Abstract
Termites belong to the infraorder Isoptera within the order Blattodea. Reticulitermes chinensis Snyder, a species in the Rhinotermitidae family, remains a major pest causing severe damage to wooden structures in buildings. Here, the chromosome-level genome of R. chinensis was assembled using PacBio and Hi-C technologies. The final genome comprises 21 pseudochromosomes, with a total size of 1.02 Gb. The scaffold N50 is 47.29 Mb, the GC content is 29.46%, and 94% of sequences were anchored to pseudochromosomes. The BUSCO completeness score is 97.6%. The genome contains 23,733 predicted protein-coding genes, and 48.74% of it consists of repetitive sequences. This high-quality genome is conducive to understanding unique termite traits such as social behavior, efficient lignocellulose digestion, and evolutionary adaptations.
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Data availability
The dataset has been deposited to National Genomics Data Center as a BioProject under accession number PRJNA1335780. The final Genome assembly data of the termite Reticulitermes chinensis Snyder is available in the GenBank under the accession number JBRIKC000000000.1. The raw reads generated from three platform specific sequencing runs have been deposited in the NCBI Sequence Read Archive (SRA, accession numbers: SRR35653615 - SRR35653619).
Code availability
No custom code was developed for this study. All analyses used publicly available bioinformatics tools, with software versions and parameters detailed in the Methods section to ensure reproducibility.
References
Govorushko, S. Economic and ecological importance of termites: A global review. Entomological Science 22, 21–35 (2019).
Lo, N. et al. Evidence from multiple gene sequences indicates that termites evolved from wood-feeding cockroaches. Current Biology 10, 801–804 (2000).
Khan, Z. et al. A comprehensive review on the documented characteristics of four Reticulitermes termites (Rhinotermitidae, Blattodea) of China. Brazilian Journal of Biology 84, e256354 (2022).
Shigenobu, S. et al. Genomic and transcriptomic analyses of the subterranean termite Reticulitermes speratus: Gene duplication facilitates social evolution. Proceedings of the National Academy of Sciences 119, e2110361119 (2022).
Martelossi, J. et al. Wood feeding and social living: Draft genome of the subterranean termite Reticulitermes lucifugus (Blattodea; Termitoidae). Insect Molecular Biology 32, 118–131 (2023).
Konishi, T., Tasaki, E., Takata, M. & Matsuura, K. King-and queen-specific degradation of uric acid contributes to reproduction in termites. Proceedings of the Royal Society B 290, 20221942 (2023).
Peñafiel, N., Flores, D. M., Rivero De Aguilar, J., Guayasamin, J. M. & Bonaccorso, E. A cost-effective protocol for total DNA isolation from animal tissue. Neotropical Biodiversity 5, 69–74 (2019).
Chen, S., Zhou, Y., Chen, Y. & Gu, J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34, i884–i890 (2018).
Marçais, G. & Kingsford, C. A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics 27, 764–770 (2011).
Ranallo-Benavidez, T. R., Jaron, K. S. & Schatz, M. C. GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes. Nature communications 11, 1432 (2020).
Cheng, H., Concepcion, G. T., Feng, X., Zhang, H. & Li, H. Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nature methods 18, 170–175 (2021).
Guan, D. et al. Identifying and removing haplotypic duplication in primary genome assemblies. Bioinformatics 36, 2896–2898 (2020).
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows–Wheeler transform. bioinformatics 25, 1754–1760 (2009).
Zhou, C., McCarthy, S. A. & Durbin, R. YaHS: yet another Hi-C scaffolding tool. Bioinformatics 39, btac808 (2023).
Durand, N. C. et al. Juicebox provides a visualization system for Hi-C contact maps with unlimited zoom. Cell systems 3, 99–101 (2016).
Martins, V.G. Karyotype evolution in the Termitidae (Isoptera). (1999).
Jankásek, M. & Varadínová, Z. K. Blattodea karyotype database. European Journal of Entomology 118, 192–199 (2021).
Manni, M., Berkeley, M. R., Seppey, M., Simão, F. A. & Zdobnov, E. M. BUSCO update: novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes. Molecular biology and evolution 38, 4647–4654 (2021).
Sawada, Y. et al. Unsupervised AI reveals insect species-specific genome signatures. PeerJ 12, e17025 (2024).
Kiełbasa, S. M., Wan, R., Sato, K., Horton, P. & Frith, M. C. Adaptive seeds tame genomic sequence comparison. Genome research 21, 487–493 (2011).
Krzywinski, M. et al. Circos: an information aesthetic for comparative genomics. Genome research 19, 1639–1645 (2009).
