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      Stage-specific transcriptome of Bursaphelenchus xylophilus reveals temporal regulation of effector genes and roles of the dauer-like stages in the lifecycle

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          Abstract

          The pine wood nematode Bursaphelenchus xylophilus is the causal agent of pine wilt disease, one of the most devastating forest diseases in East Asian and West European countries. The lifecycle of B. xylophilus includes four propagative larval stages and gonochoristic adults which are involved in the pathogenicity, and two stages of dispersal larvae involved in the spread of the disease. To elucidate the ecological roles of each developmental stage in the pathogenic life cycle, we performed a comprehensive transcriptome analysis using RNA-seq generated from all developmental stages of B. xylophilus and compared transcriptomes between stages. We found more than 9000 genes are differentially expressed in at least one stage of the life cycle including genes involved in general nematode biology such as reproduction and moulting but also effector genes likely to be involved in parasitism. The dispersal-stage transcriptome revealed its analogy to C. elegans dauer and the distinct roles of the two larval stages from each other regarding survival and transmission. This study provides important insights and resources to understand B. xylophilus parasitic biology.

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          Toward almost closed genomes with GapFiller

          De novo assembly is a commonly used application of next-generation sequencing experiments. The ultimate goal is to puzzle millions of reads into one complete genome, although draft assemblies usually result in a number of gapped scaffold sequences. In this paper we propose an automated strategy, called GapFiller, to reliably close gaps within scaffolds using paired reads. The method shows good results on both bacterial and eukaryotic datasets, allowing only few errors. As a consequence, the amount of additional wetlab work needed to close a genome is drastically reduced. The software is available at http://www.baseclear.com/bioinformatics-tools/.
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            STEM: a tool for the analysis of short time series gene expression data

            Background Time series microarray experiments are widely used to study dynamical biological processes. Due to the cost of microarray experiments, and also in some cases the limited availability of biological material, about 80% of microarray time series experiments are short (3–8 time points). Previously short time series gene expression data has been mainly analyzed using more general gene expression analysis tools not designed for the unique challenges and opportunities inherent in short time series gene expression data. Results We introduce the Short Time-series Expression Miner (STEM) the first software program specifically designed for the analysis of short time series microarray gene expression data. STEM implements unique methods to cluster, compare, and visualize such data. STEM also supports efficient and statistically rigorous biological interpretations of short time series data through its integration with the Gene Ontology. Conclusion The unique algorithms STEM implements to cluster and compare short time series gene expression data combined with its visualization capabilities and integration with the Gene Ontology should make STEM useful in the analysis of data from a significant portion of all microarray studies. STEM is available for download for free to academic and non-profit users at .
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              Top 10 plant-parasitic nematodes in molecular plant pathology.

              The aim of this review was to undertake a survey of researchers working with plant-parasitic nematodes in order to determine a 'top 10' list of these pathogens based on scientific and economic importance. Any such list will not be definitive as economic importance will vary depending on the region of the world in which a researcher is based. However, care was taken to include researchers from as many parts of the world as possible when carrying out the survey. The top 10 list emerging from the survey is composed of: (1) root-knot nematodes (Meloidogyne spp.); (2) cyst nematodes (Heterodera and Globodera spp.); (3) root lesion nematodes (Pratylenchus spp.); (4) the burrowing nematode Radopholus similis; (5) Ditylenchus dipsaci; (6) the pine wilt nematode Bursaphelenchus xylophilus; (7) the reniform nematode Rotylenchulus reniformis; (8) Xiphinema index (the only virus vector nematode to make the list); (9) Nacobbus aberrans; and (10) Aphelenchoides besseyi. The biology of each nematode (or nematode group) is reviewed briefly. © 2013 BSPP AND JOHN WILEY & SONS LTD.
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                Author and article information

                Contributors
                taisei_kikuchi@med.miyazaki-u.ac.jp
                Journal
                Sci Rep
                Sci Rep
                Scientific Reports
                Nature Publishing Group UK (London )
                2045-2322
                15 April 2019
                15 April 2019
                2019
                : 9
                : 6080
                Affiliations
                [1 ]ISNI 0000 0001 2151 536X, GRID grid.26999.3d, Laboratory of Forest Botany, Graduate School of Agricultural and Life Sciences, , the University of Tokyo, ; Tokyo, 113-8657 Japan
                [2 ]ISNI 0000 0001 0657 3887, GRID grid.410849.0, Division of Parasitology, Faculty of Medicine, , University of Miyazaki, ; Miyazaki, 889-1692 Japan
                [3 ]ISNI 0000 0001 1710 3792, GRID grid.412121.5, Forestry Vocational School, , Duzce University, ; 81620 Duzce, Turkey
                [4 ]ISNI 0000 0001 2287 1366, GRID grid.28665.3f, Biodiversity Research Center, , Academia Sinica, ; Taipei, Taiwan
                [5 ]ISNI 0000 0004 0372 2033, GRID grid.258799.8, Laboratory of Terrestrial Microbial Ecology, , Graduate School of Agriculture, Kyoto University, ; Kyoto, 606-8502 Japan
                [6 ]ISNI 0000 0000 9150 188X, GRID grid.417935.d, Kansai Research Center, , Forestry and Forest Products Research Institute, ; Kyoto, 612-0855 Japan
                Author information
                http://orcid.org/0000-0002-6843-5049
                http://orcid.org/0000-0002-2123-5058
                http://orcid.org/0000-0001-8752-1674
                http://orcid.org/0000-0003-2759-9167
                Article
                42570
                10.1038/s41598-019-42570-7
                6465311
                30988401
                300b4234-11f5-4a9e-897f-87ca382eba7f
                © The Author(s) 2019

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 17 July 2018
                : 1 April 2019
                Funding
                Funded by: FundRef https://doi.org/10.13039/501100001691, MEXT | Japan Society for the Promotion of Science (JSPS);
                Award ID: 15H04514’
                Award ID: 26292178
                Award ID: 16H04722
                Award ID: 15H04521
                Award Recipient :
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