Dataset Information

Multigene phylogeny, taxonomy and reclassification of Hyaloperonospora on Cardamine.

ABSTRACT: Based on sequence data from cox1, cox2, ITS and LSU rDNA, it is shown that at least six species of Hyaloperonospora occur on the genus Cardamine, most of which were commonly classified under Peronospora dentariae. Based on sequences from their type hosts, Peronospora dentariae, Peronospora cardamines-laciniatae, Peronospora dentariae-macrophyllae, Peronospora malyi and Peronospora nasturtii-aquatici are combined into Hyaloperonospora, and their circumscription is clarified. Hyaloperonospora cardamines-enneaphyllos is described as a new species from Cardamine enneaphyllos. The host range of Hyaloperonospora nasturtii-aquatici, described from Nasturtium officinale, is shown to extend to various Cardamine species. Host range of species is shown to be highly diagnostic, with no overlap in their host range, but species commonly cannot be distinguished by morphology alone. Both cox1 and cox2 are confirmed to be good markers for phylogenetic species delimitation of closely related Hyaloperonospora species on Cardamine.

SUBMITTER: Voglmayr H

PROVIDER: S-EPMC3935337 | biostudies-literature | 2014 Feb

REPOSITORIES: biostudies-literature

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Multigene phylogeny, taxonomy and reclassification of Hyaloperonospora on Cardamine.

Voglmayr Hermann H Choi Young-Joon YJ Shin Hyeon-Dong HD

Mycological progress 20140201 1

Based on sequence data from cox1, cox2, ITS and LSU rDNA, it is shown that at least six species of Hyaloperonospora occur on the genus Cardamine, most of which were commonly classified under Peronospora dentariae. Based on sequences from their type hosts, Peronospora dentariae, Peronospora cardamines-laciniatae, Peronospora dentariae-macrophyllae, Peronospora malyi and Peronospora nasturtii-aquatici are combined into Hyaloperonosp ...[more]

PMID: 24587792

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Project description:BACKGROUND:Recent advances in genome sequencing technologies and the cost drop in high-throughput sequencing continue to give rise to a deluge of data available for downstream analyses. Among others, evolutionary biologists often make use of genomic data to uncover phenotypic diversity and adaptive evolution in protein-coding genes. Therefore, multiple sequence alignments (MSA) and phylogenetic trees (PT) need to be estimated with optimal results. However, the preparation of an initial dataset of multiple sequence file(s) (MSF) and the steps involved can be challenging when considering extensive amount of data. Thus, it becomes necessary the development of a tool that removes the potential source of error and automates the time-consuming steps of a typical workflow with high-throughput and optimal MSA and PT estimations. RESULTS:We introduce LMAP_S (Lightweight Multigene Alignment and Phylogeny eStimation), a user-friendly command-line and interactive package, designed to handle an improved alignment and phylogeny estimation workflow: MSF preparation, MSA estimation, outlier detection, refinement, consensus, phylogeny estimation, comparison and editing, among which file and directory organization, execution, manipulation of information are automated, with minimal manual user intervention. LMAP_S was developed for the workstation multi-core environment and provides a unique advantage for processing multiple datasets. Our software, proved to be efficient throughout the workflow, including, the (unlimited) handling of more than 20 datasets. CONCLUSIONS:We have developed a simple and versatile LMAP_S package enabling researchers to effectively estimate multiple datasets MSAs and PTs in a high-throughput fashion. LMAP_S integrates more than 25 software providing overall more than 65 algorithm choices distributed in five stages. At minimum, one FASTA file is required within a single input directory. To our knowledge, no other software combines MSA and phylogeny estimation with as many alternatives and provides means to find optimal MSAs and phylogenies. Moreover, we used a case study comparing methodologies that highlighted the usefulness of our software. LMAP_S has been developed as an open-source package, allowing its integration into more complex open-source bioinformatics pipelines. LMAP_S package is released under GPLv3 license and is freely available at https://lmap-s.sourceforge.io/.

Dataset Information

Multigene phylogeny, taxonomy and reclassification of Hyaloperonospora on Cardamine.

Publications

Multigene phylogeny, taxonomy and reclassification of <i>Hyaloperonospora</i> on Cardamine.

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Dataset Information

Multigene phylogeny, taxonomy and reclassification of Hyaloperonospora on Cardamine.

Publications

Multigene phylogeny, taxonomy and reclassification of &lt;i&gt;Hyaloperonospora&lt;/i&gt; on Cardamine.

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OmicsDI is part of the ELIXIR infrastructure

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Multigene phylogeny, taxonomy and reclassification of <i>Hyaloperonospora</i> on Cardamine.