Access to this full-text is provided by Springer Nature.
Content available from Scientific Data
This content is subject to copyright. Terms and conditions apply.
1
SCIENTIFIC DATA | (2025) 12:446 | https://doi.org/10.1038/s41597-025-04814-2
www.nature.com/scientificdata
A chromosome-level genome
assembly of eriophyoid mite
Setoptus koraiensis
Zi-Kai Shao, Lei Chen , Jing-Tao Sun & Xiao-Feng Xue ✉
Eriophyoidea represents a highly diverse superfamily of herbivorous mites in the Acariformes,
chromosome-level genome assembly of Setoptus koraiensis
Eriophyoid mites (Acariformes, Eriophyoidea) are among the largest superfamilies in the Arachnida, compris-
ing over 5,000 name species1,2 and exhibiting a worldwide distribution3. ese tiny (~200 um in length, among
the smallest arthropods), vermiform to fusiform mites have only two pairs of legs, and are strictly phytopha-
gous, reecting high hostplant specicity4,5; some of them can cause massive economic losses in agriculture and
forestry6.
Despite the need to understand the ecology and evolution among eriophyoid mites, there are no
chromosome-level assembled genomes for eriophyoid mites yet. A near chromosome genome assembly has
been published for tomato russet mite Aculops lycopersici7, but the lack of high-quality chromosome-level
genome resources has limited further comparative genomic analyses among eriophyoid mites.
In this study, we assembled a chromosome-level genome for the Setoptus koraiensis (Eriophyoidea,
Phytoptidae) using PacBio long-reads sequencing, Illumina short-reads sequencing, and high-throughput
chromatin conformation capture (Hi-C) sequencing. Our assembly resulted in a genome size of 47 Mb across
two chromosomes, with scaold N50 lengths of 24.53 Mb (Table1). is genome is the rst chromosome-level
genome among eriophyoid mites, providing signicant new data resources for understanding the Eriophyoidea.
At least 100,000 wild S. koraiensis individuals, including eggs, juveniles and adults,
were collected from Pinus koraiensis Siebold & Zucc. (Pinaceae), in Lishui, Nanjing city, Jiangsu province,
China (31.3921°N, 118.5417°E). Samples were identied by morphological characteristics with molecular evi-
dence (mitochondrial COI). Vouchers were deposited in the Arthropod/Mite Collection of the Department of
Entomology, Nanjing Agricultural University, Jiangsu Province, China.
Genomic DNA was extracted from more than 100,000 individuals using MagAttract
HMW DNA Kit. The Pacbio 30 kb SMRTbell library was prepared with more than 5 μg gDNA using the
SMRTbellTM Prep Kit 2.0 (Pacic Biosciences). e mode of Continuous Long Read (CLR) was run on the Sequel
II platform. Illumina whole-genome sequencing was prepared using a 350 bp-insert fragment library (150 bp
paired-end) by Truseq DNA PCR-free Kit, which was further sequenced on an Illumina NovaSeq 6000 platform.
High-throughput chromosome conformation capture (Hi-C) included cross-linking, HindIII restriction enzyme
digestion, end repair, DNA cyclization, purication and capture. e Hi-C library with 300–700 bp insert size
library was sequenced on the NovaSeq 6000 platform. Finally, we generated 24.25 Gb (~496X) PacBio long reads,
9.5 Gb (~194X) Illumina short reads, and 9 Gb Hi-C (~184X) reads for our genome assembly.
Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China. ✉e-mail: xfxue@
njau.edu.cn
Content courtesy of Springer Nature, terms of use apply. Rights reserved
2
SCIENTIFIC DATA | (2025) 12:446 | https://doi.org/10.1038/s41597-025-04814-2
www.nature.com/scientificdata
www.nature.com/scientificdata/
Duplicate and low-quality Illumina raw reads (base quality < Q20, length < 15 bp, polymer
A/G/C/ > 10 bp) were trimmed and removed using BBtools package v38.828. e 21-mer depth distribution was
counted using script ‘khist.sh’ of BBtools. Genome Scope v2.09 was used to estimate the genome size and hete-
rozygosity of S. koraiensis with the maximum kmer coverage at 1,000×. Based on the distribution of kmer cover-
age and frequency, the estimated genome size of S. koraiensis was 45.72 Mb, with a heterozygosity rate of around
1.13% and a repeat content proportion of approximately 3.3% (Fig.1).
e CLR reads were set as input to Flye v2.610 to assemble continuous long reads. One
round of built-in long reads polishing was performed by Flye v2.6. en, two rounds of short reads were used
to polish and ll in gaps of the primary assembly with NextPolish v1.4.111. Haplotigs and duplication caused by
haplotype divergence were eliminated by Purge_dups v1.2.512 using the alignment program Minimap2 v2.2813.
