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Arnqvist G, Westerberg I, Galbraith J, Sayadi A, Scofield DG, Olsen RA, Immonen E, Bonath F, Ewels P, Suh A. A chromosome-level assembly of the seed beetle Callosobruchus maculatus genome with annotation of its repetitive elements. G3 (BETHESDA, MD.) 2024; 14:jkad266. [PMID: 38092066 PMCID: PMC10849321 DOI: 10.1093/g3journal/jkad266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 10/30/2023] [Indexed: 02/09/2024]
Abstract
Callosobruchus maculatus is a major agricultural pest of legume crops worldwide and an established model system in ecology and evolution. Yet, current molecular biological resources for this species are limited. Here, we employ Hi-C sequencing to generate a greatly improved genome assembly and we annotate its repetitive elements in a dedicated in-depth effort where we manually curate and classify the most abundant unclassified repeat subfamilies. We present a scaffolded chromosome-level assembly, which is 1.01 Gb in total length with 86% being contained within the 9 autosomes and the X chromosome. Repetitive sequences accounted for 70% of the total assembly. DNA transposons covered 18% of the genome, with the most abundant superfamily being Tc1-Mariner (9.75% of the genome). This new chromosome-level genome assembly of C. maculatus will enable future genetic and evolutionary studies not only of this important species but of beetles more generally.
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Affiliation(s)
- Göran Arnqvist
- Animal Ecology, Department of Ecology and Genetics, Uppsala University, Uppsala SE75236, Sweden
| | - Ivar Westerberg
- Systematic Biology, Department of Organismal Biology, Uppsala University, Uppsala SE75236, Sweden
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm SE10691, Sweden
| | - James Galbraith
- School of Biological Sciences, University of Adelaide, Adelaide 5005, Australia
- Faculty of Environment, Science and Economy, University of Exeter, Cornwall TR10 9FE, UK
| | - Ahmed Sayadi
- Rheumatology, Department of Medical Sciences, Uppsala University, Uppsala SE75236, Sweden
| | - Douglas G Scofield
- Evolutionary Biology, Department of Ecology and Genetics, Uppsala University, Uppsala SE75236, Sweden
- Uppsala Multidisciplinary Center for Advanced Computational Science, Uppsala University, Uppsala SE75236, Sweden
| | - Remi-André Olsen
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm SE10691, Sweden
| | - Elina Immonen
- Evolutionary Biology, Department of Ecology and Genetics, Uppsala University, Uppsala SE75236, Sweden
| | - Franziska Bonath
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm SE10691, Sweden
| | | | - Alexander Suh
- Systematic Biology, Department of Organismal Biology, Uppsala University, Uppsala SE75236, Sweden
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Sahoo RK, Manu S, Chandrakumaran NK, Vasudevan K. Nuclear and Mitochondrial Genome Assemblies of the Beetle, Zygogramma bicolorata, a Globally Important Biocontrol Agent of Invasive Weed Parthenium hysterophorus. Genome Biol Evol 2023; 15:evad188. [PMID: 37831427 PMCID: PMC10603765 DOI: 10.1093/gbe/evad188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/05/2023] [Accepted: 10/09/2023] [Indexed: 10/14/2023] Open
Abstract
Implementing a genetic-based approach to achieve the full potential of classical biocontrol programs has been advocated for decades. The availability of genome-level information brings the opportunity to scrutinize biocontrol traits for their efficacy and evolvability. However, implementation of this advocacy remains limited to few instances. Biocontrol of a globally noxious weed, Parthenium hysterophorus, by the leaf-feeding beetle, Zygogramma bicolorata, has been in place for more than four decades now, with varying levels of success. As the first step in providing genetic-based improvement to this biocontrol program, we describe the nuclear and mitochondrial assemblies of Z. bicolorata. We assembled the genome from the long-read sequence data, error corrected with high-throughput short reads and checked for contaminants and sequence duplication to produce a 936 Mb nuclear genome. With 96.5% Benchmarking Universal Single-Copy Orthologs completeness and the long terminal repeat assembly index 12.91, we present a reference-quality assembly that appeared to be repeat rich at 62.7% genome-wide and consists of 29,437 protein-coding regions. We detected signature of nuclear insertion of mitochondrial fragments in 80 nuclear positions comprising 13 kb out of 17.9 kb mitochondria genome sequence. This genome, along with its annotations, provides a valuable resource to gain further insights into the biocontrol traits of Z. bicolorata for improving the control of the invasive weed P. hysterophorus.
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Affiliation(s)
- Ranjit Kumar Sahoo
- Laboratory for the Conservation of Endangered Species (LaCONES), CSIR-Centre for Cellular and Molecular Biology (CCMB), Hyderabad, India
| | - Shivakumara Manu
- Laboratory for the Conservation of Endangered Species (LaCONES), CSIR-Centre for Cellular and Molecular Biology (CCMB), Hyderabad, India
| | - Naveen Kumar Chandrakumaran
- Laboratory for the Conservation of Endangered Species (LaCONES), CSIR-Centre for Cellular and Molecular Biology (CCMB), Hyderabad, India
| | - Karthikeyan Vasudevan
- Laboratory for the Conservation of Endangered Species (LaCONES), CSIR-Centre for Cellular and Molecular Biology (CCMB), Hyderabad, India
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