The first telomere-to-telomere genome assembly of the soybean male-sterile germplasm 88-428BY by massive parallel sequencing

doi:10.1016/j.pld.2026.04.006

Plant Diversity ›› 2026, Vol. 48 ›› Issue (04): 836-845.DOI: 10.1016/j.pld.2026.04.006

• Short communication • Previous Articles Next Articles

The first telomere-to-telomere genome assembly of the soybean male-sterile germplasm 88-428BY by massive parallel sequencing

Yuhua Yang, Zhiyuan Bai, Yan Chen, Mengen Nie, Haigang Wang, Haiping Zhang, Ruijun Zhang, Zhixin Mu

Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Taiyuan 030031, China

Received:2026-01-04 Revised:2026-04-06 Accepted:2026-04-13 Online:2026-04-28 Published:2026-07-25
Contact: Haiping Zhang,E-mail:nkyzhp@126.com;Ruijun Zhang,E-mail:zrj013835@126.com;Zhixin Mu,E-mail:muzx2008@sina.com
Supported by:
This work was supported by Major Science and Technology Special Program of Shanxi Province (No.202201140601025), the Natural Science Foundation of Shanxi Province (No.202303021211085), the China Postdoctoral Science Foundation and Shanxi Agricultural University Outstanding Doctoral Startup Project (2023BQ95). We thank Baoguo Wei for his kind provision of the 88-428BY.

The first telomere-to-telomere genome assembly of the soybean male-sterile germplasm 88-428BY by massive parallel sequencing

Yuhua Yang, Zhiyuan Bai, Yan Chen, Mengen Nie, Haigang Wang, Haiping Zhang, Ruijun Zhang, Zhixin Mu

Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Taiyuan 030031, China

通讯作者: Haiping Zhang,E-mail:nkyzhp@126.com;Ruijun Zhang,E-mail:zrj013835@126.com;Zhixin Mu,E-mail:muzx2008@sina.com
基金资助:
This work was supported by Major Science and Technology Special Program of Shanxi Province (No.202201140601025), the Natural Science Foundation of Shanxi Province (No.202303021211085), the China Postdoctoral Science Foundation and Shanxi Agricultural University Outstanding Doctoral Startup Project (2023BQ95). We thank Baoguo Wei for his kind provision of the 88-428BY.

Abstract

Abstract: Soybean (Glycine max) is a key source of plant protein and oil, yet genomic resources for male-sterile germplasms remain scarce. This study addresses this gap by presenting the first telomere-to-telomere (T2T) genome assembly of the landrace soybean 88-428BY, a Chinese photoperiod-sensitive genic male sterility (PGMS) germplasm with photoperiod-dependent fertility. Using a hybrid strategy combining PacBio HiFi, Oxford Nanopore ultra-long reads, and Hi-C scaffolding, we generated a high-quality reference genome of 1.01 Gb (N50 = 52.05 Mb), achieving 99.88% BUSCO completeness and assembling telomeres at both ends of 80% of the chromosomes. Annotation revealed 55,292 protein-coding genes and a high repetitive content (63.03%), which was dominated by LTR retrotransposons. Comparative genomics identified 35,236 structural variations (SVs), with hotspot regions harboring genes showing suppressed expression. Transcriptomic analysis under long-day and short-day conditions uncovered co-expression modules enriched in flavonoid biosynthesis and protease inhibitors, alongside key transcription factors (e.g., NAC25, ERF113) potentially associated with fertility regulation. This T2T genome provides a critical resource for elucidating the molecular basis of photoperiod-sensitive male sterility and advancing functional genomics and molecular breeding in soybean.

Key words: Glycine max, 88-428BY, Telomere-to-telomere, Structure variations, Photoperiod treatment

摘要： Soybean (Glycine max) is a key source of plant protein and oil, yet genomic resources for male-sterile germplasms remain scarce. This study addresses this gap by presenting the first telomere-to-telomere (T2T) genome assembly of the landrace soybean 88-428BY, a Chinese photoperiod-sensitive genic male sterility (PGMS) germplasm with photoperiod-dependent fertility. Using a hybrid strategy combining PacBio HiFi, Oxford Nanopore ultra-long reads, and Hi-C scaffolding, we generated a high-quality reference genome of 1.01 Gb (N50 = 52.05 Mb), achieving 99.88% BUSCO completeness and assembling telomeres at both ends of 80% of the chromosomes. Annotation revealed 55,292 protein-coding genes and a high repetitive content (63.03%), which was dominated by LTR retrotransposons. Comparative genomics identified 35,236 structural variations (SVs), with hotspot regions harboring genes showing suppressed expression. Transcriptomic analysis under long-day and short-day conditions uncovered co-expression modules enriched in flavonoid biosynthesis and protease inhibitors, alongside key transcription factors (e.g., NAC25, ERF113) potentially associated with fertility regulation. This T2T genome provides a critical resource for elucidating the molecular basis of photoperiod-sensitive male sterility and advancing functional genomics and molecular breeding in soybean.

