The first haplotype-resolved genome assembly of Prunus s.l. subgenus Laurocerasus (Prunus spinulosa)

doi:10.1016/j.pld.2025.09.007

Abstract

Abstract: Prunus spinulosa (2n = 4x = 32) is an evergreen species of significant medicinal usage and ecological value. However, the lacking of a high-quality genome of P. spinulosa has obstructed further exploration of its ecological study and phylogenetic relationship of Prunus. In this study, we present the first haplotype-resolved genome assembly of Prunus s.l. subgenus Laurocerasus, the tetraploid genome of P. spinulosa was phased into 32 pseudochromosomes with 4 haplotypes, the genome size of each haplotype ranged from 249.82 Mb to 259.69 Mb, and N50 fluctuated from 31.35 Mb to 33.25 Mb, the protein-coding genes vary from 21,272 to 22,668. Different evaluation methods showed that the P. spinulosa genome assembly has high quality of completeness, continuity and accuracy. Being the first complete genome of P. spinulosa, it provides a valuable genetic resource for the Prunus tetraploid species database and supports further functional genomic study of this species.

Key words: Haplotype-resolved genome, Phylogenomics, Prunus, Subgenus Laurocerasus, Rosaceae, Tetraploidy

摘要： Prunus spinulosa (2n = 4x = 32) is an evergreen species of significant medicinal usage and ecological value. However, the lacking of a high-quality genome of P. spinulosa has obstructed further exploration of its ecological study and phylogenetic relationship of Prunus. In this study, we present the first haplotype-resolved genome assembly of Prunus s.l. subgenus Laurocerasus, the tetraploid genome of P. spinulosa was phased into 32 pseudochromosomes with 4 haplotypes, the genome size of each haplotype ranged from 249.82 Mb to 259.69 Mb, and N50 fluctuated from 31.35 Mb to 33.25 Mb, the protein-coding genes vary from 21,272 to 22,668. Different evaluation methods showed that the P. spinulosa genome assembly has high quality of completeness, continuity and accuracy. Being the first complete genome of P. spinulosa, it provides a valuable genetic resource for the Prunus tetraploid species database and supports further functional genomic study of this species.

关键词: Haplotype-resolved genome, Phylogenomics, Prunus, Subgenus Laurocerasus, Rosaceae, Tetraploidy

Sining Zhang, Jun Chen, Pan Li. The first haplotype-resolved genome assembly of Prunus s.l. subgenus Laurocerasus (Prunus spinulosa)[J]. Plant Diversity, 2025, 47(06): 991-994.

