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  • 1
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    Online Resource
    To blend or not to blend? The role of morphological traits for the detection of marine macrobenthos in bulk DNA and eDNA from the ethanol preservative
    Pensoft Publishers ; 2021
    In:  ARPHA Conference Abstracts Vol. 4 ( 2021-03-04)
    Details
    In: ARPHA Conference Abstracts, Pensoft Publishers, Vol. 4 ( 2021-03-04)
    Abstract: The impact of methodological choices on the reliability and reproducibility of DNA metabarcoding need to be well understood to allow successful implementation in routine monitoring frameworks. For macrobenthos communities, the metabarcoding protocol focuses on a fragment of the mitochondrial COI gene and depending on the primer set used for amplification of COI, different taxa can be detected. To identify the primer set that allows the best diversity estimates for macrobenthos in the North Sea region, we sampled four distinct and well characterised communities and identified macrobenthos using traditional morpho-taxonomy before molecular processing. Of the five primer sets tested, the Leray primer set yielded the highest number of non-chimeric reads, detected the highest number of macrobenthos species and best recovered beta diversity patterns. Despite the availability of a nearly complete reference database, 19 out of the 59 morphological species were not picked up with DNA metabarcoding. Next to primer choice, the DNA source used in metabarcoding studies can affect whether or not a species is detected. DNA can be extracted from bulk specimens or from the ethanol preservative in which the macrobenthos sample was preserved. The latter DNA source would greatly speed up processing time of samples in the laboratory. We therefore compared species detection in bulk DNA and eDNA from the ethanol preservative from the four macrobenthos communities in the North Sea. Our results show that community composition differed significantly between bulk DNA and eDNA samples, but both sample types are able to differentiate the four macrobenthos communities from the North Sea. Of the 49 species that are detected in both sample types, 27 are also found in the morphological dataset. The 14 species that are exclusively detected in the ethanol preservative are mainly pelagic species. In view of the low read numbers allocated to these species (at most 153 reads) they most likely represent “contaminant” DNA molecules that are attached to the specimens or the organic debris. To better understand the different results between bulk DNA and eDNA from the ethanol preservative, we investigated the importance of four categorical traits in explaining the probability of detecting a species in the two sample types: body, larval stage (benthic or pelagic), longevity and body skeleton (chitin, CaCO 3 or soft tissue). A generalized linear mixed effects model approach shows that the probability of detecting a species in the eDNA from the ethanol preservative is significantly lower than for bulk DNA for macrobenthos species having small to medium body size and for species having chitine or CaCO 3 in their skeleton. In contrast, detection in the bulk DNA samples is not affected by the investigated traits. Although the ethanol preservative can be used to characterize beta diversity patterns, our results show that monitoring of macrobenthos species will be most robust when using bulk DNA as template for metabarcoding.
    Type of Medium: Online Resource
    ISSN: 2603-3925
    URL: Article
    DOI: 10.3897/aca.4.e65127
    Language: Unknown
    Publisher: Pensoft Publishers
    Publication Date: 2021
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  • 2
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    Table_8.DOCX
    Frontiers Media SA ; 2021
    In:  Frontiers in Marine Science Vol. 8 ( 2021-6-15)
    Details
    In: Frontiers in Marine Science, Frontiers Media SA, Vol. 8 ( 2021-6-15)
    Abstract: DNA metabarcoding is a promising method to increase cost and time efficiency of marine monitoring. While substantial evidence exists that bulk DNA samples adequately reflect diversity patterns of marine macrobenthos, the potential of eDNA in the ethanol preservative of benthic samples for biodiversity monitoring remains largely unexplored. We investigated species detection in bulk DNA and eDNA from the ethanol preservative in samples from four distinct macrobenthic communities in the North Sea. Bulk DNA and eDNA were extracted with different extraction kits and five COI primer sets were tested. Despite the availability of a nearly complete reference database, at most 22% of the amplicon sequence variants (ASVs) were assigned taxonomy at the phylum level. However, the unassigned ASVs represented only a small fraction of the total reads (13%). The Leray primer set outperformed the four other primer sets in the number of non-chimeric reads and species detected, and in the recovery of beta diversity patterns. Community composition differed significantly between bulk DNA and eDNA samples, but both sample types were able to differentiate the four communities. The probability of detecting a species in the eDNA from the ethanol preservative was significantly lower than for bulk DNA for macrobenthos species having small to medium body size and for species having chitine or CaCO 3 in their cuticula. Detection in the bulk DNA samples was not affected by the investigated morphological traits, indicating that monitoring of macrobenthos species will be most robust when using bulk DNA as template for metabarcoding.
