Journal of nematology最新文献_第9页

Impact of non-fumigant nematicides on reproduction and pathogenicity of Meloidogyne enterolobii and disease severity in tobacco. 非熏蒸杀线虫剂对烟根结线虫繁殖和致病性及烟草病害严重程度的影响。

IF 1.4 4区生物学

Journal of nematology Pub Date : 2023-06-05 eCollection Date: 2023-02-01 DOI: 10.2478/jofnem-2023-0025

Md Shah Alam, Churamani Khanal, Joseph Roberts, William Rutter

{"title":"Impact of non-fumigant nematicides on reproduction and pathogenicity of Meloidogyne enterolobii and disease severity in tobacco.","authors":"Md Shah Alam, Churamani Khanal, Joseph Roberts, William Rutter","doi":"10.2478/jofnem-2023-0025","DOIUrl":"10.2478/jofnem-2023-0025","url":null,"abstract":"Meloidogyne enterolobii is a highly aggressive quarantine pathogen which threatens the multibillion-dollar tobacco industry and is not manageable with the currently available management methods in tobacco. There is currently no known host plant resistance in tobacco and previous studies have shown that the lower level of the currently recommended rate of non-fumigant nematicides does not provide satisfactory management of M. enterolobii. The current study was conducted with the hypothesis that M. enterolobii can be better managed using a single soil application of the maximum allowed rate of non-fumigant nematicides. Treatments involved three non-fumigant chemical nematicides (oxamyl, fluopyram, and fluensulfone), a biological nematicide derived from Burkholderia, and a non-treated control. Fluensulfone significantly suppressed the nematode reproduction relative to the control, the suppression being 71% for eggs and 86% for the second stage juveniles (J2). Fluopyram also suppressed nematode reproduction, although this was statistically insignificant, with the suppression being 26% and 37% for eggs and J2, respectively. Oxamyl significantly suppressed J2 (80%), but not eggs (50%) in relation to the control. The most significant reduction of disease severity was achieved by the application of fluensulfone (64%), followed by oxamyl (54%) and fluopyram (48%). Except for fluensulfone, which significantly reduced the root biomass, none of the nematicides significantly impacted root and shoot biomass. The biological nematicide did not significantly affect nematode reproduction, pathogenicity, or disease severity. The results from the current study suggest that while the non-fumigant nematicides provided a good level of the nematode suppression, more research is needed to improve the efficacy of non-fumigant nematicides through employing better application methods or finding better chemistries.","PeriodicalId":16475,"journal":{"name":"Journal of nematology","volume":"55 1","pages":"20230025"},"PeriodicalIF":1.4,"publicationDate":"2023-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10241305/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10238286","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Morphological and Molecular Characterization of Talanema eshtiaghii sp. n. (Dorylaimida, Qudsianematidae) from Iran. 伊朗Talanema eshtiaghii sp.n.（Dorylaimida，Qudsianemalidae）的形态学和分子特征。

IF 1.3 4区生物学

Journal of nematology Pub Date : 2023-06-05 eCollection Date: 2023-02-01 DOI: 10.2478/jofnem-2023-0022

Nasir Vazifeh, Gholamreza Niknam, Habibeh Jabbari, Reyes Peña-Santiago

{"title":"Morphological and Molecular Characterization of Talanema eshtiaghii sp. n. (Dorylaimida, Qudsianematidae) from Iran.","authors":"Nasir Vazifeh, Gholamreza Niknam, Habibeh Jabbari, Reyes Peña-Santiago","doi":"10.2478/jofnem-2023-0022","DOIUrl":"10.2478/jofnem-2023-0022","url":null,"abstract":"A new species of the genus Talanema, recovered from the northwest of Iran, was described based on morphological, morphometric, and molecular data. Talanema eshtiaghii sp. n. was characterized by its 1.45-1.68 mm long body, lip region offset by constriction and 13-15 μm wide, odontostyle 15-18 μm long, double guiding ring, neck 312-362 μm long, pharyngeal expansion occupying 41-43% of the total neck length, uterus tripartite, and 111-189 μm long or 2.1-3.2 body diameters, vulva transverse (V = 55-58), tail similar in both sexes, conical with a dorsal concavity (30-44 μm, c = 33-56, c' = 1.0-1.6), spicules 49-56 μm long, and 14-18 shortly spaced ventromedian supplements in front of the level of the anterior end of spicules, with distinct hiatus. It was compared to four closely similar species, with emphasis on the most relevant traits to distinguish them. Molecular phylogenetic studies using partial sequence of the 28S rDNA (D2-D3 segment) revealed that the new species forms a clade with other currently sequenced representatives of Talanema, tentatively supporting the monophyly of this genus.","PeriodicalId":16475,"journal":{"name":"Journal of nematology","volume":"55 1","pages":"20230022"},"PeriodicalIF":1.3,"publicationDate":"2023-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10241306/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10238285","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A New Biological Product Shows Promising Control of the Northern Root-Knot Nematode, Meloidogyne hapla, in Greenhouse Tomatoes. 一种新的生物制品有望控制温室番茄中的北方根结线虫。

