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      Bremia itoana (Oomycota, Peronosporales), a Specialized Downy Mildew Pathogen on an East Asian Plant, Crepidiastrum sonchifolium (Asteraceae)

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          Abstract

          Crepidiastrum sonchifolium, a flowering plant in the daisy family (Asteraceae), is native to East Asia. In Korea, this plant is a locally cultivated vegetable, and its market size is gradually growing. Since the plants with downy mildew infection were initially found at a private farm of Chuncheon city, the occurrences have continued in commercial farms of other regions, highlighting that this disease is spreading throughout Korea. The pathogen was attributed to a member of the genus Bremia that contains many specialized species, each of which displays a narrow host spectrum on Asteraceae. Based on morphological and molecular phylogenetic analyses, along with the high host specificity recently proven for Bremia species, the identity of the causal agent was confirmed as a so far undescribed species of Bremia. Here, we introduce Bremia itoana sp. nov., specific to C. sonchifolium.

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          SequenceMatrix: concatenation software for the fast assembly of multi-gene datasets with character set and codon information

          Gaurav Vaidya, David Lohman, Rudolf Meier (2011)
          We present SequenceMatrix, software that is designed to facilitate the assembly and analysis of multi-gene datasets. Genes are concatenated by dragging and dropping FASTA, NEXUS, or TNT files with aligned sequences into the program window. A multi-gene dataset is concatenated and displayed in a spreadsheet; each sequence is represented by a cell that provides information on sequence length, number of indels, the number of ambiguous bases ("Ns"), and the availability of codon information. Alternatively, GenBank numbers for the sequences can be displayed and exported. Matrices with hundreds of genes and taxa can be concatenated within minutes and exported in TNT, NEXUS, or PHYLIP formats, preserving both character set and codon information for TNT and NEXUS files. SequenceMatrix also creates taxon sets listing taxa with a minimum number of characters or gene fragments, which helps assess preliminary datasets. Entire taxa, whole gene fragments, or individual sequences for a particular gene and species can be excluded from export. Data matrices can be re-split into their component genes and the gene fragments can be exported as individual gene files. SequenceMatrix also includes two tools that help to identify sequences that may have been compromised through laboratory contamination or data management error. One tool lists identical or near-identical sequences within genes, while the other compares the pairwise distance pattern of one gene against the pattern for all remaining genes combined. SequenceMatrix is Java-based and compatible with the Microsoft Windows, Apple MacOS X and Linux operating systems. The software is freely available from http://code.google.com/p/sequencematrix/. © The Willi Hennig Society 2010.
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            Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework

            Kazutaka Katoh, Hiroyuki Toh (2008)
            Background Structural alignment of RNAs is becoming important, since the discovery of functional non-coding RNAs (ncRNAs). Recent studies, mainly based on various approximations of the Sankoff algorithm, have resulted in considerable improvement in the accuracy of pairwise structural alignment. In contrast, for the cases with more than two sequences, the practical merit of structural alignment remains unclear as compared to traditional sequence-based methods, although the importance of multiple structural alignment is widely recognized. Results We took a different approach from a straightforward extension of the Sankoff algorithm to the multiple alignments from the viewpoints of accuracy and time complexity. As a new option of the MAFFT alignment program, we developed a multiple RNA alignment framework, X-INS-i, which builds a multiple alignment with an iterative method incorporating structural information through two components: (1) pairwise structural alignments by an external pairwise alignment method such as SCARNA or LaRA and (2) a new objective function, Four-way Consistency, derived from the base-pairing probability of every sub-aligned group at every multiple alignment stage. Conclusion The BRAliBASE benchmark showed that X-INS-i outperforms other methods currently available in the sum-of-pairs score (SPS) criterion. As a basis for predicting common secondary structure, the accuracy of the present method is comparable to or rather higher than those of the current leading methods such as RNA Sampler. The X-INS-i framework can be used for building a multiple RNA alignment from any combination of algorithms for pairwise RNA alignment and base-pairing probability. The source code is available at the webpage found in the Availability and requirements section.
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              Host Jumps and Radiation, Not Co‐Divergence Drives Diversification of Obligate Pathogens. A Case Study in Downy Mildews and Asteraceae

