BMC Genomics (Jan 2020)
Enhanced genome assembly and a new official gene set for Tribolium castaneum
- Nicolae Herndon,
- Jennifer Shelton,
- Lizzy Gerischer,
- Panos Ioannidis,
- Maria Ninova,
- Jürgen Dönitz,
- Robert M. Waterhouse,
- Chun Liang,
- Carsten Damm,
- Janna Siemanowski,
- Peter Kitzmann,
- Julia Ulrich,
- Stefan Dippel,
- Georg Oberhofer,
- Yonggang Hu,
- Jonas Schwirz,
- Magdalena Schacht,
- Sabrina Lehmann,
- Alice Montino,
- Nico Posnien,
- Daniela Gurska,
- Thorsten Horn,
- Jan Seibert,
- Iris M. Vargas Jentzsch,
- Kristen A. Panfilio,
- Jianwei Li,
- Ernst A. Wimmer,
- Dominik Stappert,
- Siegfried Roth,
- Reinhard Schröder,
- Yoonseong Park,
- Michael Schoppmeier,
- Ho-Ryun Chung,
- Martin Klingler,
- Sebastian Kittelmann,
- Markus Friedrich,
- Rui Chen,
- Boran Altincicek,
- Andreas Vilcinskas,
- Evgeny Zdobnov,
- Sam Griffiths-Jones,
- Matthew Ronshaugen,
- Mario Stanke,
- Sue J. Brown,
- Gregor Bucher
Affiliations
- Nicolae Herndon
- Department of Computer Science, East Carolina University
- Jennifer Shelton
- Division of Biology, Kansas State University
- Lizzy Gerischer
- Institut für Mathematik und Informatik, Universität Greifswald
- Panos Ioannidis
- Department of Genetic Medicine and Development, University of Geneva Medical School and Swiss Institute of Bioinformatics
- Maria Ninova
- Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building
- Jürgen Dönitz
- Department of Evolutionary Developmental Genetics, GZMB, University of Göttingen
- Robert M. Waterhouse
- Department of Ecology and Evolution, University of Lausanne and Swiss Institute of Bioinformatics
- Chun Liang
- Department of Biology, Miami University
- Carsten Damm
- Institut für Informatik, Fakultät für Mathematik und Informatik, Georg-August-Universität Göttingen
- Janna Siemanowski
- Department of Evolutionary Developmental Genetics, GZMB, University of Göttingen
- Peter Kitzmann
- Department of Evolutionary Developmental Genetics, GZMB, University of Göttingen
- Julia Ulrich
- Department of Evolutionary Developmental Genetics, GZMB, University of Göttingen
- Stefan Dippel
- Göttinger Graduiertenschule fur Neurowissenschaften Biophysik und Molekulare Biowissenschaften, Georg-August-Universität Göttingen
- Georg Oberhofer
- Department of Evolutionary Developmental Genetics, GZMB, University of Göttingen
- Yonggang Hu
- Department of Evolutionary Developmental Genetics, GZMB, University of Göttingen
- Jonas Schwirz
- Department of Evolutionary Developmental Genetics, GZMB, University of Göttingen
- Magdalena Schacht
- Department of Evolutionary Developmental Genetics, GZMB, University of Göttingen
- Sabrina Lehmann
- Department of Evolutionary Developmental Genetics, GZMB, University of Göttingen
- Alice Montino
- Department of Evolutionary Developmental Genetics, GZMB, University of Göttingen
- Nico Posnien
- Department of Developmental Biology, GZMB, University of Göttingen
- Daniela Gurska
- Institute for Zoology: Developmental Biology, University of Cologne
- Thorsten Horn
- Institute for Zoology: Developmental Biology, University of Cologne
- Jan Seibert
- Institute for Zoology: Developmental Biology, University of Cologne
- Iris M. Vargas Jentzsch
- Institute for Zoology: Developmental Biology, University of Cologne
- Kristen A. Panfilio
- School of Life Sciences, University of Warwick
- Jianwei Li
- Department Developmental Biology, GZMB, University of Göttingen
- Ernst A. Wimmer
- Department of Developmental Biology, University of Göttingen
- Dominik Stappert
- Institute of Zoology: Developmental Biology, University of Cologne
- Siegfried Roth
- Institute of Zoology: Developmental Biology, University of Cologne
- Reinhard Schröder
- Institut für Biowissenschaften, Universität Rostock
- Yoonseong Park
- Department of Entomology, Kansas State University
- Michael Schoppmeier
- Department of Biology, Divison of Developmental Biology, Friedrich-Alexander-University of Erlangen-Nürnberg
- Ho-Ryun Chung
- Department of Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics
- Martin Klingler
- Department of Biology, Division of Developmental Biology, Friedrich-Alexander-University of Erlangen-Nürnberg
- Sebastian Kittelmann
- Oxford Brookes University, Centre for Functional Genomics
- Markus Friedrich
- Department of Anatomy and Cell Biology, Wayne State University
- Rui Chen
- Baylor College of Medicine
- Boran Altincicek
- Institute of Crop Science and Resource Conservation (INRES-Phytomedicine), Rheinische Friedrich-Wilhelms-University of Bonn
- Andreas Vilcinskas
- Institute for Insect Biotechnology, Justus-Liebig University of Giessen
- Evgeny Zdobnov
- Department of Genetic Medicine and Development, University of Geneva Medical School and Swiss Institute of Bioinformatics
- Sam Griffiths-Jones
- Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building
- Matthew Ronshaugen
- Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building
- Mario Stanke
- Institut für Mathematik und Informatik, Universität Greifswald
- Sue J. Brown
- Division of Biology, Kansas State University
- Gregor Bucher
- Georg-August-Universität Göttingen
- DOI
- https://doi.org/10.1186/s12864-019-6394-6
- Journal volume & issue
-
Vol. 21,
no. 1
pp. 1 – 13
Abstract
Abstract Background The red flour beetle Tribolium castaneum has emerged as an important model organism for the study of gene function in development and physiology, for ecological and evolutionary genomics, for pest control and a plethora of other topics. RNA interference (RNAi), transgenesis and genome editing are well established and the resources for genome-wide RNAi screening have become available in this model. All these techniques depend on a high quality genome assembly and precise gene models. However, the first version of the genome assembly was generated by Sanger sequencing, and with a small set of RNA sequence data limiting annotation quality. Results Here, we present an improved genome assembly (Tcas5.2) and an enhanced genome annotation resulting in a new official gene set (OGS3) for Tribolium castaneum, which significantly increase the quality of the genomic resources. By adding large-distance jumping library DNA sequencing to join scaffolds and fill small gaps, the gaps in the genome assembly were reduced and the N50 increased to 4753kbp. The precision of the gene models was enhanced by the use of a large body of RNA-Seq reads of different life history stages and tissue types, leading to the discovery of 1452 novel gene sequences. We also added new features such as alternative splicing, well defined UTRs and microRNA target predictions. For quality control, 399 gene models were evaluated by manual inspection. The current gene set was submitted to Genbank and accepted as a RefSeq genome by NCBI. Conclusions The new genome assembly (Tcas5.2) and the official gene set (OGS3) provide enhanced genomic resources for genetic work in Tribolium castaneum. The much improved information on transcription start sites supports transgenic and gene editing approaches. Further, novel types of information such as splice variants and microRNA target genes open additional possibilities for analysis.
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