    Type of Medium: Online Resource
    ISSN: 2296-7745
    URL: Article
    URL: Article
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    URL: Article
    DOI: 10.3389/fmars.2021.637858
    DOI: 10.3389/fmars.2021.637858.s001
    DOI: 10.3389/fmars.2021.637858.s002
    DOI: 10.3389/fmars.2021.637858.s003
    DOI: 10.3389/fmars.2021.637858.s004
    DOI: 10.3389/fmars.2021.637858.s005
    DOI: 10.3389/fmars.2021.637858.s006
    DOI: 10.3389/fmars.2021.637858.s007
    DOI: 10.3389/fmars.2021.637858.s008
    DOI: 10.3389/fmars.2021.637858.s009
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2021
    detail.hit.zdb_id: 2757748-X
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  • 3
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    Analysis of the transcriptome of the root lesion nematode Pratylenchus coffeae generated by 454 sequencing technology
    Elsevier BV ; 2011
    In:  Molecular and Biochemical Parasitology Vol. 178, No. 1-2 ( 2011-7), p. 7-14
    Details
    In: Molecular and Biochemical Parasitology, Elsevier BV, Vol. 178, No. 1-2 ( 2011-7), p. 7-14
    Type of Medium: Online Resource
    ISSN: 0166-6851
    URL: Article
    DOI: 10.1016/j.molbiopara.2011.04.001
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2011
    detail.hit.zdb_id: 1491098-6
    SSG: 12
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  • 4
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    Facilitating the adoption of high‐throughput sequencing technologies as a plant pest diagnostic test in laboratories: A step‐by‐step description
    Wiley ; 2022
    In:  EPPO Bulletin Vol. 52, No. 2 ( 2022-08), p. 394-418
    Details
    In: EPPO Bulletin, Wiley, Vol. 52, No. 2 ( 2022-08), p. 394-418
    Abstract: Высокопроизводительное секвенирование (HTS) ‐ это мощный инструмент, позволяющий одновременно обнаруживать и потенциально идентифицировать любые организмы, присутствующие в образце. Растущий интерес к применению технологий HTS для рутинной диагностики в лабораториях, занимающихся здоровьем растений, требует разработку рекомендаций по подготовке лабораторий к проведению HTS‐тестирования. В данном документе описаны общие и технические рекомендации, которые помогут лабораториям пройти сложный процесс подготовки лаборатории к проведению HTS‐тестов в рамках существующих систем обеспечения качества. Рассматриваются все этапы для обеспечения надежных и воспроизводимых результатов, начиная с выделения нуклеиновых кислот и заканчивая анализом и интерпретацией данных. Настоящее руководство актуально для обнаружения и идентификации любого вредного организма растений (например, членистоногих, бактерий, грибов, нематод, инвазивных растений или сорняков, простейших, вироидов, вирусов) и из любого типа матрицы (например, чистая культура микроорганизмов, ткани растений, почва, вода), независимо от технологии ВПC (например, ампликонное секвенирование, дробовое секвенирование) и области применения (например, программа надзора, фитосанитарная сертификация, карантин, контроль импорта). Настоящее руководство составлено в общих терминах, чтобы облегчить внедрение технологий HTS в рутинную диагностику вредителей растений и обеспечить её более широкое применение во всех областях защиты растений, включая научные исследования. В дополнительных материалах приводится глоссарий соответствующих терминов.
    Type of Medium: Online Resource
    ISSN: 0250-8052 , 1365-2338
    URL: Issue
    URL: Article
    DOI: 10.1111/epp.v52.2
    DOI: 10.1111/epp.12863
    Language: English
    Publisher: Wiley
    Publication Date: 2022
    detail.hit.zdb_id: 2033181-2
    SSG: 12
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  • 5
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    Reduced-Particle-Size Wheat Bran Is Efficiently Colonized by a Lactic Acid-Producing Community and Reduces Levels of Enterobacteriaceae in the Cecal Microbiota of Broilers
    American Society for Microbiology ; 2018
    In:  Applied and Environmental Microbiology Vol. 84, No. 21 ( 2018-11)
    Details
    In: Applied and Environmental Microbiology, American Society for Microbiology, Vol. 84, No. 21 ( 2018-11)
    Abstract: In the present study, we investigated whether reducing the particle size of wheat bran affects the colonizing microbial community using batch fermentations with cecal inocula from seven different chickens. We also investigated the effect of in-feed administration of regular wheat bran (WB; 1,690 μm) and wheat bran with reduced particle size (WB280; 280 μm) on the cecal microbial community composition of broilers. During batch fermentation, WB280 was colonized by a lactic acid-producing community ( Bifidobacteriaceae and Lactobacillaceae ) and by Lachnospiraceae that contain lactic acid-consuming butyric acid-producing species. The relative abundances of the Enterobacteriaceae decreased in the particle-associated communities for both WB and WB280 compared to that of the control. In addition, the community attached to wheat bran was enriched in xylan-degrading bacteria. When administered as a feed additive to broilers, WB280 significantly increased the richness of the cecal microbiota and the abundance of bacteria containing the butyryl-coenzyme A (CoA):acetate CoA-transferase gene, a key gene involved in bacterial butyrate production, while decreasing the abundances of Enterobacteriaceae family members in the ceca. Particle size reduction of wheat bran thus resulted in the colonization of the bran particles by a very specific lactic acid- and butyric acid-producing community and can be used to steer toward beneficial microbial shifts. This can potentially increase the resilience against pathogens and increase animal performance when the reduced-particle-size wheat bran is administered as a feed additive to broilers. IMPORTANCE Prebiotic dietary fibers are known to improve the gastrointestinal health of both humans and animals in many different ways. They can increase the bulking capacity, improve transit times, and, depending on the fiber, even stimulate the growth and activity of resident beneficial bacteria. Wheat bran is a readily available by-product of flour processing and is a highly concentrated source of (in)soluble dietary fiber. The intake of fiber-rich diets has been associated with increased Firmicutes and decreased Proteobacteria numbers. Here, we show that applying only 1% of a relatively simple substrate which was technically modified using relatively simple techniques reduces the concentration of Enterobacteriaceae . This could imply that in future intervention studies, one should take the particle size of dietary fibers into account.