              Young-Joon Choi, Marco Thines (2015)
              Even though the microevolution of plant hosts and pathogens has been intensely studied, knowledge regarding macro-evolutionary patterns is limited. Having the highest species diversity and host-specificity among Oomycetes, downy mildews are a useful a model for investigating long-term host-pathogen coevolution. We show that phylogenies of Bremia and Asteraceae are significantly congruent. The accepted hypothesis is that pathogens have diverged contemporarily with their hosts. But maximum clade age estimation and sequence divergence comparison reveal that congruence is not due to long-term coevolution but rather due to host-shift driven speciation (pseudo-cospeciation). This pattern results from parasite radiation in related hosts, long after radiation and speciation of the hosts. As large host shifts free pathogens from hosts with effector triggered immunity subsequent radiation and diversification in related hosts with similar innate immunity may follow, resulting in a pattern mimicking true co-divergence, which is probably limited to the terminal nodes in many pathogen groups.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Mycobiology
                Journal ID (iso-abbrev): Mycobiology
                Journal ID (publisher-id): TMYB
                Journal ID (publisher-id): tmyb20
                Title: Mycobiology
                Publisher: Taylor & Francis
                ISSN (Print): 1229-8093
                ISSN (Electronic): 2092-9323
                Publication date Collection: 2018
                Publication date (Electronic): 11 December 2018
                Volume: 46
                Issue: 4
                Pages: 416-420
                Affiliations
                [a ]Department of Biology, Kunsan National University , Gunsan, Korea;
                [b ]Center for Convergent Agrobioengineering (CECA), Kunsan National University , Gunsan, Korea;
                [c ]Department of Crop Life Safety, Crop Protection Division National Institute of Agricultural Science, RDA , Wanju, Korea;
                [d ]Division of Environmental Science and Ecological Engineering College of Life Sciences and Biotechnology, Korea University , Seoul, Korea
                Author notes
                CONTACT Young-Joon Choi yjchoi@ 123456kunsan.ac.kr ; Hyeon-Dong Shin hdshin@ 123456korea.ac.kr
                Author information
                http://orcid.org/0000-0002-0909-4723
                http://orcid.org/0000-0002-6378-3175
                http://orcid.org/0000-0003-3419-4299
                http://orcid.org/0000-0002-7778-2747
                Article
                Publisher ID: 1547485
                DOI: 10.1080/12298093.2018.1547485
                PMC ID: 6319453
                SO-VID: 5e03b28e-e3e4-49d0-8a9c-a4906653e0cf
                Copyright © © 2018 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group on behalf of the Korean Society of Mycology.
                License:

                This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License ( http://creativecommons.org/licenses/by-nc/4.0/), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Date received : 01 October 2018
                Date revision received : 31 October 2018
                Date accepted : 02 November 2018
                Page count
                Figures: 2, Tables: 2, Pages: 4, Words: 2916
                Funding
                Funded by: National Institute of Biological Resources 10.13039/501100005880
                Funded by: Ministry of Environment 10.13039/501100003562
                Funded by: National Research Foundation of Korea 10.13039/501100003725
                Funded by: Ministry of Science, ICT & Future Planning 10.13039/100010669
                Award ID: 2016R1C1B2008013
                YJC was supported by a grant from the National Institute of Biological Resources (NIBR), funded by of the Ministry of Environment (MOE), and the National Research Foundation of Korea (NRF), funded by the Ministry of Science, ICT & Future Planning [Project No. 2016R1C1B2008013], Republic of Korea. YJC and JL were supported by a grant from the Agenda programme [Project No. PJ013476], Rural Development Administration, Republic of Korea.
                Categories
                Subject: Research Articles

                ScienceOpen disciplines: Plant science & Botany
                Keywords: barcoding,cichorioideae,cox2 mtdna,downy mildew,newly emerging disease
                Data availability:
                ScienceOpen disciplines: Plant science & Botany
                Keywords: barcoding, cichorioideae, cox2 mtdna, downy mildew, newly emerging disease

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