关键词: Glycine max, 88-428BY, Telomere-to-telomere, Structure variations, Photoperiod treatment

Yuhua Yang, Zhiyuan Bai, Yan Chen, Mengen Nie, Haigang Wang, Haiping Zhang, Ruijun Zhang, Zhixin Mu. The first telomere-to-telomere genome assembly of the soybean male-sterile germplasm 88-428BY by massive parallel sequencing[J]. Plant Diversity, 2026, 48(04): 836-845.

References

[1] Alonge, M., Wang, X., Benoit, M., et al., 2020. Major impacts of widespread structural variation on gene expression and crop improvement in tomato. Cell, 182, 145-161.e123. https://doi.org/10.1016/j.cell.2020.05.021.
[2] Altschul, S. F., Gish, W., Miller, W., et al., 1990. Basic local alignment search tool. J. Mol. Biol., 215, 403-410. https://doi.org/10.1016/S0022-2836(05)80360-2.
[3] Anders, S., Pyl, P. T., Huber, W., 2015. HTSeq-a Python framework to work with high-throughput sequencing data. Bioinformatics, 31, 166-169. https://doi.org/10.1093/bioinformatics/btu638.
[4] Benson, G., 1999. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res., 27, 573-580. https://doi.org/10.1093/nar/27.2.573.
[5] Buchfink, B., Xie, C., Huson, D. H., 2015. Fast and sensitive protein alignment using DIAMOND. Nat. Methods, 12, 59-60. https://doi.org/10.1038/nmeth.3176.
[6] Chen, S., Zhou, Y., Chen, Y., et al., 2018. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics, 34, 884-890. https://doi.org/10.1093/bioinformatics/bty560.
[7] Cheng, H., Concepcion, G. T., Feng, X., et al., 2021. Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nat. Methods, 18, 170-175. https://doi.org/10.1038/s41592-020-01056-5.
[8] Chin, C.H., Chen, S.H., Wu, H.H., et al., 2014. cytoHubba: identifying hub objects and sub-networks from complex interactome. BMC Syst. Biol., 8, 11. https://doi.org/10.1186/1752-0509-8-S4-S11.
[9] De Coster, W., D'Hert, S., Schultz, D. T., et al., 2018. NanoPack: visualizing and processing long-read sequencing data. Bioinformatics, 34, 2666-2669. https://doi.org/10.1093/bioinformatics/bty149.
[10] Du, H., Fang, C., Li, Y., et al., 2023. Understandings and future challenges in soybean functional genomics and molecular breeding. J. Integr. Plant Biol., 65, 468-495. https://doi.org/10.1111/jipb.13433.
[11] Dudchenko, O., Batra, S., Omer, A., et al., 2017. De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science, 356, eaal3327. https://doi.org/10.1126/science.aal3327.
[12] Durand, N., Shamim, S., Machol, I., et al., 2016. Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments. Cell Syst., 3, 95-98. https://doi.org/10.1016/j.cels.2016.07.002.
[13] Durand, N. C., Robinson, J. T., Shamim, M. S., et al., 2016. Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom. Cell Syst., 3, 99-101. https://doi.org/10.1016/j.cels.2015.07.012.
[14] Fang, X., Sun, X., Yang, X., et al., 2021. MS1 is essential for male fertility by regulating the microsporocyte cell plate expansion in soybean. Sci. China Life Sci., 64, 1533-1545. https://doi.org/10.1007/s11427-021-1973-0.
[15] Gel, B., Serra, E., 2017. karyoploteR: an R/Bioconductor package to plot customizable genomes displaying arbitrary data. Bioinformatics, 33, 3088-3090. https://doi.org/10.1093/bioinformatics/btx346.
[16] Goel, M., Sun, H., Jiao, W.-B., et al., 2019. SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies. Genome Biol., 20, 277. https://doi.org/10.1186/s13059-019-1911-0.
[17] Grabherr, M. G., Haas, B. J., Yassour, M., et al., 2011. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol., 29, 644-652. https://doi.org/10.1038/nbt.1883.
[18] Haas, B. J., Salzberg, S. L., Zhu, W., et al., 2008. Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments. Genome Biol., 9, 7. https://doi.org/10.1186/gb-2008-9-1-r7.
