Chromosome Level Genome Assembly of Oriental Armyworm Mythimna Separata

Overview

Journal Sci Data

Specialty Science

Date 2023 Sep 8

PMID 37684242

Authors

Chao Xu

Jichao Ji

Xiangzhen Zhu

Ningbo Huangfu

Hui Xue

Li Wang

Kaixin Zhang

Dongyang Li

Lin Niu

Ran Chen

Xueke Gao

Junyu Luo

Jinjie Cui

Affiliations

Soon will be listed here.

Abstract

The oriental armyworm, Mythimna separata, is an extremely destructive polyphagous pest with a broad host range that seriously threatens the safety of agricultural production. Here, a high-quality chromosome-level genome was assembled using Illumina, PacBio HiFi long sequencing, and Hi-C scaffolding technologies. The genome size was 706.30 Mb with a contig N50 of 22.08 Mb, and 99.2% of the assembled sequences were anchored to 31 chromosomes. In addition, 20,375 protein-coding genes and 258.68 Mb transposable elements were identified. The chromosome-level genome assembly of M. separata provides a significant genetic resource for future studies of this insect and contributes to the development of management strategies.

Citing Articles

Biological Control Potential of the Reduviid Predator (Fabricius) in Managing Noctuid Pests: Insights Into Predation and Prey Preference.

Xue C, Mao J, Xu B, Zhou L, Zhou H, Mao J Insects. 2025; 16(2).

PMID: 40003853 PMC: 11856166. DOI: 10.3390/insects16020224.

Fitness of (Lepidoptera: Noctuidae) on Cultivated Wheat and a Weed, Wild Oat (), and Its Implications for Pest Management.

Pan Q, Shen J, Su L, Nie Z, Shikano I, Liu T Biology (Basel). 2025; 13(12.

PMID: 39765704 PMC: 11673161. DOI: 10.3390/biology13121037.

Chromosome-level genome assembly of the tetraploid medicinal and natural dye plant Persicaria tinctoria.

Li Q, Huang H, Fan R, Ye Q, Hu Y, Wu Z Sci Data. 2024; 11(1):1440.

PMID: 39730378 PMC: 11680826. DOI: 10.1038/s41597-024-04317-6.

Chromosome-level genome assembly of cotton thrips Thrips tabaci (Thysanoptera: Thripidae).

Gao Y, Ji J, Xu C, Wang L, Zhang K, Li D Sci Data. 2024; 11(1):1003.

PMID: 39294155 PMC: 11411069. DOI: 10.1038/s41597-024-03737-8.

Four New Furofuran Lignans from Inhibit the Accumulation of Molting Hormones in Armyworm.

Zhang J, Cong Q, Sun Y, Hua J, Luo S Int J Mol Sci. 2024; 25(13).

PMID: 39000185 PMC: 11240949. DOI: 10.3390/ijms25137081.

References

Wang Y, Tang H, DeBarry J, Tan X, Li J, Wang X . MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res. 2012; 40(7):e49. PMC: 3326336. DOI: 10.1093/nar/gkr1293. View

Bernt M, Donath A, Juhling F, Externbrink F, Florentz C, Fritzsch G . MITOS: improved de novo metazoan mitochondrial genome annotation. Mol Phylogenet Evol. 2012; 69(2):313-9. DOI: 10.1016/j.ympev.2012.08.023. View

Simao F, Waterhouse R, Ioannidis P, Kriventseva E, Zdobnov E . BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics. 2015; 31(19):3210-2. DOI: 10.1093/bioinformatics/btv351. View

Tong D, Zhang L, Wu N, Xie D, Fang G, Coates B . The oriental armyworm genome yields insights into the long-distance migration of noctuid moths. Cell Rep. 2022; 41(12):111843. DOI: 10.1016/j.celrep.2022.111843. View

Emms D, Kelly S . OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol. 2019; 20(1):238. PMC: 6857279. DOI: 10.1186/s13059-019-1832-y. View

Nguyen L, Schmidt H, von Haeseler A, Minh B . IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 2014; 32(1):268-74. PMC: 4271533. DOI: 10.1093/molbev/msu300. View

Yokoi K, Furukawa S, Zhou R, Jouraku A, Bono H . Reference Genome Sequences of the Oriental Armyworm, (Lepidoptera: Noctuidae). Insects. 2022; 13(12). PMC: 9853324. DOI: 10.3390/insects13121172. View

Neumann P, Novak P, Hostakova N, Macas J . Systematic survey of plant LTR-retrotransposons elucidates phylogenetic relationships of their polyprotein domains and provides a reference for element classification. Mob DNA. 2019; 10:1. PMC: 6317226. DOI: 10.1186/s13100-018-0144-1. View

Korf I . Gene finding in novel genomes. BMC Bioinformatics. 2004; 5:59. PMC: 421630. DOI: 10.1186/1471-2105-5-59. View

10.

Tillich M, Lehwark P, Pellizzer T, Ulbricht-Jones E, Fischer A, Bock R . GeSeq - versatile and accurate annotation of organelle genomes. Nucleic Acids Res. 2017; 45(W1):W6-W11. PMC: 5570176. DOI: 10.1093/nar/gkx391. View

11.

Katoh K, Asimenos G, Toh H . Multiple alignment of DNA sequences with MAFFT. Methods Mol Biol. 2009; 537:39-64. DOI: 10.1007/978-1-59745-251-9_3. View

12.

Talavera G, Castresana J . Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol. 2007; 56(4):564-77. DOI: 10.1080/10635150701472164. View

13.

Li H, Durbin R . Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009; 25(14):1754-60. PMC: 2705234. DOI: 10.1093/bioinformatics/btp324. View

14.

Bao W, Kojima K, Kohany O . Repbase Update, a database of repetitive elements in eukaryotic genomes. Mob DNA. 2015; 6:11. PMC: 4455052. DOI: 10.1186/s13100-015-0041-9. View

15.

Ou S, Jiang N . LTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons. Plant Physiol. 2017; 176(2):1410-1422. PMC: 5813529. DOI: 10.1104/pp.17.01310. View

16.

Vurture G, Sedlazeck F, Nattestad M, Underwood C, Fang H, Gurtowski J . GenomeScope: fast reference-free genome profiling from short reads. Bioinformatics. 2017; 33(14):2202-2204. PMC: 5870704. DOI: 10.1093/bioinformatics/btx153. View

17.

Zhao H, Liu H, Liu Y, Wang C, Ma B, Zhang M . Chromosome-level genomes of two armyworms, Mythimna separata and Mythimna loreyi, provide insights into the biosynthesis and reception of sex pheromones. Mol Ecol Resour. 2023; 23(6):1423-1441. DOI: 10.1111/1755-0998.13809. View

18.

Stanke M, Diekhans M, Baertsch R, Haussler D . Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics. 2008; 24(5):637-44. DOI: 10.1093/bioinformatics/btn013. View

19.

Rao S, Huntley M, Durand N, Stamenova E, Bochkov I, Robinson J . A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell. 2014; 159(7):1665-80. PMC: 5635824. DOI: 10.1016/j.cell.2014.11.021. View

20.

Keilwagen J, Wenk M, Erickson J, Schattat M, Grau J, Hartung F . Using intron position conservation for homology-based gene prediction. Nucleic Acids Res. 2016; 44(9):e89. PMC: 4872089. DOI: 10.1093/nar/gkw092. View