IF 1.3 4区生物学

Journal of nematology Pub Date : 2023-05-26 eCollection Date: 2023-02-01 DOI: 10.2478/jofnem-2023-0023

Elisabeth Darling, Abigail Palmisano, Henry Chung, Marisol Quintanilla-Tornel

引用次数: 0

Characterization of Hoplolaimus seinhorsti and Hoplolaimus pararobustus (Tylenchina: Hoplolaimidae) from banana, with phylogeny and species delineation in the genus Hoplolaimus. 香蕉Hoplolaimus seinhorsti和Hoplolaimus pararobustus的特征（中国：Hoplolaimicae），以及Hoplolaimuns属的系统发育和物种划分。

IF 1.3 4区生物学

Journal of nematology Pub Date : 2023-05-23 eCollection Date: 2023-02-01 DOI: 10.2478/jofnem-2023-0019

Emmanuel Olajide, Phougeishangbam Rolish Singh, Yao A Kolombia, Merlin Kornelia Rumbarar, Marjolein Couvreur, Wim Bert

{"title":"Characterization of Hoplolaimus seinhorsti and Hoplolaimus pararobustus (Tylenchina: Hoplolaimidae) from banana, with phylogeny and species delineation in the genus Hoplolaimus.","authors":"Emmanuel Olajide, Phougeishangbam Rolish Singh, Yao A Kolombia, Merlin Kornelia Rumbarar, Marjolein Couvreur, Wim Bert","doi":"10.2478/jofnem-2023-0019","DOIUrl":"10.2478/jofnem-2023-0019","url":null,"abstract":"The morphological and molecular characterisations of two lance nematode species isolated from the rhizosphere of banana, Hoplolaimus seinhorsti and H. pararobustus, are provided based on an integrative study that includes light and scanning electron microscopy, phylogenetic analysis and two tree-based molecular species delimitation methods (GMYC and bPTP). Nineteen new sequences were obtained, including 5 partial 18S rRNA, 6 D2-D3 of 28S rRNA, 1 ITS rRNA and 7 COI mtDNA (the first COI sequences of H. seinhorsti and H. pararobustus), and an updated morphological character comparison of 37 Hoplolaimus species is presented. The tree-based molecular species-delimitation approaches employed gave markedly differing results, and also showed remarkable discrepancies among the investigated genes, although the bPTP output was found to agree well with established morphological species delimitations. Both species-delimitation approaches did, however, provide the same output for the COI mtDNA sequences, and the COI mtDNA gene sequence was also found to correspond better to established morphological species. It is therefore recommended by this paper as representing the most suitable barcode marker for Hoplolaimus species identification. This integrative study also resulted in the corrective reassignment of 17 gene sequences that were previously unidentified or incorrectly classified, as well as concluding that H. pararobustus consists of two cryptic species.","PeriodicalId":16475,"journal":{"name":"Journal of nematology","volume":"55 1","pages":"20230019"},"PeriodicalIF":1.3,"publicationDate":"2023-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10448604/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10586616","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Morphological and Molecular Characterization of Diplogasteroides sp., a Cryptic Population of the Haslacheri Group (Diplogastridae), and Parasitorhabditis terebranus (Rhabditidae) from Korea. 韩国Haslacheri群（双壳虫科）的一个隐蔽种群——双壳拟杆菌属（Diplogastridae）和圆棒线虫（Rhabditidae）的形态学和分子特征。

IF 1.4 4区生物学

Journal of nematology Pub Date : 2023-05-23 eCollection Date: 2023-02-01 DOI: 10.2478/jofnem-2023-0017

Abraham Okki Mwamula, Sang Myeong Lee, Young Hak Jung, Ho-Wook Lee, Yi Seul Kim, Young Ho Kim, Dong Woon Lee