[19] Hou, X., Wang, D., Cheng, Z., et al., 2022. A near-complete assembly of an Arabidopsis thaliana genome. Mol. Plant, 15, 1247-1250. https://doi.org/10.1016/j.molp.2022.05.014.
[20] Huang, Y., Koo, D.H., Mao, Y., et al., 2024. A complete reference genome for the soybean cv. Jack. Plant Commun., 5, 100765. https://doi.org/10.1016/j.xplc.2023.100765.
[21] Jeffares, D. C., Jolly, C., Hoti, M.,et al., 2017. Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast. Nat. Commun., 8, 14061. https://doi.org/10.1038/ncomms14061.
[22] Jia, K.H., Zhang, X., Li, L.L., et al., 2024. Telomere-to-telomere genome assemblies of cultivated and wild soybean provide insights into evolution and domestication under structural variation. Plant Commun., 5, 100919. https://doi.org/10.1016/j.xplc.2024.100919.
[23] Jin, J., Tian, F., Yang, D. C., et al., 2017. PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants. Nucleic Acids Res., 45, 1040-1045. https://doi.org/10.1093/nar/gkw982.
[24] Keilwagen, J., Hartung, F., Grau, J., 2019. GeMoMa: Homology-Based Gene Prediction Utilizing Intron Position Conservation and RNA-seq Data. In M. Kollmar (Ed.), Methods Mol. Biol., 1964, 161-177. Springer New York. https://doi.org/10.1007/978-1-4939-9173-0_9.
[25] Khan, A. H., Min, L., Ma, Y., et al., 2023. High-temperature stress in crops: male sterility, yield loss and potential remedy approaches. Plant Biotechnol. J., 21, 680-697. https://doi.org/10.1111/pbi.13946.
[26] Kim, D., Langmead, B., Salzberg, S. L., 2015. HISAT: a fast spliced aligner with low memory requirements. Nat. Methods, 12, 357-360. https://doi.org/10.1038/nmeth.3317.
[27] Kovaka, S., Zimin, A. V., Pertea, G. M., et al., 2019. Transcriptome assembly from long-read RNA-seq alignments with StringTie2. Genome Biol., 20, 278. https://doi.org/10.1186/s13059-019-1910-1.
[28] Langfelder, P., Horvath, S., 2008. WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics, 9, 559. https://doi.org/10.1186/1471-2105-9-559.
[29] Li, H., 2018. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics, 34, 3094-3100. https://doi.org/10.1093/bioinformatics/bty191.
[30] Li, M., Chen, C., Wang, H., et al., 2024. Telomere-to-telomere genome assembly of sorghum. Sci. Data, 11, 835. https://doi.org/10.1038/s41597-024-03664-8.
[31] Lian, Y., Wu, Y., Li, C., et al., 2025. A telomere-to-telomere genome of wild soybean with resistance to soybean cyst nematode X12. Sci. Data, 12, 1412. https://doi.org/10.1038/s41597-025-05741-y.
[32] Liang, S., Duan, Z., He, X., et al., 2024. Natural variation in GmSW17 controls seed size in soybean. Nat. Commun., 15, 7417. https://doi.org/10.1038/s41467-024-51798-5.
[33] Lin, Y., Ye, C., Li, X., et al., 2023. quarTeT: a telomere-to-telomere toolkit for gap-free genome assembly and centromeric repeat identification. Hortic. Res., 10, uhad127. https://doi.org/10.1093/hr/uhad127.
[34] Livak, K.J., Schmittgen, T.D., 2001. Analysis of relative gene expression data using real-time quantitative PCR and the 2-ΔΔCT method. Methods 25, 402-408. doi:10.1006/meth.2001.1262.
[35] Love, M. I., Huber, W., Anders, S., 2014. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol., 15, 550. https://doi.org/10.1186/s13059-014-0550-8.
[36] Lowe, T. M., Eddy, S. R., 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res., 25, 955-964. https://doi.org/10.1093/nar/25.5.955.
[37] Ma, Z., Hu, L., Jiang, W., 2024. Understanding AP2/ERF Transcription Factor Responses and Tolerance to Various Abiotic Stresses in Plants: A Comprehensive Review. Int. J. Mol. Sci., 25, 893. https://doi.org/10.3390/ijms25020893.
[38] Marcais, G., Delcher, A. L., Phillippy, A. M., et al., 2018. MUMmer4: A fast and versatile genome alignment system. PLoS Comput. Biol., 14, e1005944. https://doi.org/10.1371/journal.pcbi.1005944.
