Juglans mandshurica plantation, (C) East Asian woody plant species zone; (D) PK, 20 km west of MTS, artificial lake on the way to Glukhovka and Rakovka; (E–H) SO, Sakhalin Isl., Susunay mountain range: (E–G) pass "Verblud", sampling and camping area, (H) foothills of the Susunay mountain range, the Erman's birch groove. Personalities: (C) S. Gorokhova, (F) V. Sheiko, (H) N. Kirichenko (the photographs are published with the permission of SG, VS and NK). (PK) Primorskii Krai, (SO) Sakhalinskaya Oblast (includes Sakhalin Island and Kuril Islands).
FIGURE 9 in Exploring species diversity and host plant associations of leaf-mining micromoths (Lepidoptera: Gracillariidae) in the Russian Far East using DNA barcoding
FIGURE 9. Number of gracillariid species found on various plant plants in the Russian Far East in 2010–2017. In some cases, the same gracillariid species were found on more than one plant genus (for example, Gracillaria sp. on Syringa and Fraxinus, Phyllonorycter pastorella on Salix and Populus etc.), therefore the sum of all bars is more than the total number of species identified in the study.
FIGURE 5 in Exploring species diversity and host plant associations of leaf-mining micromoths (Lepidoptera: Gracillariidae) in the Russian Far East using DNA barcoding
FIGURE 5. Female genitalia of gracillariids sampled in the Russian Far East. (A) Micrurapteryx caraganella, host plant Caragana arborescens, Skovorodino, Amurskaya Oblast, 26.VI.2016; genitalia slide [39-female]; (B) Phyllonorycter nipponicella, Quercus mongolica, PK, Gornotaezhnoe, 23.VII.2016, [8-2016-female]. Scale bars: (A) 550, (B) 100 µm.
FIGURE 6 in Exploring species diversity and host plant associations of leaf-mining micromoths (Lepidoptera: Gracillariidae) in the Russian Far East using DNA barcoding
FIGURE 6. Male genitalia of Caloptilia and Phyllonorycter spp. from the Russian Far East. (A) Caloptilia gloriosa, host plant Acer pseudosieboldianum, genitalia slide [13-male]; (B) Phyllonorycter cavella, Betula dahurica, [11-2016-male]; (C) Ph. japonica, Corylus mandshurica, [4-2016-male]; (D) Ph. jozanae, Crataegus sp. [14Pj-2016-male]; (E) Ph. issikii, T. mandshurica, [NK596-male]. Sampling locations: PK, Gornotaezhnoe, (A–D) 22–25.VII.2016, (E) 21.VIII.2015. Scale bars: (A) 350, (B–E) 200 µm.
FIGURE 14 in Exploring species diversity and host plant associations of leaf-mining micromoths (Lepidoptera: Gracillariidae) in the Russian Far East using DNA barcoding
FIGURE 14. Mines, leaf shelters and pupation sites of Phyllonorycter, Chrysaster and Cameraria spp. from the Russian Far East. (A) Phyllonorycter sp. 7, host plant Ulmus glabra; (B–C) Phyllonorycter sp. 8, Juglans mandshurica; (D–E) Chrysaster hagicola, Lespedeza bicolor; (F–G) Cameraria niphonica, Acer pseudosieboldianum and A. caudatum subsp. ukurundense, respectively; (H) Phyllocnistis sp. 1, Salix sp. Indications: (m) mine; (b) blotch part of the mine; (t) epidermal tunnel; (l) larva; (p) pupation site. Close up: (C–G) mine; (H) pupation site. Sampling locations: (A) SO, Sakhalin Isl., Yuzhno-Sakhalinsk, 11–20.VII.2017; (B–H) PK, Gornotaezhnoe, MTS and forest, 22–26.VII.2016.
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