{"title":"Morphological and Molecular Characterization of Diplogasteroides sp., a Cryptic Population of the Haslacheri Group (Diplogastridae), and Parasitorhabditis terebranus (Rhabditidae) from Korea.","authors":"Abraham Okki Mwamula, Sang Myeong Lee, Young Hak Jung, Ho-Wook Lee, Yi Seul Kim, Young Ho Kim, Dong Woon Lee","doi":"10.2478/jofnem-2023-0017","DOIUrl":"10.2478/jofnem-2023-0017","url":null,"abstract":"Diplogasteroides sp., a cryptic population of D. haslacheri, and Parasitorhabditis terebranus were reported from the frass of Monochamus alternatus galleries in dead Pinus thunbergii for the first time in Korea. Females and males are morphologically characterized and their linked DNA barcodes (18S-rRNA, 28S-rRNA, ITS-rRNA and COI) supplied. Females and males of the two species from Korea conform to the original species descriptions from Europe and the USA, with variations in a few details in morphometrics. Specifically, Diplogasteroides sp. is morphologically very similar to D. haslacheri. However, it cannot be designated as D. haslacheri due to the existence of cryptic species complex within the haslacheri group (D. haslacheri, D. asiaticus, D. nix, D. andrassyi, and D. carinthiacus), a condition requiring hybridization studies to test species identity within the group. Based on analysis of COI sequences, differences among these cryptic species are evident. Thus, in addition to hybridization tests, the COI might be a powerful DNA barcoding marker for the precise identification of these cryptic species within the genus. Additionally, this is the first molecular characterization of P. terebranus, and the species is herein recorded for the first time outside its type locality.","PeriodicalId":16475,"journal":{"name":"Journal of nematology","volume":"55 1","pages":"20230017"},"PeriodicalIF":1.4,"publicationDate":"2023-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10277748/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10602703","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Ultrastructural study of anther parasitism of Ficus laevigata by Ficophagus laevigatus (Aphelenchoididae). 金翅榕花药寄生的超微结构研究。

IF 1.3 4区生物学

Journal of nematology Pub Date : 2023-05-18 eCollection Date: 2023-02-01 DOI: 10.2478/jofnem-2023-0010

Robin M Giblin-Davis, Natsumi Kanzaki, Donna S Williams

{"title":"Ultrastructural study of anther parasitism of Ficus laevigata by Ficophagus laevigatus (Aphelenchoididae).","authors":"Robin M Giblin-Davis, Natsumi Kanzaki, Donna S Williams","doi":"10.2478/jofnem-2023-0010","DOIUrl":"10.2478/jofnem-2023-0010","url":null,"abstract":"Transmission electron microscopy (TEM) was used to compare the ultrastructural differences between healthy male florets (anthers) and one floret parasitized by Ficophagus laevigatus in late phase C syconia of Ficus laevigata from southern Florida. Previous light-microscopic examination of paraffin-sectioned material showed that F. laevigatus-infested anthers of F. laevigata manifested as malformed, often with aberrant pollen and hypertrophied epidermal cells closest to regions containing propagating nematodes. Female florets or fig wasp-parasitized female florets were not observed to be parasitized by nematodes. Considering that plant-feeding in the Aphelenchoididae is purportedly much less specialized than in certain groups of the Tylenchomorpha, where specialized hypertrophied feeder cells are produced in response to nematode feeding, we examined the putative induced response in this unusual aphelenchoidid system with the higher resolution afforded by TEM. TEM confirmed the expression of significant epidermal cell hypertrophy of the anther and anther filament in the presence of propagating nematodes, which was expressed as cell enlargement (2-5X), fractionation of large electron-dense stores into smaller aggregates, irregularly shaped nuclei enclosed by an elongated nuclear envelope, nucleolus enlargement, increased organelle production, and apparent metabolism with increased numbers of mitochondria, pro-plastids, and endoplasmic reticulum, as well as increased thickening of the cell walls. Pathological effects were observed in adjacent cells/tissue (e.g., anther and anther filament parenchymal cells, pollen tubes, pollen, and endothecium) with apparent diminishment as the distance from propagating nematodes increased (which was also probably affected by number of nematodes). Some TEM sections captured previously undocumented ultrastructural highlights of propagating individuals of F. laevigatus.","PeriodicalId":16475,"journal":{"name":"Journal of nematology","volume":"55 1","pages":"20230010"},"PeriodicalIF":1.3,"publicationDate":"2023-05-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10193554/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10290456","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Morphological and Molecular Characterization of Filenchus multistriatus n. sp. (Tylenchomorpha: Tylenchidae) and Data on a Known Species of the Genus from Bushehr Province, Southern Iran. 伊朗南部布什尔省Filenchus multistatus n.sp.的形态和分子特征（Tylenchomorpha：Tylenchidae）以及该属一已知物种的数据。

