Redefining Ormyridae (Hymenoptera, Chalcidoidea) with establishment of subfamilies and description of new genera

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Abstract

The circumscription of the family Ormyridae (Hymenoptera: Chalcidoidea) is revised after phylogenetic analysis based on ultra‐conserved elements (UCEs) and comparative morphological assessment of the chalcid ‘Gall Clade’. Six genera are treated in the family, including two new genera, Halleriaphagus van Noort and Burks, gen. nov., and Ouma Mitroiu, gen. nov. One genus, Eubeckerella Narendran, is re‐assigned to the family, and Ormyrulus Bouček is synonymised with Ormyrus Westwood, syn. nov., resulting in the new combination Ormyrus gibbus (Bouček), comb. nov. The six genera are classified in three subfamilies, two of which are newly described, Asparagobiinae van Noort, Burks, Mitroiu and Rasplus, subfam. nov., and Hemadinae van Noort, Burks, Mitroiu and Rasplus, subfam. nov. Halleriaphagus is established for the newly described type species Halleriaphagus phagolucida van Noort and Burks, sp. nov., and Ouma is erected for O. daleskeyae Mitroiu, sp. nov., and O. emazantsi Mitroiu, sp. nov. Asparagobius is revised with description of Asparagobius bouceki van Noort, sp. nov., and Asparagobius copelandi Rasplus and van Noort, sp. nov. Asparagobius and Halleriaphagus are classified in Asparagobiinae, Hemadas in Hemadinae and Eubeckerella, Ormyrus and Ouma in Ormyrinae. The molecular support defining the ormyrid clade is corroborated by the proposed morphological synapomorphy of a foliaceous prepectus overlying the tegula base. Identification keys to the genera of Ormyridae and to the species of Asparagobius and Ouma are provided. Online Lucid identification keys and images of all the species treated herein are available at: http://www.waspweb.org.

Zoobank Registration: LSID urn:lsid:zoobank.org:pub:8811695B-EE57-4C18-A6B6-E63D267E2373.

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Anthony M. Bolger, Marc Lohse, Bjoern Usadel (2014)

Motivation: Although many next-generation sequencing (NGS) read preprocessing tools already existed, we could not find any tool or combination of tools that met our requirements in terms of flexibility, correct handling of paired-end data and high performance. We have developed Trimmomatic as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data. Results: The value of NGS read preprocessing is demonstrated for both reference-based and reference-free tasks. Trimmomatic is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested. Availability and implementation: Trimmomatic is licensed under GPL V3. It is cross-platform (Java 1.5+ required) and available at http://www.usadellab.org/cms/index.php?page=trimmomatic Contact: usadel@bio1.rwth-aachen.de Supplementary information: Supplementary data are available at Bioinformatics online.

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MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

Kazutaka Katoh, Daron Standley (2013)

We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.

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FLASH: fast length adjustment of short reads to improve genome assemblies.

T. Magoc, S. L. Salzberg (2013)

Next-generation sequencing technologies generate very large numbers of short reads. Even with very deep genome coverage, short read lengths cause problems in de novo assemblies. The use of paired-end libraries with a fragment size shorter than twice the read length provides an opportunity to generate much longer reads by overlapping and merging read pairs before assembling a genome. We present FLASH, a fast computational tool to extend the length of short reads by overlapping paired-end reads from fragment libraries that are sufficiently short. We tested the correctness of the tool on one million simulated read pairs, and we then applied it as a pre-processor for genome assemblies of Illumina reads from the bacterium Staphylococcus aureus and human chromosome 14. FLASH correctly extended and merged reads >99% of the time on simulated reads with an error rate of <1%. With adequately set parameters, FLASH correctly merged reads over 90% of the time even when the reads contained up to 5% errors. When FLASH was used to extend reads prior to assembly, the resulting assemblies had substantially greater N50 lengths for both contigs and scaffolds. The FLASH system is implemented in C and is freely available as open-source code at http://www.cbcb.umd.edu/software/flash. t.magoc@gmail.com.

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Author and article information

Contributors

Simon van Noort: (View ORCID Profile)

Mircea‐Dan Mitroiu: (View ORCID Profile)

Roger Burks: (View ORCID Profile)

Gary Gibson: (View ORCID Profile)

Paul Hanson: (View ORCID Profile)

John Heraty: (View ORCID Profile)

Petr Janšta: (View ORCID Profile)

Astrid Cruaud: (View ORCID Profile)

Jean‐Yves Rasplus: (View ORCID Profile)

Journal

Title: Systematic Entomology

Abbreviated Title: Systematic Entomology

Publisher: Wiley

ISSN (Print): 0307-6970

ISSN (Electronic): 1365-3113

Publication date Created: July 2024

Publication date (Electronic): April 30 2024

Publication date (Print): July 2024

Volume: 49

Issue: 3

Pages: 447-494

Affiliations

[1 ] Research and Exhibitions Department, South African Museum Iziko Museums of South Africa Cape Town South Africa

[2 ] Department of Biological Sciences University of Cape Town Cape Town South Africa

[3 ] Faculty of Biology Alexandru Ioan Cuza University of Iași Iași Romania

[4 ] Riverside Department of Entomology University of California Riverside California USA

[5 ] Honorary Research Associate, Agriculture and Agri‐Food Canada Canadian National Collection of Insects, Arachnids and Nematodes Ottawa Ontario Canada

[6 ] School of Biology University of Costa Rica San Jose Costa Rica

[7 ] Department of Entomology University of California Riverside California USA

[8 ] Department of Zoology, Faculty of Science Charles University Prague Czech Republic

[9 ] Department of Entomology State Museum of Natural History Stuttgart Germany

[10 ] CBGP, Center for Biology and Management of Populations, INRAE, CIRAD, IRD, Montpellier SupAgro University Montpellier Montpellier France

Article

DOI: 10.1111/syen.12630

SO-VID: b3368427-b76e-42d7-afd5-8aaeb2c45a20

License:

http://creativecommons.org/licenses/by-nc-nd/4.0/

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