{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,21]],"date-time":"2025-10-21T15:41:15Z","timestamp":1761061275147,"version":"3.41.2"},"reference-count":49,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2021,2,2]],"date-time":"2021-02-02T00:00:00Z","timestamp":1612224000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31970401","31501847"],"award-info":[{"award-number":["31970401","31501847"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100007129","name":"Natural Science Foundation of Shandong Province","doi-asserted-by":"publisher","award":["ZR2020MC046"],"award-info":[{"award-number":["ZR2020MC046"]}],"id":[{"id":"10.13039\/501100007129","id-type":"DOI","asserted-by":"publisher"}]},{"name":"National Science and Technology Fundamental Resources Investigation Program of China","award":["2018FY100300"],"award-info":[{"award-number":["2018FY100300"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>As a polyphagous soil-dwelling predatory mite, Stratiolaelaps scimitus (Womersley) (Acari: Laelapidae), formerly known as Stratiolaelaps miles (Berlese), is native to the Northern hemisphere and preys on soil invertebrates, including fungus gnats, springtails, thrips nymphs, nematodes, and other species of mites. Already mass-produced and commercialized in North America, Europe, Oceania and China, S. scimitus will highly likely be introduced to other countries and regions as a biocontrol agent against edaphic pests in the near future. The introduction, however, can lead to unexpected genetic changes within populations of biological control agents, which might decrease the efficacy of pest management or increase the risks to local environments. To better understand the genetic basis of its biology and behavior, we sequenced and assembled the draft genome of S.\u00a0scimitus using the PacBio Sequel platform II. We generated \u223c150\u00d7 (64.81\u2009Gb) PacBio long reads with an average read length of 12.60\u2009kb. Reads longer than 5\u2009kb were assembled into contigs, resulting in the final assembly of 158 contigs with an N50 length of 7.66\u2009Mb, and captured 93.1% of the BUSCO (Benchmarking Universal Single-Copy Orthologs) gene set (n\u2009=\u20091,066). We identified 16.39% (69.91\u2009Mb) repetitive elements, 1,686 noncoding RNAs, and 13,305 protein-coding genes, which represented 95.8% BUSCO completeness. Combining analyses of genome family evolution and function enrichment of gene ontology and pathway, a total of 135 families experienced significant expansions, which were mainly involved in digestion, detoxification, immunity, and venom. Major expansions of the detoxification enzymes, that is, P450s and carboxylesterases, suggest a possible genetic mechanism underlying polyphagy and ecological adaptions. Our high-quality genome assembly and annotation provide new insights on the evolutionary biology, soil ecology, and biological control for predaceous mites.<\/jats:p>","DOI":"10.1093\/gbe\/evab011","type":"journal-article","created":{"date-parts":[[2021,1,22]],"date-time":"2021-01-22T23:18:07Z","timestamp":1611357487000},"source":"Crossref","is-referenced-by-count":3,"title":["A Highly Contiguous Genome Assembly of a Polyphagous Predatory Mite <i>Stratiolaelaps scimitus<\/i> (Womersley) (Acari: Laelapidae)"],"prefix":"10.1093","volume":"13","author":[{"given":"Yi","family":"Yan","sequence":"first","affiliation":[{"name":"Department of Entomology, College of Plant Protection, Shandong Agricultural University, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, Taian, China"},{"name":"Department of Entomology, Agricultural Science Center North, University of Kentucky, Lexington, Kentucky, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Na","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Entomology, College of Plant Protection, Shandong Agricultural University, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, Taian, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chenglin","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Entomology, College of Plant Protection, Shandong Agricultural University, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, Taian, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xinran","family":"Wu","sequence":"additional","affiliation":[{"name":"Department of Entomology, College of Plant Protection, Shandong Agricultural University, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, Taian, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kai","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Entomology, College of Plant Protection, Shandong Agricultural University, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, Taian, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhan","family":"Yin","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Hebei University, Baoding, Hebei, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xuguo","family":"Zhou","sequence":"additional","affiliation":[{"name":"Department of Entomology, Agricultural Science Center North, University of Kentucky, Lexington, Kentucky, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lixia","family":"Xie","sequence":"additional","affiliation":[{"name":"Department of Entomology, College of Plant Protection, Shandong Agricultural University, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, Taian, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2021,2,2]]},"reference":[{"issue":"1","key":"2021030604534289500_evab011-B1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s13100-015-0041-9","article-title":"Repbase update, a database of repetitive elements in eukaryotic genomes","volume":"6","author":"Bao","year":"2015","journal-title":"Mobile DNA"},{"issue":"1","key":"2021030604534289500_evab011-B2","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1038\/nmeth.3176","article-title":"Fast and sensitive protein alignment using DIAMOND","volume":"12","author":"Buchfink","year":"2015","journal-title":"Nat Methods"},{"year":"2014","author":"Bushnell","key":"2021030604534289500_evab011-B3"},{"issue":"1\u20132","key":"2021030604534289500_evab011-B4","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1007\/s10493-005-0242-x","article-title":"Development and reproduction of Stratiolaelaps scimitus (Acari: laelapidae) with fungus gnat larvae (Diptera: sciaridae), potworms (Oligochaeta: enchytraeidae) or Sancassaniaaff Sphaerogaster (Acari: acaridae) as the sole food source","volume":"36","author":"Cabrera","year":"2005","journal-title":"Exp Appl Acarol"},{"issue":"1","key":"2021030604534289500_evab011-B5","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1186\/1471-2105-10-421","article-title":"BLAST+: architecture and applications","volume":"10","author":"Camacho","year":"2009","journal-title":"BMC Bioinformatics"},{"issue":"15","key":"2021030604534289500_evab011-B6","doi-asserted-by":"crossref","first-page":"1972","DOI":"10.1093\/bioinformatics\/btp348","article-title":"trimA l: a tool for automated alignment trimming in large-scale phylogenetic analyses","volume":"25","author":"Capella-Guti\u00e9rrez","year":"2009","journal-title":"Bioinformatics"},{"key":"2021030604534289500_evab011-B7","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/978-1-4939-9173-0_1","article-title":"tRNAscan-SE: searching for tRNA genes in genomic sequences","volume":"1962","author":"Chan","year":"2019","journal-title":"Methods Mol Biol"},{"issue":"16","key":"2021030604534289500_evab011-B8","doi-asserted-by":"crossref","first-page":"7762","DOI":"10.1093\/nar\/gkv784","article-title":"High speed BLASTN: an accelerated MegaBLAST search tool","volume":"43","author":"Chen","year":"2015","journal-title":"Nucleic Acids Res"},{"issue":"12","key":"2021030604534289500_evab011-B10","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/gigascience\/giy127","article-title":"Genomes of trombidid mites reveal novel predicted allergens and laterally transferred genes associated with secondary metabolism","volume":"7","author":"Dong","year":"2018","journal-title":"GigaScience"},{"issue":"D1","key":"2021030604534289500_evab011-B11","doi-asserted-by":"crossref","first-page":"D427","DOI":"10.1093\/nar\/gky995","article-title":"The Pfam protein families database in 