IF 1.3 4区生物学

Journal of nematology Pub Date : 2023-05-17 eCollection Date: 2023-02-01 DOI: 10.2478/jofnem-2023-0008

Somayeh Monemi, Mohammad Reza Atighi, Joaquín Abolafia, Pablo Castillo, Majid Pedram

{"title":"Morphological and Molecular Characterization of Filenchus multistriatus n. sp. (Tylenchomorpha: Tylenchidae) and Data on a Known Species of the Genus from Bushehr Province, Southern Iran.","authors":"Somayeh Monemi, Mohammad Reza Atighi, Joaquín Abolafia, Pablo Castillo, Majid Pedram","doi":"10.2478/jofnem-2023-0008","DOIUrl":"10.2478/jofnem-2023-0008","url":null,"abstract":"During a nematological survey in southern Iran, a population belonging to the family Tylenchidae was recovered from a tomato field in Bushehr province. The recovered population belongs to the genus Filenchus, was described and illustrated herein as F. multistriatus n. sp. It is mainly characterized by having a wide and low annulated lip region continuous with adjacent body; amphidial openings confined to the labial plate; four lines in lateral fields forming three bands, with the two outer bands broken by transverse, and the inner one broken by both transverse and longitudinal lines; and median bulb oval with visible valve and elongate-conoid tail uniformly and gradually narrowing toward the distal region, ending in a widely rounded tip. Its morphological and morphometric differences with three closely similar species were discussed. The phylogenetic relationships of the new species with other relevant genera and species were reconstructed using partial sequences of small, and large subunit ribosomal DNA (SSU and LSU rDNA) sequences. Morphometric and morphological data were also provided for an Iranian population of F. sandneri recovered from Bushehr province. Both populations were characterised using SEM data.","PeriodicalId":16475,"journal":{"name":"Journal of nematology","volume":"55 1","pages":"20230008"},"PeriodicalIF":1.3,"publicationDate":"2023-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10191216/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10234280","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Distribution of Plant-Parasitic Nematodes in Michigan Corn Fields. 密歇根玉米地植物寄生线虫的分布。

IF 1.4 4区生物学

Journal of nematology Pub Date : 2023-05-02 eCollection Date: 2023-02-01 DOI: 10.2478/jofnem-2023-0015

Sita Thapa, Elisabeth Darling, Emilie Cole, Kristin Poley, Marisol Quintanilla

{"title":"Distribution of Plant-Parasitic Nematodes in Michigan Corn Fields.","authors":"Sita Thapa, Elisabeth Darling, Emilie Cole, Kristin Poley, Marisol Quintanilla","doi":"10.2478/jofnem-2023-0015","DOIUrl":"10.2478/jofnem-2023-0015","url":null,"abstract":"Plant-parasitic nematodes (PPNs) can cause substantial economic yield losses to many agronomic crops in the United States. A regional-scale survey was completed across 20 counties to determine PPNs prevalence in Michigan corn and how factors such as soil type, tillage, irrigation, and cropping systems influence their distribution. Ten different major genera of PPNs were identified in Michigan corn fields: Longidorus (needle), Helicotylenchus (spiral), Pratylenchus (lesion), Meloidogyne (root-knot), Heterodera (cyst), Hoplolaimus (lance), Tylenchorhynchus or Merlinius (stunt), Paratylenchus (pin), Criconemella (ring), and Xiphinema (dagger). No significant differences among different categories of tillage for lesion, stunt, or needle nematode prevalence was detected. Lesion nematodes were most prevalent in muck soil, while stunt nematode prevalence was significantly affected by the soil type. Needle nematodes were least abundant in irrigated soils and in contrast, stunt nematodes were higher in non-irrigated soils. Spiral nematodes were the most common PPNs in Michigan corn in all cropping systems. These findings will be helpful in planning future nematode studies in Michigan and in developing and evaluating corn nematode management strategies.","PeriodicalId":16475,"journal":{"name":"Journal of nematology","volume":"55 1","pages":"20230015"},"PeriodicalIF":1.4,"publicationDate":"2023-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10353600/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10291495","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Reaction of Winter Cover Crops to Meloidogyne enterolobii and Glasshouse Bioassay for Evaluating Utility in Managing M. enterolobii in Soybeans. 冬覆盖作物对肠根结线虫的反应和用于评估大豆中肠根结霉菌管理效用的玻璃屋生物测定。

IF 1.4 4区生物学

Journal of nematology Pub Date : 2023-05-02 eCollection Date: 2023-02-01 DOI: 10.2478/jofnem-2023-0014