Hi-C reads were aligned to the purged genome using BWA v0.7.1814 and Juicer v1.615 to anchor, order and orient
contigs into chromosomal assembly following 3D-DNA16 pipeline. en, we manually reviewed and corrected
assembled errors using Juicebox v2.1717. Contaminations were checked and deleted against the UniVec and NCBI
nucleotide databases using BLAST + v2.11.018 and MMseqs2 v1619. e completeness of genome assembly was
evaluated by BUSCO version 5.2.220 using the eukaryota_odb10 dataset (creation date 2020-09-10). e reads
from the whole genome sequencing were aligned back to the genome assembly to access the mapping rate. Aer
de novo assembly, polishing and contaminant removal, the S. koraiensis genome has a genome size of 49.9 Mb
with 565 scaolds, an N50 length of 24.53 Mb, with 94.2% of assembled genomes anchored to two chromosomes
(Fig.2) resulting in a nal genome size of 47 Mb (Table1).
e repetitive elements were identied using RepeatModeler v2.0.521, which discov-
ered the complete long terminal repeats (LTR) with the ‘-LTRstruct’ pipeline. RepeatMasker v4.1.622 was searched
against the custom repeat library of Dfam 3.823 and Repbase v2018102624 with options ‘-no_is -norna -xsmall -q’
to so mask repeats of the genome assembly.
For gene structure annotation, we performed a pipeline integrating ab initio and homolog-based meth-
ods. Braker v2.1.525 was used to obtain ab initio gene predictions employing GeneMark-ES/ET/EP v4.3326 and
Augustus v3.4.027 based on reference proteins from the OrthoDB v11 database28. GeMoMa v1.929 was used for
Characteristics Setoptus koraiensis
Genome Size (Mb) 47
Number of contigs 266
Number of chromosomes 2
Scaold N50 length (Mb) 24.53
BUSCO completeness (%) 89
Repetitive elements Size (Mb) 6.42 (13.82%)
Tab le 1. Statistics of Setoptus koraiensis genome assembly. State: We would be happy to be published without
further edits.
Fig. 1 GenomeScope genome size estimates for Setoptus koraiensis.
Content courtesy of Springer Nature, terms of use apply. Rights reserved
3
SCIENTIFIC DATA | (2025) 12:446 | https://doi.org/10.1038/s41597-025-04814-2
www.nature.com/scientificdata
www.nature.com/scientificdata/
homology prediction with the parameters “GeMoMa.c = 0.4 GeMoMa.p = 10”, and the protein sequences of six
species (Aculops lycopersici (GCA_015350385.1), Tetranychus urticae (GCA_039701765.1), Tetranychus piercei
(GCA_036759885.1), Panonychus citri (GCA_014898815.1), Pyemotes zhonghuajia (GCA_025170145.1), Blomia
tropicalis (GCA_029204025.1)) were provided to assist gene prediction. e results obtained from BRAKER and
GeMoMa were combined and provided to MAKER v3.01.0330. e functional annotation of predicted protein
sequences was searched against UniProt, InterProScan and eggNOG databases. Diamond v2.1.1031 was used to
assign the gene function of the best hits in the UniProt database under the ‘very sensitive’ mode. Gene Ontology
(GO) and pathway (KEGG) were annotated using InterProScan v5.7232 and eggnog-mapper v2.1.1233 against
Pfam34, SMART35, Superfamily36, CDD37, and EggNOG 5.0.2 database38.
Data Records
The raw reads and genome assembly have been deposited in the NCBI databases under BioProject
PRJNA1196018. The PacBio, Illumina, and Hi-C data are available under identification numbers
SRR32458739-SRR3245874139. e nal chromosome assembly has been deposited at GenBank under the
accession number GCA_048013815.140. e mitochondrial COI sequence has been deposited at GenBank
under the accession number PV16383341. e genome assembly and annotation les are available in Figshare42.
Fig. 2 Genome-wide chromosomal heatmap of Setoptus koraiensis, the blue boxes show super scaolds.