2019","volume":"47","author":"El-Gebali","year":"2019","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"2021030604534289500_evab011-B12","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s13059-019-1832-y","article-title":"OrthoFinder: phylogenetic orthology inference for comparative genomics","volume":"20","author":"Emms","year":"2019","journal-title":"Genome Biol"},{"key":"2021030604534289500_evab011-B13","first-page":"1","volume-title":"Comprehensive molecular insect science","author":"Feyereisen","year":"2005"},{"issue":"D1","key":"2021030604534289500_evab011-B14","doi-asserted-by":"crossref","first-page":"D190","DOI":"10.1093\/nar\/gkw1107","article-title":"InterPro in 2017-beyond protein family and domain annotations","volume":"45","author":"Finn","year":"2017","journal-title":"Nucleic Acids Res"},{"issue":"17","key":"2021030604534289500_evab011-B15","doi-asserted-by":"crossref","first-page":"9451","DOI":"10.1073\/pnas.1921046117","article-title":"Repeat Modeler 2 for automated genomic discovery of transposable element families","volume":"117","author":"Flynn","year":"2020","journal-title":"Proc Natl Acad Sci USA"},{"issue":"8","key":"2021030604534289500_evab011-B16","doi-asserted-by":"crossref","first-page":"1987","DOI":"10.1093\/molbev\/mst100","article-title":"Estimating gene gain and loss rates in the presence of error in genome assembly and annotation using CAFE 3","volume":"30","author":"Han","year":"2013","journal-title":"Mol Biol Evol"},{"issue":"5","key":"2021030604534289500_evab011-B17","doi-asserted-by":"crossref","first-page":"767","DOI":"10.1093\/bioinformatics\/btv661","article-title":"BRAKER1: unsupervised RNA-Seq-based genome annotation with GeneMark-ET and AUGUSTUS","volume":"32","author":"Hoff","year":"2016","journal-title":"Bioinformatics"},{"issue":"1","key":"2021030604534289500_evab011-B18","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1471-2105-12-491","article-title":"MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects","volume":"12","author":"Holt","year":"2011","journal-title":"BMC Bioinformatics"},{"issue":"6","key":"2021030604534289500_evab011-B19","doi-asserted-by":"crossref","first-page":"1762","DOI":"10.1093\/gbe\/evw048","article-title":"Genome sequencing of the phytoseiid predatory mite Metaseiulus occidentalis reveals completely atomized Hox genes and superdynamic intron evolution","volume":"8","author":"Hoy","year":"2016","journal-title":"Genome Biol Evol"},{"issue":"7","key":"2021030604534289500_evab011-B20","doi-asserted-by":"crossref","first-page":"2253","DOI":"10.1093\/bioinformatics\/btz891","article-title":"NextPolish: a fast and efficient genome polishing tool for long read assembly","volume":"36","author":"Hu","year":"2020","journal-title":"Bioinformatics"},{"issue":"D1","key":"2021030604534289500_evab011-B21","doi-asserted-by":"crossref","first-page":"D81","DOI":"10.1093\/nar\/gkv1272","article-title":"The Dfam database of repetitive DNA families","volume":"44","author":"Hubley","year":"2016","journal-title":"Nucleic Acids Res"},{"issue":"8","key":"2021030604534289500_evab011-B22","doi-asserted-by":"crossref","first-page":"2115","DOI":"10.1093\/molbev\/msx148","article-title":"Fast genome-wide functional annotation through or thology assignment by eggNOG-mapper","volume":"34","author":"Huerta-Cepas","year":"2017","journal-title":"Mol Biol Evol"},{"issue":"D1","key":"2021030604534289500_evab011-B23","doi-asserted-by":"crossref","first-page":"D309","DOI":"10.1093\/nar\/gky1085","article-title":"eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses","volume":"47","author":"Huerta-Cepas","year":"2019","journal-title":"Nucleic Acids Res"},{"issue":"4","key":"2021030604534289500_evab011-B24","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1093\/molbev\/mst010","article-title":"MAFFT multiple sequence alignment software version 7: improvements in performance and usability","volume":"30","author":"Katoh","year":"2013","journal-title":"Mol Biol Evol"},{"issue":"1","key":"2021030604534289500_evab011-B25","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1186\/s12983-014-0081-x","article-title":"FASconCAT-G: extensive functions for multiple sequence alignment preparations concerning phylogenetic