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408 results for “Cyst”
Data from: A metagenetics approach to determine the diversity and distribution of cyst nematodes at the level of the country, the field and the individual
Distinct populations of the potato cyst nematode (PCN) Globodera pallida exist in the UK that differ in their ability to overcome various sources of resistance. An efficient method for distinguishing between populations would enable pathogen-informed cultivar choice in the field. Science and Advice for Scottish Agriculture (SASA) annually undertake national DNA diagnostic tests to determine the presence of PCN in potato seed and ware land by extracting DNA from soil floats. These DNA samples provide a unique resource for monitoring the distribution of PCN and further interrogation of the diversity within species. We identify a region of mitochondrial DNA descriptive of three main groups of G. pallida present in the UK, and adopt a metagenetics approach to the sequencing and analysis of all SASA samples simultaneously. Using this approach we describe the distribution of G. pallida mitotypes across Scotland with field-scale resolution. Most fields contain a single mitotype, one fifth contain a mix of mitotypes, and less than 3 % contain all three mitotypes. Within mixed fields we were able to quantify the relative abundance of each mitotype across an order of magnitude. Local areas within mixed fields are dominated by certain mitotypes and indicate towards a complex underlying "pathoscape". Finally, we assess mitotype distribution at the level of the individual cyst, and provide evidence of "hybrids". This study provides a method for accurate, quantitative and high throughput typing of up to one thousand fields simultaneously, while revealing novel insights into the national genetic variability of an economically important plant-parasite.
FIGURE 1. Heterodera fengi n in Heterodera fengi n. sp. (Nematoda: Heteroderinae) from bamboo in Guangdong Province, China a new cyst nematode in the Cyperi group
FIGURE 1. Heterodera fengi n. sp. A: Cysts; B: Anterior region of white female; C: Vulval cone; D: Pharyngeal region of J2; E: Anterior region of J2; F: Lateral field and tail of J2; G: Pharyngeal region male; H: Anterior region of male; I: Lateral field and tail of male.
FIGURE 4. J2s in Heterodera fengi n. sp. (Nematoda: Heteroderinae) from bamboo in Guangdong Province, China a new cyst nematode in the Cyperi group
FIGURE 4. J2s of Heterodera fengi n. sp. under light microscope. A: Entire body; B: Pharyngeal region; C-D: Anterior region; E: Lateral lines; F: Tail. (Scale bar: A = 100 μm; B, F = 20 μm; C-E = 10 μm.).
FIGURE 7 in Heterodera fengi n. sp. (Nematoda: Heteroderinae) from bamboo in Guangdong Province, China a new cyst nematode in the Cyperi group
FIGURE 7. RFLP-ITS-rRNA pattern of Heterodera fengi n. sp. Lanes: M = 100 bp DNA ladder (NEB); 1 = ITS-rRNA amplification product; 2 = AluI; 3 = AvaI; 4 = Bsh1236I (BstuI); 5 =BsuRI (HaeIII); 6 = CfoI (HhaI); 7 = MvaI; 8 = RsaI (AfaI).
FIGURE 3 in Heterodera fengi n. sp. (Nematoda: Heteroderinae) from bamboo in Guangdong Province, China a new cyst nematode in the Cyperi group
FIGURE 3. Males of Heterodera fengi n. sp. under light microscope. A: Entire body; B: Pharyngeal region; C: Lateral lines in the middle body; D: Lateral lines in the posterior body. E–F: Tail. (Scale bar: A = 100 μm; B–F= 20 μm.).
FIGURE 2 in Heterodera fengi n. sp. (Nematoda: Heteroderinae) from bamboo in Guangdong Province, China a new cyst nematode in the Cyperi group
FIGURE 2. Cysts and females of Heterodera fengi n. sp. under light microscrope. A: Female (arrow) parasitizing roots of bamboo; B: Female with large egg sac; C: Eggs in female; D: Lip region of female; E: Stylet knobs and DGO of female; F-G: Median bulb of females; H: Entire cysts; I: Cuticle pattern of cyst in vulval region; J-L: En face view of vulval cone; K-M: Same as J and L, respectively, deeper level, with underbridge. (Scale bar: A, H = 100 μm; B = 200 μm; C = 100 μm; D-G, I-M = 10 μm.).