    Type of Medium: Online Resource
    ISSN: 0099-2240 , 1098-5336
    URL: Article
    DOI: 10.1128/AEM.01343-18
    RVK:
    WA 15000
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2018
    detail.hit.zdb_id: 223011-2
    detail.hit.zdb_id: 1478346-0
    SSG: 12
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  • 6
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    DataSheet_1.pdf
    Frontiers Media SA ; 2023
    In:  Frontiers in Plant Science Vol. 14 ( 2023-6-22)
    Details
    In: Frontiers in Plant Science, Frontiers Media SA, Vol. 14 ( 2023-6-22)
    Abstract: Industrial chicory ( Cichorium intybus var. sativum ) and witloof ( C. intybus var. foliosum ) are crops with an important economic value, mainly cultivated for inulin production and as a leafy vegetable, respectively. Both crops are rich in nutritionally relevant specialized metabolites with beneficial effects for human health. However, their bitter taste, caused by the sesquiterpene lactones (SLs) produced in leaves and taproot, limits wider applications in the food industry. Changing the bitterness would thus create new opportunities with a great economic impact. Known genes encoding enzymes involved in the SL biosynthetic pathway are GERMACRENE A SYNTHASE (GAS), GERMACRENE A OXIDASE (GAO) , COSTUNOLIDE SYNTHASE (COS) and KAUNIOLIDE SYNTHASE ( KLS ). In this study, we integrated genome and transcriptome mining to further unravel SL biosynthesis. We found that C. intybus SL biosynthesis is controlled by the phytohormone methyl jasmonate (MeJA). Gene family annotation and MeJA inducibility enabled the pinpointing of candidate genes related with the SL biosynthetic pathway. We specifically focused on members of subclade CYP71 of the cytochrome P450 family. We verified the biochemical activity of 14 C . intybus CYP71 enzymes transiently produced in Nicotiana benthamiana and identified several functional paralogs for each of the GAO , COS and KLS genes, pointing to redundancy in and robustness of the SL biosynthetic pathway. Gene functionality was further analyzed using CRISPR/Cas9 genome editing in C. intybus . Metabolite profiling of mutant C. intybus lines demonstrated a successful reduction in SL metabolite production. Together, this study increases our insights into the C. intybus SL biosynthetic pathway and paves the way for the engineering of C. intybus bitterness.