Neel Saha, Tanner Schwarz, Samantha Mowery, Adrienne M Gorny

{"title":"Reaction of Winter Cover Crops to Meloidogyne enterolobii and Glasshouse Bioassay for Evaluating Utility in Managing M. enterolobii in Soybeans.","authors":"Neel Saha, Tanner Schwarz, Samantha Mowery, Adrienne M Gorny","doi":"10.2478/jofnem-2023-0014","DOIUrl":"10.2478/jofnem-2023-0014","url":null,"abstract":"Meloidogyne enterolobii is an invasive and highly aggressive root-knot nematode pathogen impacting the Southeastern United States. Winter cover cropping may be a cost-effective method for reducing populations of M. enterolobii in between summer cash crops, yet a gap in the knowledge remains about the response of these cover crops to M. enterolobii and their utility in suppressing nematode populations prior to a cash crop. A \"two-step\" glasshouse bioassay was performed to evaluate eight winter cover crops popular in North Carolina for their direct response to M. enterolobii infection, and to quantify their effect in reducing nematode populations for the following soybean plants. Data on cover crop root galling, soybean root galling, soybean shoot fresh weight, soybean root fresh weight, eggs per gram of soybean root, and a modified reproductive factor were collected. Cereal cover crops did not display root galling, and there was significantly less root galling in those soybean plants following cereal winter cover crops when compared to those following broadleaf winter cover crops. Broadleaf winter cover crops resulted in significantly higher eggs per gram of soybean root and modified reproductive factor in the soybean plants, compared to cereal cover crops and non-inoculated controls. Results from this study suggest that cereal winter cover crops may be poor-hosts to M. enterolobii and may significantly reduce M. enterolobii populations before a soybean crop, compared to broadleaf winter cover crops. This study lays the groundwork for management recommendations and future field trials to assess management of M. enterolobii through winter cover cropping.","PeriodicalId":16475,"journal":{"name":"Journal of nematology","volume":"55 1","pages":"20230014"},"PeriodicalIF":1.4,"publicationDate":"2023-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10236376/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10236399","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

18S-NemaBase: Curated 18S rRNA Database of Nematode Sequences. 18S NemaBase：线虫序列的18S rRNA Curated数据库。

IF 1.4 4区生物学

Journal of nematology Pub Date : 2023-04-21 eCollection Date: 2023-02-01 DOI: 10.2478/jofnem-2023-0006

Kaitlin Gattoni, Eli M S Gendron, Rebeca Sandoval-Ruiz, Abigail Borgemeier, J Parr McQueen, Rachel M Shepherd, Dieter Slos, Thomas O Powers, Dorota L Porazinska

{"title":"18S-NemaBase: Curated 18S rRNA Database of Nematode Sequences.","authors":"Kaitlin Gattoni, Eli M S Gendron, Rebeca Sandoval-Ruiz, Abigail Borgemeier, J Parr McQueen, Rachel M Shepherd, Dieter Slos, Thomas O Powers, Dorota L Porazinska","doi":"10.2478/jofnem-2023-0006","DOIUrl":"10.2478/jofnem-2023-0006","url":null,"abstract":"Nematodes are the most abundant and diverse animals on the planet but lack representation in biodiversity research. This presents a problem for studying nematode diversity, particularly when molecular tools (i.e., barcoding and metabarcoding) rely on well-populated and curated reference databases, which are absent for nematodes. To improve molecular identification and the assessment of nematode diversity, we created and curated an 18S rRNA database specific to nematodes (18S-NemaBase) using sequences sourced from the most recent publicly available 18S rRNA SILVA v138 database. As part of the curation process, taxonomic strings were standardized to contain a fixed number of taxonomic ranks relevant to nematology and updated for the most recent accepted nematode classifications. In addition, apparent erroneous sequences were removed. To test the efficacy and accuracy of 18S-NemaBase, we compared it to an older but also curated SILVA v111 and the newest SILVA v138 by assigning taxonomies and analyzing the diversity of a nematode dataset from the Western Nebraska Sandhills. We showed that 18S-NemaBase provided more accurate taxonomic assignments and diversity assessments than either version of SILVA, with a much easier workflow and no need for manual corrections. Additionally, observed diversity further improved when 18S-NemaBase was supplemented with reference sequences from nematodes present in the study site. Although the 18S-NemaBase is a step in the right direction, a concerted effort to increase the number of high-quality, accessible, full-length nematode reference sequences is more important now than ever.","PeriodicalId":16475,"journal":{"name":"Journal of nematology","volume":"55 1","pages":"20230006"},"PeriodicalIF":1.4,"publicationDate":"2023-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10152464/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10601724","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0