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[en] We present a reference genome assembly from an individual male Violet Carpenter Bee (Xylocopa violacea, Linnaeus 1758). The assembly is 1.02 gigabases in span. 48% of the assembly is scaffolded into 17 pseudo-chromosomal units. The mitochondrial genome has also been assembled and is 21.8 kilobases in length. The genome is highly repetitive, likely representing a highly heterochromatic architecture expected of bees from the genus Xylocopa. We also use an evidence-based methodology to annotate 10,152 high confidence coding genes. This genome was sequenced as part of the pilot project of the European Reference Genome Atlas (ERGA) and represents an important addition to the genomic resources available for Hymenoptera.
Disciplines :
Zoology
Author, co-author :
Nash, Will J ; The Earlham Institute, Norwich Research Park, Colney Lane, Norwich, NR4 7UZ, UK. will.nash@earlham.ac.uk
Man, Angela ; The Earlham Institute, Norwich Research Park, Colney Lane, Norwich, NR4 7UZ, UK
McTaggart, Seanna ; The Earlham Institute, Norwich Research Park, Colney Lane, Norwich, NR4 7UZ, UK
Baker, Kendall ; The Earlham Institute, Norwich Research Park, Colney Lane, Norwich, NR4 7UZ, UK
Barker, Tom; The Earlham Institute, Norwich Research Park, Colney Lane, Norwich, NR4 7UZ, UK
Catchpole, Leah; The Earlham Institute, Norwich Research Park, Colney Lane, Norwich, NR4 7UZ, UK
Durrant, Alex; The Earlham Institute, Norwich Research Park, Colney Lane, Norwich, NR4 7UZ, UK
Gharbi, Karim ; The Earlham Institute, Norwich Research Park, Colney Lane, Norwich, NR4 7UZ, UK
Irish, Naomi; The Earlham Institute, Norwich Research Park, Colney Lane, Norwich, NR4 7UZ, UK
Kaithakottil, Gemy; The Earlham Institute, Norwich Research Park, Colney Lane, Norwich, NR4 7UZ, UK
Ku, Debby ; The Earlham Institute, Norwich Research Park, Colney Lane, Norwich, NR4 7UZ, UK
Providence, Aaliyah ; The Earlham Institute, Norwich Research Park, Colney Lane, Norwich, NR4 7UZ, UK
Shaw, Felix; The Earlham Institute, Norwich Research Park, Colney Lane, Norwich, NR4 7UZ, UK
Swarbreck, David ; The Earlham Institute, Norwich Research Park, Colney Lane, Norwich, NR4 7UZ, UK
Watkins, Chris; The Earlham Institute, Norwich Research Park, Colney Lane, Norwich, NR4 7UZ, UK
McCartney, Ann M; Genomics Institute, University of California, Santa Cruz, CA, 95060, USA
Formenti, Giulio; The Vertebrate Genome Laboratory, The Rockefeller University, 1240 York Ave, New York, NY, 10065, USA ; Department of Biology, University of Florence, Sesto Fiorentino, Italy
Mouton, Alice ; Université de Liège - ULiège > Département des sciences et gestion de l'environnement (Arlon Campus Environnement) > Socio-économie, Environnement et Développement (SEED) ; Department of Biology, University of Florence, Sesto Fiorentino, Italy
Vella, Noel; Conservation Biology Research Group, Biology Department, University of Malta, Msida, MSD 2080, Malta
von Reumont, Björn M; LOEWE Center for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325, Frankfurt, Germany ; Applied Bioinformatics Group, Faculty of Biological Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 13, 60438, Frankfurt, Germany
Vella, Adriana; Conservation Biology Research Group, Biology Department, University of Malta, Msida, MSD 2080, Malta. adriana.vella@um.edu.mt
Haerty, Wilfried; The Earlham Institute, Norwich Research Park, Colney Lane, Norwich, NR4 7UZ, UK. wilfried.haerty@earlham.ac.uk ; School of Biological Sciences, The University of East Anglia, Norwich, NR4 7TJ, UK. wilfried.haerty@earlham.ac.uk
RCUK | Biotechnology and Biological Sciences Research Council Innovate UK Deutsche Forschungsgemeinschaft
Funding text :
We acknowledge Fiona Fraser (Earlham Institute, Norwich) and Michael Quail (Wellcome Sanger Institute, Hinxton) for valuable conversations and advice in developing Hi-C library preparation. The authors would also like to acknowledge the GRiT (Wellcome Sanger Institute, Hinxton), particularly Jo Wood, Tom Mathers, Dominic Absolon, Camilla Santos, Michael Paulini for invaluable mentorship in Hi-C scaffolding and curation. The authors also acknowledge Kamil Hepak (Norwich Bioscience Institutes, Scientific Computing) for significant HPC support.The authors acknowledge support from the Biotechnology and Biological Sciences Research Council (BBSRC), part of UK Research and Innovation, Core Capability Grant BB/CCG2220/1 at the Earlham Institute and its constituent work packages (BBS/E/T/000PR9818 and BBS/E/T/000PR9819), and the Core Capability Grant BB/CCG1720/1 and the National Capability at the Earlham Institute BBS/E/T/000PR9816 (NC1\u2014Supporting EI\u2019s ISPs and the UK Community with Genomics and Single Cell Analysis), BBS/E/T/000PR9811 (NC4\u2014Enabling and Advancing Life Scientists in data-driven research through Advanced Genomics and Computational Training), and BBS/E/T/000PR9814 (NC 3 - Development and deployment of versatile digital platforms for \u2018omics-based data sharing and analysis). Authors also acknowledge support from BBSRC Core Capability Grant BB/CCG1720/1 and the work delivered via the Scientific Computing group, as well as support for the physical HPC infrastructure and data centre delivered via the NBI Computing infrastructure for Science (CiS) group. AV and NV acknowledge funding from the BioCon_Innovate Research Excellence Grant (I18LU06-01) from the University of Malta. BMvR acknowledges funding from the DFG (RE3454/6-1).
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