Content courtesy of Springer Nature, terms of use apply. Rights reserved
4
SCIENTIFIC DATA | (2025) 12:446 | https://doi.org/10.1038/s41597-025-04814-2
www.nature.com/scientificdata
www.nature.com/scientificdata/
Technical Validation
We mapped the Illumina sequencing data to the nal assembly with BWA v0.7.18, and the mapping rate was
92.9%. We assessed the completeness of the genome assembly using BUSCO v5.4.2 with the ‘eukaryota_odb10’
database, and a total of 89% (83.9% single-copied genes, 5.1% duplicated genes, 5.5% fragmented, and 5.5%
missing genes) completed BUSCOs were identied, which is higher than that of A. lycopersici (86.3%). We
masked 13.82% (6.42 Mb) repetitive regions of the S. koraiensis genome. Among them, 0.2% of repeat sequences
were short interspersed elements (SINEs), 1.29% were long interspersed elements (LINEs), 0.92% were long
terminal repeats (LTRs), 1.61% were DNA transposons, and 5.14% were unclassied (Fig.3). We identied 5,954
protein-coding genes, with 4,770 genes that could be functionally annotated. e BUSCO completeness for pro-
tein sequence is 77.3% (71.4% single-copied genes, 5.9% duplicated genes, 3.9% fragmented, and 18.8% missing
genes) with the ‘eukaryota_odb10’ database. All evidence strongly supported the completeness and accuracy of
S. koraiensis genome assembly.
Code availability
No custom scripts or code were used in this study.
Received: 27 December 2024; Accepted: 12 March 2025;
Published: xx xx xxxx
References
1. Zhang, Z.-Q. Eriophyoidea and allies: where do they belong? Syst. Appl. Acarol. 22, 1091–1095 (2017).
2. Zhang, Z.-Q. Phylum Arthropoda von Siebold, 1848. in Animal biodibersity: An Outline of Higher-Level Classication and Survey of
Taxonomic ichness (ed. Zhang, Z.-Q.) 99–103 (Magnolia Press, 2011)
3. Li, N., Sun, J.-T., Yin, Y., Hong, X.-Y. & Xue, X.-F. Global patterns and drivers of herbivorous eriophyoid mite species diversity.
J. Biogeogr. 50, 330–340 (2022).
4. Soraca, A., Smith, L., Oldeld, G., Cristofaro, M. & Amrine, J. W. Host-plant specicity and specialization in eriophyoid mites and
their importance for the use of eriophyoid mites as biocontrol agents of weeds. Exp. Appl. Acarol. 51, 93–113 (2010).
5. Yin, Y. et al. DNA barcoding uncovers cryptic diversity in minute herbivorous mites (Acari, Eriophyoidea). Mol. Ecol. esour. 22,
1986–1998 (2022).
6. de Lillo, E., Pozzebon, A., Valenzano, D. & Duso, C. An intimate relationship between eriophyoid mites and their host plants–a
review. Front. Plant. Sci. 9, 1786 (2018).
7. Greenhalgh, . et al. Genome streamlining in a minute herbivore that manipulates its host plant. Elife 9 (2020).
8. Bushnell, B. BBtools. Available online: https://sourceforge.net/projects/bbmap/ (accessed on 1 October 2024) (2014).
9. anallo-Benavidez, T. ., Jaron, . S. & Schatz, M. C. GenomeScope 2.0 and Smudgeplot for reference-free proling of polyploid
genomes. Nat. Commun. 11, 1432 (2020).
10. olmogorov, M., Yuan, J., Lin, Y. & Pevzner, P. A. Assembly of long, error-prone reads using repeat graphs. Nat. Biotechnol. 37,
540–546 (2019).
11. Hu, J., Fan, J., Sun, Z. & Liu, S. NextPolish: a fast and ecient genome polishing tool for long-read assembly. Bioinformatics 36,
2253–2255 (2020).
12. Gua n , D. et al. Identifying and removing haplotypic duplication in primary genome assemblies. Bioinformatics 36, 2896–2898
(2020).
13. Li, H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34, 3094–3100 (2018).
14. Li, H. & Durbin, . Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
Fig. 3 Circular karyotype representation of the chromosomes of Setoptus koraiensis. Tracks from inside to
outside are GC content (GC), density of protein-coding genes (GENE), DNA transposons (DNA), LTR/LINE/
SINE retrotransposons (LTR, LINE, SINE), and simple repeats (Simple).
Content courtesy of Springer Nature, terms of use apply. Rights reserved
5
SCIENTIFIC DATA | (2025) 12:446 | https://doi.org/10.1038/s41597-025-04814-2
www.nature.com/scientificdata
www.nature.com/scientificdata/
15. Durand, N. C. et al. Juicer provides a one-clic system for analyzing loop-resolution Hi-C experiments. Cell. Syst. 3, 95–98 (2016).
16. Dudcheno, O. et al. De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaolds. Science 356,
92–95 (2017).