FIGURE 5 in Using Gordiid cysts to discover the hidden diversity, potential distribution, and new species of Gordiids (Phylum Nematomorpha)
FIGURE 5. Maxent model summary of gordiid infected snail geography showing known occurrence points (black circles) and predicted potential geographic distribution (green areas of streams) in Payne County, Oklahoma. Blue areas of streams are identified as unsuitable. Purple and red arrows indicate locations of free-living adults of Gordius n. sp. and Chordodes morgani, respectively. Note that all Gordius n. sp. were collected in the predicted geographic distribution, and C. morgani was collected from a dog water bowl from a home near a region of a stream with predicted distribution for gordiids. Scale bar = 6.7 km.
FIGURE 4 in Using Gordiid cysts to discover the hidden diversity, potential distribution, and new species of Gordiids (Phylum Nematomorpha)
FIGURE 4. Scanning electron and light microscope micrographs of adult free-living gordiids reared from field collected cysts or collected as free-living adults from Payne County, Oklahoma. (A) Dorsal view of the posterior region of a female Paragordius varius. Note the three posterior tail lobes (Tl). Scale bar = 500 Μm. (B) Ventral view of the posterior region of a male Paragordius varius. Note the two long posterior tail lobes (Tl), cloaca (c), and spines on the ventral midline (white arrows). Scale bar = 200 Μm. (C) Midbody cuticular structures of a male P. varius. Note the hemisphirical structures (Hs). Scale bar = 10 Μm. (D) Tapered anterior end and cuticular patern of a male Chordodes morgani. Scale bar = 100 Μm. (E) Midbody region of a male C. morgani showing the characteristic leopard pattern. Scale bar = 300 Μm. (F) Midbody region of a male C. morgani showing the characteristic crown areole pattern. Scale bar = 100 Μm. (G) Ventral view of the posterior region of a male C. morgaini. Note no tail lobes and an oval cloaca (c). Scale bar = 200 Μm. (H) Cloaca opening surrounded by circumcloacal spines. Scale bar = 10 Μm. (I) Cuticular structures on the posterior region of a male C. morgaini. Note the crown areoles (Ca), bulging areoles (BA), and bristles (white arrow). Scale bar = 8 Μm. (J) Tapered anterior end and cuticular patern of a male Gordius n. sp. Scale bar = 10 Μm. (K) Areole pattern on the posterior body region of a male Gordius n. sp. Note the weakly developed areoles (A) and the presence of bristles (white arrows). Scale bar = 20 Μm. (L) Ventral view of the posterior region of a male Gordius n. sp. Note the two posterior tail lobes (Tl), cloaca (c), and post cloacal crescent (Pcc). Scale bar = 120 Μm.
FIGURE 3 in Using Gordiid cysts to discover the hidden diversity, potential distribution, and new species of Gordiids (Phylum Nematomorpha)
FIGURE 3. (A) Female Acheta domesticus releasing a single female Paragordius varius. (B) A gordian knot of male and female P. var ius after emerging from a female A. domesticus. Note that males are the darker and thiner individuals. Scale bars = 1 cm.
FIGURE 1 in Using Gordiid cysts to discover the hidden diversity, potential distribution, and new species of Gordiids (Phylum Nematomorpha)
FIGURE 1. Photomicrographs of gordiid cyst and larval types recovered from Physa acuta snails collected in Payne County, Oklahoma. (A) Cyst of Gordius sp. Note the lack of spines on the preseptum and tighly double folded larva. Scale bar = 25 Μm. (B) Cyst of Paragordius sp. Note the characterisitc spines on the preseptum (black arrow) and double folding of the postseptum (white arrow) never reaching the posterior end of the preseptum. Scale bar = 15 Μm. (C) Cyst of Chordodes/Neochordodes sp. Note the single folding position of the postseptum and relatively small spines on the preseptum. Scale bar = 10 Μm. (D) Larva of Gordius sp. in the process of folding. Note the characteristic single spine on the posterior end of the postseptum (arrow). Scale bar = 15 Μm. (E) Unencysted larva of Paragordius sp. Note the characteristically long spines of the outer hooks of the preseptum (black arrow) and characteristic granules of the pseudointestine (white arrow). Scale bar = 15 Μm. (F) Unencysted larva of Chordodes/Neochordodes sp. Note the equal length ratio of the prespeptum and postseptum and relatively small spines on the preseptum. Scale bar = 10 Μm.