studies","volume":"11","author":"K\u00fcck","year":"2014","journal-title":"Front Zool"},{"issue":"8","key":"2021030604534289500_evab011-B26","doi-asserted-by":"crossref","first-page":"907","DOI":"10.1038\/s41587-019-0201-4","article-title":"Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype","volume":"37","author":"Kim","year":"2019","journal-title":"Nat Biotechnol"},{"issue":"5","key":"2021030604534289500_evab011-B27","doi-asserted-by":"crossref","first-page":"540","DOI":"10.1038\/s41587-019-0072-8","article-title":"Assembly of long error-prone reads using repeat graphs","volume":"37","author":"Kolmogorov","year":"2019","journal-title":"Nat Biotechnol"},{"issue":"1","key":"2021030604534289500_evab011-B28","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s13059-019-1910-1","article-title":"Transcriptome assembly from long-read RNA-seq alignments with StringTie2","volume":"20","author":"Kovaka","year":"2019","journal-title":"Genome Biol"},{"issue":"D1","key":"2021030604534289500_evab011-B29","doi-asserted-by":"crossref","first-page":"D807","DOI":"10.1093\/nar\/gky1053","article-title":"OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs","volume":"47","author":"Kriventseva","year":"2019","journal-title":"Nucleic Acids Res"},{"issue":"D1","key":"2021030604534289500_evab011-B30","doi-asserted-by":"crossref","first-page":"D435","DOI":"10.1093\/nar\/gkx1069","article-title":"Gene3D: extensive prediction of globular domains in proteins","volume":"46","author":"Lewis","year":"2018","journal-title":"Nucleic Acids Res"},{"issue":"18","key":"2021030604534289500_evab011-B31","doi-asserted-by":"crossref","first-page":"3094","DOI":"10.1093\/bioinformatics\/bty191","article-title":"Minimap2: pairwise alignment for nucleotide sequences. Minimap2: pairwise alignment for nucleotide sequences","volume":"34","author":"Li","year":"2018","journal-title":"Bioinformatics"},{"key":"2021030604534289500_evab011-B32","first-page":"124","volume-title":"A manual of acarology","author":"Lindquist","year":"2009","edition":"3rd edition"},{"issue":"20","key":"2021030604534289500_evab011-B33","doi-asserted-by":"crossref","first-page":"6494","DOI":"10.1093\/nar\/gki937","article-title":"Gene identification in novel eukaryotic genomes by self-training algorithm","volume":"33","author":"Lomsadze","year":"2005","journal-title":"Nucleic Acids Res"},{"issue":"D1","key":"2021030604534289500_evab011-B34","doi-asserted-by":"crossref","first-page":"D200","DOI":"10.1093\/nar\/gkw1129","article-title":"CDD\/SPARCLE: functional classification of proteins via subfamily domain architectures","volume":"45","author":"Marchler-Bauer","year":"2017","journal-title":"Nucleic Acids Res"},{"issue":"5","key":"2021030604534289500_evab011-B36","doi-asserted-by":"crossref","first-page":"1530","DOI":"10.1093\/molbev\/msaa015","article-title":"IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era","volume":"37","author":"Minh","year":"2020","journal-title":"Mol Biol Evol"},{"issue":"22","key":"2021030604534289500_evab011-B37","doi-asserted-by":"crossref","first-page":"2933","DOI":"10.1093\/bioinformatics\/btt509","article-title":"Infernal 1.1: 100-fold faster RNA homology searches","volume":"29","author":"Nawrocki","year":"2013","journal-title":"Bioinformatics"},{"issue":"1","key":"2021030604534289500_evab011-B38","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s12859-018-2485-7","article-title":"Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies","volume":"19","author":"Roach","year":"2018","journal-title":"BMC Bioinformatics"},{"year":"2013","author":"Smit","key":"2021030604534289500_evab011-B39"},{"issue":"Web Server","key":"2021030604534289500_evab011-B40","doi-asserted-by":"crossref","first-page":"W309","DOI":"10.1093\/nar\/gkh379","article-title":"AUGUSTUS: a web server for gene finding in eukaryotes","volume":"32","author":"Stanke","year":"2004","journal-title":"Nucleic Acids Res"},{"issue":"14","key":"2021030604534289500_evab011-B41","doi-asserted-by":"crossref","first-page":"2202","DOI":"10.1093\/bioinformatics\/btx153","article-title":"GenomeScope: fast reference-free genome profling from short