17. Durand, N. C. et al. Juicebox provides a visualization system for Hi-C contact maps with unlimited zoom. Cell. Syst. 3, 99–101 (2016).
18. Camacho, C. et al. BLAST+: architecture and applications. BMC Bioinformatics 10, 421 (2009).
19. Steinegger, M. & Soding, J. MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nat.
Biotechnol. 35, 1026–1028 (2017).
20. Manni, M., Bereley, M. ., Seppey, M., Simao, F. A. & Zdobnov, E. M. BUSCO update: novel and streamlined worows along with
broader and deeper phylogenetic coverage for scoring of euaryotic, proaryotic, and viral genomes. Mol. Biol. Evol. 38, 4647–4654 (2021) .
21. Flynn, J. M. et al. epeatModeler2 for automated genomic discovery of transposable element families. Proc Natl Acad Sci USA 117,
9451–9457 (2020).
22. Smit, A. F. A., Hubley, . & Green, P. epeatMaser Open-4.0. Available online: http://www.repeatmaser.org (accessed on 1
October 2024) (2013–2015).
23. Hubley, . et al. e Dfam database of repetitive DNA families. Nucleic. Acids. es. 44, D81–89 (2016).
24. Bao, W., ojima, . . & ohany, O. epbase Update, a database of repetitive elements in euaryotic genomes. Mob DNA 6, 11 (2015).
25. Bruna, T., Ho, . J., Lomsadze, A., Stane, M. & Borodovsy, M. BAE2: automatic euaryotic genome annotation with
GeneMar-EP+ and AUGUSTUS supported by a protein database. NA. Genom. Bioinform. 3, lqaa108 (2021).
26. Bruna, T., Lomsadze, A. & Borodovsy, M. GeneMar-EP+: euaryotic gene prediction with self-training in the space of genes and
proteins. NA. Genom. Bioinform. 2, lqaa026 (2020).
27. Stane, M., Steinamp, ., Waac, S. & Morgenstern, B. AUGUSTUS: a web server for gene nding in euaryotes. Nucleic. Acids.
es. 32, W309–312 (2004).
28. uznetsov, D. et al. OrthoDB v11: annotation of orthologs in the widest sampling of organismal diversity. Nucleic. Acids. es. 51,
D445–D451 (2023).
29. eilwagen, J. et al. Using intron position conservation for homology-based gene prediction. Nucleic. Acids. es. 44, e89 (2016).
30. Holt, C. & Yandell, M. MAE2: an annotation pipeline and genome-database management tool for second-generation genome
projects. BMC Bioinformatics 12, 491 (2011).
31. Buchn, B., euter, . & Drost, H. G. Sensitive protein alignments at tree-of-life scale using DIAMOND. Nat. Methods 18, 366–368 (2021).
32. Finn, . D. et al. InterPro in 2017-beyond protein family and domain annotations. Nucleic. Acids. es. 45, D190–D199 (2017).
33. Cantalapiedra, C. P., Hernandez-Plaza, A., Letunic, I., Bor, P. & Huerta-Cepas, J. eggNOG-mapper v2: functional annotation,
orthology assignments, and domain prediction at the metagenomic scale. Mol. Biol. Evol. 38, 5825–5829 (2021).
34. El-Geb ali, S. et al. e Pfam protein families database in 2019. Nucleic. Acids. es. 47, D427–D432 (2019).
35. Letunic, I. & Bor, P. 20 years of the SMAT protein domain annotation resource. Nucleic. Acids. es. 46, D493–D496 (2018).
36. Wilson, D. et al. SUPEFAMILY—sophisticated comparative genomics, data mining, visualization and phylogeny. Nucleic. Acids.
es. 37, D380–386 (2009).
37. Marchler-Bauer, A. et al. CDD/SPACLE: functional classication of proteins via subfamily domain architectures. Nucleic. Acids.
es. 45, D200–D203 (2017).
38. Huerta-Cepas, J. et al. eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090
organisms and 2502 viruses. Nucleic. Acids. es. 47, D309–D314 (2019).
39. NCBI Sequence ead Archive https://identiers.org/ncbi/insdc.sra:SP565774 (2024).
40. Shao, Z.-. GenBan https://identiers.org/ncbi/insdc.gca:GCA_048013815.1 (2025).
41. Shao, Z.-. GenBan https://identiers.org/ncbi/insdc:PV163833 (2025).
42. Shao, Z.-., Chen, L., Sun, J.-T. & Xue, X.-F. A chromosome-level genome assembly of eriophyoid mite Setoptus oraiensis. gshare
https://doi.org/10.6084/m9.gshare.28087958 (2025).
is research was funded by the National Natural Science Foundation of China (32170466). is work was also
supported by the high-performance computing platform of Bioinformatics Center, Nanjing Agricultural University.