FIGURE 2 in Using Gordiid cysts to discover the hidden diversity, potential distribution, and new species of Gordiids (Phylum Nematomorpha)
FIGURE 2. Positive (black circles) and negative (white circles) localities for (A) Paragordius spp., (B) Gordius spp., and (C) Chordodes/Neochordodes spp. in Payne County, Oklahoma. Numbers represent names of each site (see Table 1). Scale bars = 6.9 km.
Microchamber slide design for cell confinement during imaging- cyst rotation
<p>The data shows a <i>Colpoda steinii</i> resting cyst rotating with internal vesicles.</p><p>We performed Imaging on a Nikon Ti2-E & Yokogawa CSU W1-SoRa microscope. The microscope was equipped with an ORCA-Fusion BT digital C-MOS camera. We used a 100x silicone objective for differential interference contrast (DIC) imaging. More microscopy information is detailed in the metadata file associated with each .nd2 files. The repository contains timelapse data. <br> </p><p> </p>
PNS-Cyst-Count (Part1): nematode cysts with orgnic debris, annotated with cyst count
<p>Data collected by the PheNeSens (Phenotyping of Nematodes with Sensors) project. The images recorded cysts of sugar beet nematode, together with organic debris from the soil sample, left after the soil processing.</p> <p>A total of 48 soil samples are recorded (30 images per sample) and number of cysts are manually counted. This is the first part, in which cysts present along with large amount of organic debris. The second part (cysts without debris) is available under link: https://zenodo.org/record/6861814</p> <p>For details of the data collection and deep learning model training, refer to our paper:</p> <p>Chen L, Daub M, Luigs H-G, Jansen M, Strauch M and Merhof D (2022) High-throughput phenotyping of nematode cysts. Front. Plant Sci. 13:965254. doi: 10.3389/fpls.2022.965254 [<a href="https://www.frontiersin.org/articles/10.3389/fpls.2022.965254/full?&utm_source=Email_to_authors_&utm_medium=Email&utm_content=T1_11.5e1_author&utm_campaign=Email_publication&field=&journalName=Frontiers_in_Plant_Science&id=965254">link</a>]</p>
PNS-Cyst-Count (Part2): hand-picked nematode cysts without organic debris, annotated with cyst count
<p>Data collected by the PheNeSens (Phenotyping of Nematodes with Sensors) project. The images recorded cysts of sugar beet nematode, together with organic debris from the soil sample, left after the soil processing.</p> <p>A total of 48 soil samples are recorded (30 images per sample) and number of cysts are manually counted. This is the second part, containing images of hand-picked cysts on filter papers. The cysts before hand-picking (with large amount of organic debris) is available under: https://zenodo.org/record/6861775</p> <p>For details of the data collection and deep learning model training, refer to our paper:</p> <p>Chen L, Daub M, Luigs H-G, Jansen M, Strauch M and Merhof D (2022) High-throughput phenotyping of nematode cysts. Front. Plant Sci. 13:965254. doi: 10.3389/fpls.2022.965254 [<a href="https://www.frontiersin.org/articles/10.3389/fpls.2022.965254/full?&utm_source=Email_to_authors_&utm_medium=Email&utm_content=T1_11.5e1_author&utm_campaign=Email_publication&field=&journalName=Frontiers_in_Plant_Science&id=965254">link</a>]</p>
PNS-Cyst-Count-Artifical: images of controlled number of nematode cysts with orgnic debris