    Type of Medium: Online Resource
    ISSN: 1664-462X
    URL: Article
    URL: Article
    DOI: 10.3389/fpls.2023.1200253
    DOI: 10.3389/fpls.2023.1200253.s001
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2023
    detail.hit.zdb_id: 2687947-5
    detail.hit.zdb_id: 2613694-6
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  • 7
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    RETRACTED ARTICLE: Molecular cloning and expression analysis of novel putative effector genes from Meloidogyne graminicola
    Springer Science and Business Media LLC ; 2013
    In:  Journal of Applied Genetics Vol. 54, No. 4 ( 2013-11), p. 493-493
    Details
    In: Journal of Applied Genetics, Springer Science and Business Media LLC, Vol. 54, No. 4 ( 2013-11), p. 493-493
    Type of Medium: Online Resource
    ISSN: 1234-1983 , 2190-3883
    URL: Article
    DOI: 10.1007/s13353-013-0160-2
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2013
    detail.hit.zdb_id: 2194407-6
    SSG: 12
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  • 8
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    Table_2.xlsx
    Frontiers Media SA ; 2018
    In:  Frontiers in Plant Science Vol. 9 ( 2018-7-12)
    Details
    In: Frontiers in Plant Science, Frontiers Media SA, Vol. 9 ( 2018-7-12)
    Type of Medium: Online Resource
    ISSN: 1664-462X
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    DOI: 10.3389/fpls.2018.01019
    DOI: 10.3389/fpls.2018.01019.s001
    DOI: 10.3389/fpls.2018.01019.s002
    DOI: 10.3389/fpls.2018.01019.s003
    DOI: 10.3389/fpls.2018.01019.s004
    DOI: 10.3389/fpls.2018.01019.s005
    DOI: 10.3389/fpls.2018.01019.s006
    DOI: 10.3389/fpls.2018.01019.s007
    DOI: 10.3389/fpls.2018.01019.s008
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2018
    detail.hit.zdb_id: 2687947-5
    detail.hit.zdb_id: 2613694-6
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  • 9
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    A Primer on the Analysis of High-Throughput Sequencing Data for Detection of Plant Viruses
    MDPI AG ; 2021
    In:  Microorganisms Vol. 9, No. 4 ( 2021-04-14), p. 841-
    Details
    In: Microorganisms, MDPI AG, Vol. 9, No. 4 ( 2021-04-14), p. 841-
    Abstract: High-throughput sequencing (HTS) technologies have become indispensable tools assisting plant virus diagnostics and research thanks to their ability to detect any plant virus in a sample without prior knowledge. As HTS technologies are heavily relying on bioinformatics analysis of the huge amount of generated sequences, it is of utmost importance that researchers can rely on efficient and reliable bioinformatic tools and can understand the principles, advantages, and disadvantages of the tools used. Here, we present a critical overview of the steps involved in HTS as employed for plant virus detection and virome characterization. We start from sample preparation and nucleic acid extraction as appropriate to the chosen HTS strategy, which is followed by basic data analysis requirements, an extensive overview of the in-depth data processing options, and taxonomic classification of viral sequences detected. By presenting the bioinformatic tools and a detailed overview of the consecutive steps that can be used to implement a well-structured HTS data analysis in an easy and accessible way, this paper is targeted at both beginners and expert scientists engaging in HTS plant virome projects.
    Type of Medium: Online Resource
    ISSN: 2076-2607
    URL: Article
    DOI: 10.3390/microorganisms9040841
    Language: English
    Publisher: MDPI AG
    Publication Date: 2021
    detail.hit.zdb_id: 2720891-6
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  • 10
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    Daring to be differential: metabarcoding analysis of soil and plant-related microbial communities using amplicon sequence variants and operational taxonomical units
    Springer Science and Business Media LLC ; 2020
    In:  BMC Genomics Vol. 21, No. 1 ( 2020-12)
    Details
    In: BMC Genomics, Springer Science and Business Media LLC, Vol. 21, No. 1 ( 2020-12)
    Abstract: Microorganisms are not only indispensable to ecosystem functioning, they are also keystones for emerging technologies. In the last 15 years, the number of studies on environmental microbial communities has increased exponentially due to advances in sequencing technologies, but the large amount of data generated remains difficult to analyze and interpret. Recently, metabarcoding analysis has shifted from clustering reads using Operational Taxonomical Units (OTUs) to Amplicon Sequence Variants (ASVs). Differences between these methods can seriously affect the biological interpretation of metabarcoding data, especially in ecosystems with high microbial diversity, as the methods are benchmarked based on low diversity datasets. Results In this work we have thoroughly examined the differences in community diversity, structure, and complexity between the OTU and ASV methods. We have examined culture-based mock and simulated datasets as well as soil- and plant-associated bacterial and fungal environmental communities. Four key findings were revealed. First, analysis of microbial datasets at family level guaranteed both consistency and adequate coverage when using either method. Second, the performance of both methods used are related to community diversity and sample sequencing depth. Third, differences in the method used affected sample diversity and number of detected differentially abundant families upon treatment; this may lead researchers to draw different biological conclusions. Fourth, the observed differences can mostly be attributed to low abundant (relative abundance 〈  0.1%) families, thus extra care is recommended when studying rare species using metabarcoding. The ASV method used outperformed the adopted OTU method concerning community diversity, especially for fungus-related sequences, but only when the sequencing depth was sufficient to capture the community complexity. Conclusions Investigation of metabarcoding data should be done with care. Correct biological interpretation depends on several factors, including in-depth sequencing of the samples, choice of the most appropriate filtering strategy for the specific research goal, and use of family level for data clustering.
    Type of Medium: Online Resource
    ISSN: 1471-2164
    URL: Article
    DOI: 10.1186/s12864-020-07126-4
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2020
    detail.hit.zdb_id: 2041499-7
    SSG: 12
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