[39] Nagayama, T., Yamatani, H., Yamaguchi, N., Igarashi, H., Tsuda, M., Kato, S., Takahashi, K., & Kaga, A. (2025). Alternative splice acceptor site in MSH4 gene is responsible for male sterility conferred by ms5 in soybean. Plant J, 122(3), e70192. https://doi.org/10.1111/tpj.70192.
[40] Nawrocki, E. P., Eddy, S. R., 2013. Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics, 29, 2933-2935. https://doi.org/10.1093/bioinformatics/btt509.
[41] Quinlan, A. R., Hall, I. M., 2010. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics, 26, 841-842. https://doi.org/10.1093/bioinformatics/btq033.
[42] Rhie, A., Walenz, B. P., Koren, S., et al., 2020. Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies. Genome Biol., 21, 245. https://doi.org/10.1186/s13059-020-02134-9.
[43] Roberts, A., Trapnell, C., Donaghey, J., et al., 2011. Improving RNA-Seq expression estimates by correcting for fragment bias. Genome Biol., 12, 22. https://doi.org/10.1186/gb-2011-12-3-r22.
[44] Schmutz, J., Cannon, S. B., Schlueter, J., et al., 2010. Genome sequence of the palaeopolyploid soybean. Nature, 463, 178-183. https://doi.org/10.1038/nature08670.
[45] Sharmin, R. A., Bhuiyan, M. R., Lv, W., Yu, Z., Chang, F., Kong, J., Bhat, J. A., Zhao, T., 2020. RNA-Seq based transcriptomic analysis revealed genes associated with seed-flooding tolerance in wild soybean (Glycine soja Sieb. & Zucc.). Environmental and Experimental Botany 171, 103906.
[46] Shen, Y., Liu, J., Geng, H., et al., 2018. De novo assembly of a Chinese soybean genome. Sci. China Life Sci., 61, 871-884. https://doi.org/10.1007/s11427-018-9360-0.
[47] Sheng, Y., Huang, Y., Jin, Z., et al., 2025. Assembly of a high-quality reference genome and characterization of a chemical-mutagenized library of an elite soybean cultivar Tianlong 1. J. Genet. Genomics., 53,458-466. https://doi.org/10.1016/j.jgg.2025.08.006.
[48] Stanke, M., Morgenstern, B., 2005. AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints. Nucleic Acids Res., 33, 465-467. https://doi.org/10.1093/nar/gki458.
[49] Sun, J., Zhang, X., Feng, J., et al., 2025. The transcription factor GmFULc regulates soybean plant height by binding the promoter of a gibberellin-responsive gene. Plant Physiol., 197, 1530-1547. https://doi.org/10.1093/plphys/kiaf021.
[50] Van Durme, M., Olvera-Carrillo, Y., Pfeiffer, et al., 2023. Fertility loss in senescing Arabidopsis ovules is controlled by the maternal sporophyte via a NAC transcription factor triad. Proc. Natl. Acad. Sci. U. S. A., 120, e2219868120. https://doi.org/10.1073/pnas.2219868120.
[51] Vaser, R., Sovic, I., Nagarajan, N., et al., 2017. Fast and accurate de novo genome assembly from long uncorrected reads. Genome Res., 27, gr.214270.214116. https://doi.org/10.1101/gr.214270.116.
[52] Vasupalli, N., Mogilicherla, K., Shaik, V.,et al., 2025. Advances in plant male sterility for hybrid seed production: an overview of conditional nuclear male sterile lines and biotechnology-based male sterile systems. Front. Plant Sci., 16, 1540693. https://doi.org/10.3389/fpls.2025.1540693.
[53] Wang, L., Zhang, M., Li, M., et al., 2023. A telomere-to-telomere gap-free assembly of soybean genome. Mol. Plant, 16, 1711-1714. https://doi.org/10.1016/j.molp.2023.08.012.
[54] Wang, Y., Hao, X., Chen, C., et al., 2025. Telomere-to-telomere genome of common bean (Phaseolus vulgaris L., YP4). GigaScience, 14, giaf001. https://doi.org/10.1093/gigascience/giaf001.
[55] Waterhouse, R. M., Seppey, M., Simao, F. A., et al., 2018. BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics. Mol. Biol. Evol., 35, 543-548. https://doi.org/10.1093/molbev/msx319.
[56] Wei, B.,1991. Preliminary study on the discovery of photoperiod sensitive male sterile line in soybean. Crop Var. Resour.(Chinese), 3, 14-15.zh.