reads","volume":"33","author":"Vurture","year":"2017","journal-title":"Bioinformatics"},{"issue":"3","key":"2021030604534289500_evab011-B42","doi-asserted-by":"crossref","first-page":"253","DOI":"10.1016\/S1049-9644(02)00171-8","article-title":"Exotic vs endemic biocontrol agents: would the real Stratiolaelaps miles (Berlese) (Acari: mesostigmata: laelapidae), please stand up?","volume":"26","author":"Walter","year":"2003","journal-title":"Biol Control"},{"issue":"3","key":"2021030604534289500_evab011-B5576015","first-page":"543","article-title":"BUSCO applications from quality assessments to gene prediction and phylogenomics","volume":"35","author":"Waterhouse","year":"2018"},{"issue":"suppl 1","key":"2021030604534289500_evab011-B43","doi-asserted-by":"crossref","first-page":"D380","DOI":"10.1093\/nar\/gkn762","article-title":"SUPERFAMILY: sophisticated comparative genomics, data mining, visualization and phylogeny","volume":"37","author":"Wilson","year":"2009","journal-title":"Nucleic Acids Res"},{"issue":"4","key":"2021030604534289500_evab011-B11192892","first-page":"779\u2013","article-title":"Development, survival and reproduction of Stratiolaelaps scimitus (Acari: Laelapidae) on four diets","volume":"23","author":"Xie","year":"2018","journal-title":"Syst Appl Acarol."},{"issue":"3","key":"2021030604534289500_evab011-B44","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1016\/j.toxicon.2004.05.023","article-title":"Structure and function of snake venom cysteine-rich secretory proteins","volume":"44","author":"Yamazaki","year":"2004","journal-title":"Toxicon"},{"issue":"1","key":"2021030604534289500_evab011-B45","doi-asserted-by":"crossref","first-page":"885","DOI":"10.1080\/23802359.2020.1717393","article-title":"Characterization of the complete mitochondrial genome of the predatory mite Stratiolaelaps scimitus (Acari: laelapidae)","volume":"5","author":"Yan","year":"2020","journal-title":"Mitochondrial DNA Part B: Resources"},{"issue":"8","key":"2021030604534289500_evab011-B46","doi-asserted-by":"crossref","first-page":"1586","DOI":"10.1093\/molbev\/msm088","article-title":"PAML 4: phylogenetic analysis by maximum likelihood","volume":"24","author":"Yang","year":"2007","journal-title":"Mol Biol Evol"},{"issue":"5","key":"2021030604534289500_evab011-B47","doi-asserted-by":"crossref","first-page":"284","DOI":"10.1089\/omi.2011.0118","article-title":"clusterProfiler: an R package for comparing biological themes among gene clusters","volume":"16","author":"Yu","year":"2012","journal-title":"OMICS"},{"issue":"4","key":"2021030604534289500_evab011-B48","first-page":"705","article-title":"Functional response of Stratiolaelaps scimitus to Bradysia odoriphaga","volume":"55","author":"Zhou","year":"2018","journal-title":"Chinese J Appl Entomol"},{"issue":"1","key":"2021030604534289500_evab011-B49","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s12864-019-6281-1","article-title":"Genomic insights into mite phylogeny, fitness, development and reproduction","volume":"20","author":"Zhang","year":"2019","journal-title":"BMC Genomics"}],"container-title":["Genome Biology and Evolution"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/gbe\/advance-article-pdf\/doi\/10.1093\/gbe\/evab011\/36321138\/evab011.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"http:\/\/academic.oup.com\/gbe\/article-pdf\/13\/3\/evab011\/36418381\/evab011.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"http:\/\/academic.oup.com\/gbe\/article-pdf\/13\/3\/evab011\/36418381\/evab011.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,3,6]],"date-time":"2021-03-06T05:12:18Z","timestamp":1615007538000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/gbe\/article\/doi\/10.1093\/gbe\/evab011\/6126405"}},"subtitle":[],"editor":[{"given":"Sujal","family":"Phadke","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2021,2,2]]},"references-count":49,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2021,3,1]]}},"URL":"https:\/\/doi.org\/10.1093\/gbe\/evab011","relation":{},"ISSN":["1759-6653"],"issn-type":[{"type":"electronic","value":"1759-6653"}],"subject":[],"published-other":{"date-parts":[[2021,3,1]]},"published":{"date-parts":[[2021,2,2]]},"article-number":"evab011"}}