Benson, G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic acids research 27, 573–580 (1999).
Flynn, J. M. et al. RepeatModeler2 for automated genomic discovery of transposable element families. Proceedings of the National Academy of Sciences 117, 9451–9457 (2020).
Xu, Z. & Wang, H. LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons. Nucleic acids research 35, W265–W268 (2007).
Bedell, J. A., Korf, I. & Gish, W. MaskerAid: a performance enhancement to RepeatMasker. Bioinformatics 16, 1040–1041 (2000).
Bao, W., Kojima, K. K. & Kohany, O. Repbase Update, a database of repetitive elements in eukaryotic genomes. Mobile Dna 6, 11 (2015).
Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842 (2010).
Hoff, K. J. & Stanke, M. Predicting genes in single genomes with AUGUSTUS. Current protocols in bioinformatics 65, e57 (2019).
Hellemans, S. et al. Genomic data provide insights into the classification of extant termites. Nature Communications 15, 6724 (2024).
Misof, B. et al. Phylogenomics resolves the timing and pattern of insect evolution. Science 346, 763–767 (2014).
Fouks, B. et al. Live-bearing cockroach genome reveals convergent evolutionary mechanisms linked to viviparity in insects and beyond. Iscience 26 (2023).
Terrapon, N. et al. Molecular traces of alternative social organization in a termite genome. Nature communications 5, 3636 (2014).
Fraser, R. et al. Evidence for a novel X chromosome in termites. Genome Biology and Evolution 16, evae265 (2024).
Kent, W. J. BLAT—the BLAST-like alignment tool. Genome research 12, 656–664 (2002).
Birney, E., Clamp, M. & Durbin, R. GeneWise and genomewise. Genome research 14, 988–995 (2004).
Haas, B. J. et al. Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments. Genome biology 9, R7 (2008).
Ashburner, M. et al. Gene ontology: tool for the unification of biology. Nature genetics 25, 25–29 (2000).
Aleksander, S. A. et al. The gene ontology knowledgebase in 2023. Genetics 224, iyad031 (2023).
Bairoch, A. & Apweiler, R. The SWISS-PROT protein sequence data bank and its supplement TrEMBL. Nucleic acids research 25, 31–36 (1997).
Bairoch, A. & Apweiler, R. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic acids research 28, 45–48 (2000).
Sayers, E. W. et al. Database resources of the National Center for Biotechnology Information in 2023. Nucleic acids research 51, D29 (2022).
Kanehisa, M. & Goto, S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic acids research 28, 27–30 (2000).
Kanehisa, M., Furumichi, M., Sato, Y., Ishiguro-Watanabe, M. & Tanabe, M. KEGG: integrating viruses and cellular organisms. Nucleic acids research 49, D545–D551 (2021).
Blum, M. et al. The InterPro protein families and domains database: 20 years on. Nucleic acids research 49, D344–D354 (2021).
Jones, P. et al. InterProScan 5: genome-scale protein function classification. Bioinformatics 30, 1236–1240 (2014).
NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP629289 (2025).
Xin, P. Reticulitermes chinensis isolate PX-2025, whole genome shotgun sequencing project. GenBank https://identifiers.org/ncbi/insdc:JBRIKC000000000 (2025).
NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRR35653617 (2025).
NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRR35653619 (2025).
NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRR35653618 (2025).
NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRR35653616 (2025).
NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRR35653615 (2025).
Acknowledgements
This work was supported by the General Program of Shaanxi Natural Science Foundation [2025JC-YBMS-247], the Fundamental Research Funds for the Central Universities, Northwestern Polytechnical University [D5000220464], the Scientific and Technological Plan Project of Xi’an Science and Technology Bureau [24GXFW0080], and the Initiation Funds for High level Talents Program of Xi’an International University [XAIU202402].
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Jia Wu, Zhiyong Yue, Chenguang Feng, and Jihu Sun contributed to the research design. Jinpei Wang, Qi Jiang, Baozhen Zhou, and Jia Wu collected the samples. Peidong Xin and Zhiyong Yue analyzed the data. Peidong Xin and Chenguang Feng contributed to data quality control. Zhiyong Yue, Peidong Xin, and Jia Wu wrote the draft manuscript and revised the manuscript. All co-authors contributed to this manuscript and approved it.
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Yue, Z., Xin, P., Wang, J. et al. Chromosome-level genome assembly and annotation of the termite Reticulitermes chinensis Snyder. Sci Data (2026). https://doi.org/10.1038/s41597-026-07026-4
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DOI: https://doi.org/10.1038/s41597-026-07026-4