<p>Data collected by the PheNeSens (Phenotyping of Nematodes with Sensors) project. The images recorded cysts of sugar beet nematode, together with organic debris from the soil sample, left after the soil processing.</p> <p>This dataset was generated by manually picking nematode cysts into organic debris, so that the cyst count is known and controlled. A total of 6x8=48 samples were synthesized. Each sample contains 30 images.</p> <p>We also collected images of real soil samples, which is available from the links:</p> <p>https://zenodo.org/record/6861775</p> <p>https://zenodo.org/record/6861814</p> <p>For details of the data collection and deep learning model training, refer to our paper:</p> <p>Chen L, Daub M, Luigs H-G, Jansen M, Strauch M and Merhof D (2022) High-throughput phenotyping of nematode cysts. Front. Plant Sci. 13:965254. doi: 10.3389/fpls.2022.965254 [<a href="https://www.frontiersin.org/articles/10.3389/fpls.2022.965254/full?&utm_source=Email_to_authors_&utm_medium=Email&utm_content=T1_11.5e1_author&utm_campaign=Email_publication&field=&journalName=Frontiers_in_Plant_Science&id=965254">link</a>]</p>
FIGURE 7 in Cactodera chenopodiae (Nematoda: Heteroderidae), a new species of cyst nematode parasitizing common lambsquarter (Chenopodium album) in Liaoning, China
FIGURE 7. Phylogenetic relationships within populations and species of Heteroderinae Filipjev & Schuurmans Stekhoven,1941. The 50% majority rule consensus trees from Bayesian analysis generated from two runs as inferred from the analysis of the ITS rRNA gene sequences under the GTR + G + I model. Three clades (A, B, C and D) are identified among Cactodera sequences. Branch support (only above 50%) is shown on branches as Bayesian inference (BI)/maximum likelihood (ML)/maximum parsimony (MP). A dash (-) indicates branch support below 50% or incongruence between BI and ML/MP analyses. Sequences produced in this study are highlighted in gray.
FIGURE 5 in Cactodera chenopodiae (Nematoda: Heteroderidae), a new species of cyst nematode parasitizing common lambsquarter (Chenopodium album) in Liaoning, China
FIGURE 5. Drawing of Cactodera chenopodiae n. sp. A: Entire body of J2; B: Anterior region of J2; C–D: Tail of J2; E: Terminal view of cone; F: Cyst; G: Face view of J2 as observed with SEM.
FIGURE 4 in Cactodera chenopodiae (Nematoda: Heteroderidae), a new species of cyst nematode parasitizing common lambsquarter (Chenopodium album) in Liaoning, China
FIGURE 4. SEM micrographs of Cactodera chenopodiae n. sp. A. Cyst; B. Vulval cone with anus; C. Cuticle surface showing wavy pattern; D. Circumfenestra of cyst; E. Anterior region of J2; F. Lateral field of second-stage juvenile (J2) showing incomplete annulation; G. Egg; H–I. Pattern on surface of egg;
FIGURE 3 in Cactodera chenopodiae (Nematoda: Heteroderidae), a new species of cyst nematode parasitizing common lambsquarter (Chenopodium album) in Liaoning, China
FIGURE 3. Light micrographs of Cactodera chenopodiae n. sp. (J3) A–C: J3 in root after root staining; D: J3 off root picked after centrifugal-flotation. (Scale bars: A–C = 100 µm, D = 50 µm)
FIGURE 6 in Cactodera chenopodiae (Nematoda: Heteroderidae), a new species of cyst nematode parasitizing common lambsquarter (Chenopodium album) in Liaoning, China
FIGURE 6. Phylogenetic relationships within populations and species of Heteroderinae Filipjev & Schuurmans Stekhoven,1941. The 50% majority rule consensus trees from Bayesian analysis generated from two runs as inferred from the analysis of the D2–D3 of 28S rRNA gene sequences under the GTR + G model. Two clades (A and B) are identified among Cactodera sequences. Branch support (only above 50%) is shown on branches as Bayesian inference (BI)/maximum likelihood (ML)/maximum parsimony (MP). A dash (-) indicates branch support below 50% or incongruence between BI and ML/MP analyses. Sequences produced in this study are highlighted in gray.
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