[57] Wu, T., Hu, E., Xu, S., et al., 2021. clusterProfiler 4.0: A universal enrichment tool for interpreting omics data. Innovation, 2, 100141. https://doi.org/10.1016/j.xinn.2021.100141.
[58] Xie, C., Mao, X., Huang, J., et al., 2011. KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases. Nucleic Acids Res., 39, 316-322. https://doi.org/10.1093/nar/gkr483.
[59] Xie, E., Chen, J., Wang, B., et al., 2023. The transcribed centromeric gene OsMRPL15 is essential for pollen development in rice. Plant Physiol., 192, 1063-1079. https://doi.org/10.1093/plphys/kiad153.
[60] Xie, L., Gong, X., Yang, K., et al., 2024. Technology-enabled great leap in deciphering plant genomes. Nat. Plants, 10, 551-566. https://doi.org/10.1038/s41477-024-01655-6.
[61] Xie, M., Chung, Y.L., Li, M.W., et al., 2019. A reference-grade wild soybean genome. Nat. Commun., 10, 1216. https://doi.org/10.1038/s41467-019-09142-9.
[62] Xu, G.C., Xu, T.J., Zhu, R., et al., 2018. LR_Gapcloser: a tiling path-based gap closer that uses long reads to complete genome assembly. GigaScience, 8, giy157. https://doi.org/10.1093/gigascience/giy157.
[63] Xu, Z., Wang, H., 2007. LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons. Nucleic Acids Res., 35, 265-268. https://doi.org/10.1093/nar/gkm286.
[64] Yang, Y., He, S., Xu, L., et al., 2025. Transcriptome and WGCNA reveals the potential genetic basis of photoperiod-sensitive male sterility in soybean. BMC Genomics, 26, 131. https://doi.org/10.1186/s12864-025-11314-5.
[65] Yuan, X., Xu, J., Yu, J., et al., 2023. The NAC transcription factor ZmNAC132 regulates leaf senescence and male fertility in maize. Plant Sci., 334, 111774. https://doi.org/10.1016/j.plantsci.2023.111774.
[66] Zhang, C., Li, W., Tan, C., et al., 2025. Natural allelic variation in SW14 determines seed weight and quality in soybean. Nat. Commun., 16, 8070. https://doi.org/10.1038/s41467-025-63582-0.
[67] Zhang, C., Shao, Z., Kong, Y., et al., 2024. High-quality genome of a modern soybean cultivar and resequencing of 547 accessions provide insights into the role of structural variation. Nat. Genet., 56, 2247-2258. https://doi.org/10.1038/s41588-024-01901-9.
[68] Zhang, C., Xie, L., Yu, H., et al., 2023. The T2T genome assembly of soybean cultivar ZH13 and its epigenetic landscapes. Mol. Plant, 16, 1715-1718. https://doi.org/10.1016/j.molp.2023.10.003.
[69] Zhang, M., Liu, S., Wang, Z., et al., 2022. Progress in soybean functional genomics over the past decade. Plant Biotechnol. J., 20, 256-282. https://doi.org/10.1111/pbi.13682.
[70] Zhang, Y., Zhao, M., Tan, J., et al., 2024. Telomere-to-telomere Citrullus super-pangenome provides direction for watermelon breeding. Nat. Genet., 56, 1750-1761. https://doi.org/10.1038/s41588-024-01823-6.
[71] Zhao, Q., Tong, Y., Yang, C., et al., 2019. Identification and mapping of a new soybean male-sterile gene, mst-M. Front. Plant Sci., 10, 94. https://doi.org/10.3389/fpls.2019.00094.

The first telomere-to-telomere genome assembly of the soybean male-sterile germplasm 88-428BY by massive parallel sequencing

The first telomere-to-telomere genome assembly of the soybean male-sterile germplasm 88-428BY by massive parallel sequencing

PDF (PC)

Knowledge

Abstract

Cite this article

share this article

References

Related Articles 2

Recommended Articles

Metrics

Comments

[1]	Yongjian Luo, Ru Wang, Daoshou Qiu. Chromosome-level genome assembly of Tadehagi triquetrum provides new insights into genome evolution and biosynthesis of tadehaginoside [J]. Plant Diversity, 2026, 48(04): 846-850.
[2]	Zhidong Li, Shenghao Wang, Shuling Wang, Chong Wang, Hongbin Zhang, Fei Chen, Wenquan Wang. Tamarindus indica telomere-to-telomere genome reveals tartaric acid accumulation in fruit [J]. Plant Diversity, 2026, 48(02): 429-432.