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Xing L, Liu B, Yu D, Tang X, Sun J, Zhang B. A near-complete genome assembly of Monochamus alternatus a major vector beetle of pinewood nematode. Sci Data 2024; 11:312. [PMID: 38531927 DOI: 10.1038/s41597-024-03150-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 03/15/2024] [Indexed: 03/28/2024] Open
Abstract
The Japanese sawyer beetle, Monochamus alternatus, is not only one of the most important wood boring pest itself, but also a major vector of the invasive pinewood nematode (PWN), which is the causal agent of the devastative pine wilt disease (PWD) and threats the global pine forest. Here, we present a near-complete genome of M. alternatus at the chromosome level. The assembled genome was 792.05 Mb with contig N50 length of 55.99 Mb, which is the largest N50 size among the sequenced Coleoptera insects currently. 99.57% of sequence was anchored onto ten pseudochromosomes (one X-chromosome and nine autosomes), and the final genome harbored only 13 gaps. BUSCO evaluation revealed the presence of 99.0% of complete core genes. Thus, our genome assembly represented the highest-contiguity genome assembly as well as high completeness in insects so far. We identified 20,471 protein-coding genes, of which 20,070 (98.04%) were functionally annotated. The genome assembly of M. alternatus provides a valuable resource for exploring the evolution of the symbiosis between PWN and the vector insects.
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Affiliation(s)
- Longsheng Xing
- College of Life Science/Hebei Basic Science Center for Biotic Interactions, Institute of Life Science and Green Development, Hebei University, Baoding, 071002, China
| | - Bo Liu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Dunyang Yu
- College of Life Science/Hebei Basic Science Center for Biotic Interactions, Institute of Life Science and Green Development, Hebei University, Baoding, 071002, China
| | - Xuan Tang
- College of Life Science/Hebei Basic Science Center for Biotic Interactions, Institute of Life Science and Green Development, Hebei University, Baoding, 071002, China
| | - Jianghua Sun
- College of Life Science/Hebei Basic Science Center for Biotic Interactions, Institute of Life Science and Green Development, Hebei University, Baoding, 071002, China.
| | - Bin Zhang
- College of Life Science/Hebei Basic Science Center for Biotic Interactions, Institute of Life Science and Green Development, Hebei University, Baoding, 071002, China.
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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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Fu N, Li J, Ren L, Li X, Wang M, Li F, Zong S, Luo Y. Chromosome-level genome assembly of Monochamus saltuarius reveals its adaptation and interaction mechanism with pine wood nematode. Int J Biol Macromol 2022; 222:325-336. [PMID: 36115455 DOI: 10.1016/j.ijbiomac.2022.09.108] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/22/2022] [Accepted: 09/10/2022] [Indexed: 11/05/2022]
Abstract
Monochamus saltuarius (Coleoptera: Cerambycidae) was reported as the vector beetle of the pine wood nematode (PWN, Bursaphelenchus xylophilus) in Japan and Europe. It was first reported to transmitted the PWN to native Pinus species in 2018 in Liaoning Province, China. However, the lack of genomic resources has limited the in-depth understanding of its interspecific relationship with PWN. Here, we obtained a chromosome-level reference genome of M. saltuarius combining Illumina, Nanopore and Hi-C sequencing technologies. We assembled the scaffolds into ten chromosomes (including an X chromosome) and obtained a 682.23 Mb chromosome-level genome with a N50 of 73.69 Mb. In total, 427.67 Mb (62.69 %) repeat sequences were identified and 14, 492 protein-coding genes were predicted, of which 93.06 % were annotated. We described the mth/mthl, P450, OBP and OR gene families associated with the vector beetle's development and resistance, as well as the host selection and adaptation, which serve as a valuable resource for understanding the host adaptation in insects during evolution. This high quality reference genome of M. saltuarius also provide new avenues for researching the mechanism of this synergistic damage between vector beetles and PWN.
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Affiliation(s)
- Ningning Fu
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing 100083, China
| | - Jiaxing Li
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing 100083, China
| | - Lili Ren
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing 100083, China.
| | | | - Ming Wang
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing 100083, China
| | - Fengqi Li
- Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, Guizhou 550025, China
| | - Shixiang Zong
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing 100083, China
| | - Youqing Luo
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing 100083, China.
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