Author contributions
Z.-K.S. and X.-F.X. conceived and designed the study. Z.-K.S. analyzed the data. X.-F.X., L.C. and J.-T.S. had
substantial contributions to the interpretation of the data, writing, and review of the nal manuscript.
Competing interests
e authors declare no competing interests.
Additional information
Correspondence and requests for materials should be addressed to X.-F.X.
Reprints and permissions information is available at www.nature.com/reprints.
Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and
institutional aliations.
Open Access is article is licensed under a Creative Commons Attribution-NonCommercial-
NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribu-
tion and reproduction in any medium or format, as long as you give appropriate credit to the original author(s)
and the source, provide a link to the Creative Commons licence, and indicate if you modied the licensed mate-
rial. You do not have permission under this licence to share adapted material derived from this article or parts of
it. e images or other third party material in this article are included in the article’s Creative Commons licence,
unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative
Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted
use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit
http://creativecommons.org/licenses/by-nc-nd/4.0/.
© e Author(s) 2025
Content courtesy of Springer Nature, terms of use apply. Rights reserved
1.
2.
3.
4.
5.
6.
Terms and Conditions
Springer Nature journal content, brought to you courtesy of Springer Nature Customer Service Center GmbH (“Springer Nature”).
Springer Nature supports a reasonable amount of sharing of research papers by authors, subscribers and authorised users (“Users”), for small-
scale personal, non-commercial use provided that all copyright, trade and service marks and other proprietary notices are maintained. By
accessing, sharing, receiving or otherwise using the Springer Nature journal content you agree to these terms of use (“Terms”). For these
purposes, Springer Nature considers academic use (by researchers and students) to be non-commercial.
These Terms are supplementary and will apply in addition to any applicable website terms and conditions, a relevant site licence or a personal
subscription. These Terms will prevail over any conflict or ambiguity with regards to the relevant terms, a site licence or a personal subscription
(to the extent of the conflict or ambiguity only). For Creative Commons-licensed articles, the terms of the Creative Commons license used will
apply.
We collect and use personal data to provide access to the Springer Nature journal content. We may also use these personal data internally within
ResearchGate and Springer Nature and as agreed share it, in an anonymised way, for purposes of tracking, analysis and reporting. We will not
otherwise disclose your personal data outside the ResearchGate or the Springer Nature group of companies unless we have your permission as
detailed in the Privacy Policy.
While Users may use the Springer Nature journal content for small scale, personal non-commercial use, it is important to note that Users may
not:
use such content for the purpose of providing other users with access on a regular or large scale basis or as a means to circumvent access
control;
use such content where to do so would be considered a criminal or statutory offence in any jurisdiction, or gives rise to civil liability, or is
otherwise unlawful;
falsely or misleadingly imply or suggest endorsement, approval , sponsorship, or association unless explicitly agreed to by Springer Nature in
writing;
use bots or other automated methods to access the content or redirect messages
override any security feature or exclusionary protocol; or
share the content in order to create substitute for Springer Nature products or services or a systematic database of Springer Nature journal
content.
In line with the restriction against commercial use, Springer Nature does not permit the creation of a product or service that creates revenue,
royalties, rent or income from our content or its inclusion as part of a paid for service or for other commercial gain. Springer Nature journal
content cannot be used for inter-library loans and librarians may not upload Springer Nature journal content on a large scale into their, or any
other, institutional repository.
These terms of use are reviewed regularly and may be amended at any time. Springer Nature is not obligated to publish any information or
content on this website and may remove it or features or functionality at our sole discretion, at any time with or without notice. Springer Nature
may revoke this licence to you at any time and remove access to any copies of the Springer Nature journal content which have been saved.
To the fullest extent permitted by law, Springer Nature makes no warranties, representations or guarantees to Users, either express or implied
with respect to the Springer nature journal content and all parties disclaim and waive any implied warranties or warranties imposed by law,
including merchantability or fitness for any particular purpose.
Please note that these rights do not automatically extend to content, data or other material published by Springer Nature that may be licensed
from third parties.
If you would like to use or distribute our Springer Nature journal content to a wider audience or on a regular basis or in any other manner not
expressly permitted by these Terms, please contact Springer Nature at
onlineservice@springernature.com
Content uploaded by Xiao-Feng Xue
Author content
All content in this area was uploaded by Xiao-Feng Xue on Mar 18, 2025
Content may be subject to copyright.