References

Alonge, M., Lebeigle, L., Kirsche, M., et al., 2022. Automated assembly scaffolding elevates a new tomato system for high-throughput genome editing. Genome Biol. 23, 258. https://doi.org/10.1186/s13059-022-02823-7.
Borowiec, M.L., 2016. AMAS: a fast tool for alignment manipulation and computing of summary statistics. PeerJ 4, e1660. https://doi.org/doi:10.7717/peerj.1660.
Capella-Gutierrez, S., Silla-Martinez, J., Gabaldon, T., 2009. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25, 1972-1973. https://doi.org/10.1093/bioinformatics/btp348.
Chen, S., Zhou, Y., Chen, Y., et al., 2018. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34, i884-i890. https://doi.org/10.1093/bioinformatics/bty560.
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.
Chin, S.W., Shaw, J., Haberle, R., et al., 2014. Diversification of almonds, peaches, plums and cherries - molecular systematics and biogeographic history of Prunus (Rosaceae). Mol. Phylogenet. Evol. 76, 34-38. https://doi.org/10.1016/j.ympev.2014.02.024.
Deng, J., Liu, C., Yang, H., et al., 2024. Floristic geographical components and distribution characteristic of species in subgen. Laurocerasus (Prunus Linn.) in China. J. Plant Resour. Environ. 33, 11-21. https://doi.org/10.3969/j.issn.1674-7895.2024.06.02.
Durand, N.C., Robinson, J.T., Shamin, 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.
Emms, D.M., Kelly, S., 2019. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol. 20, 238. https://doi.org/10.1186/s13059-019-1832-y.
Flynn, J.M., Robert, H., Clement, G., et al., 2020. RepeatModeler2 for automated genomic discovery of transposable element families. Proc. Natl. Acad. Sci. U.S.A. 117, 9451-9457. https://doi.org/10.1073/pnas.1921046117.
Govaerts, R., Nic-Lughadha, E., Black, N., et al., 2021. The World Checklist of Vascular Plants, a continuously updated resource for exploring global plant diversity. Sci. Data 8, 215. https://doi.org/10.1038/s41597-021-00997-6.
Grabherr, M., Brian, H., Moran, Y., 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.
Gurevich, A., Saveliev, V., Vyahhi, N., et al., 2013. QUAST: quality assessment tool for genome assemblies. Bioinformatics 29, 1072-1075. https://doi.org/10.1093/bioinformatics/btt086.
Haas, B.J., Delcher, A., Mount, S., et al., 2003. Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res. 31, 5654-5666. https://doi.org/10.1093/nar/gkg770.
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, 1-22. https://doi.org/10.1186/gb-2008-9-1-r7.
He, M., Yang, J., Jing, Y., et al., 2023. NGenomeSyn: an easy-to-use and flexible tool for publication-ready visualization of syntenic relationships across multiple genomes. Bioinformatics 39, btad121. https://doi.org/10.1093/bioinformatics/btad121.
Hodel, R., Zimmer, E., Wen, J., 2021. A phylogenomic approach resolves the backbone of Prunus (Rosaceae) and identifies signals of hybridization and allopolyploidy. Mol. Phylogenet. Evol. 160, 107118. https://doi.org/10.1016/j.ympev.2021.107118.
Hoff, K., Lange, S., Lomsadze, A., 2016. BRAKER1: unsupervised RNA-seq-based genome annotation with GeneMark-ET and AUGUSTUS. Bioinformatics 32, 767-769. https://doi.org/10.1093/bioinformatics/btv661.
James, M.P., Valerie, R.H., Crystal, B., et al., 2020. Measuring Genome Sizes Using Read-Depth, k-mers, and Flow Cytometry: Methodological Comparisons in Beetles (Coleoptera). G3: Genes, Genomes, Genet. 10, 3047-3060. https://doi.org/10.1534/g3.120.401028.
Jurka, J., 2000. Repbase Update: a database and an electronic journal of repetitive elements. Trends Genet. 9, 418-420. https://doi.org/10.1016/s0168-9525(00)02093-x.
Katoh, K., Misawa, K., Kuma, K., et al., 2002. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 30, 3059-3066. https://doi.org/10.1093/nar/gkf436.
Keilwagen, J., Hartung, F., Paulini, M., et al., 2018. Combining RNA-seq data and homology-based gene prediction for plants, animals and fungi. BMC Bioinformatics 19,189. https://doi.org/10.1186/s12859-018-2203-5.
Kim, D., Langmead, B., Salzberg, S., 2015. HISAT: a fast spliced aligner with low memory requirements. Nat. Methods 12, 357-360. https://doi.org/10.1038/nmeth.3317.
Li, H., 2013. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv preprint, 1303.3997. https://doi.org/10.48550/arXiv.1303.3997.
Li, H., Handsaker, B., Wysoker, A., et al., 2009. The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078-2079. https://doi.org/10.1093/bioinformatics/btp352.
Lin, S., Pu, F., Zhang, J., et al., 1991. Observations on the chromosome number of Prunus. China Fruits 2, 8-10. https://doi.org/10.16626/j.cnki.issn1000-8047.1991.02.005.
Lomsadze, A., Ter-Hovhannisyan, V., Chernoff, Y.O., et al., 2005. Gene identification in novel eukaryotic genomes by self-training algorithm. Nucleic Acids Res. 33, 6494-6506. https://doi.org/10.1093/nar/gki937.
Manni, M., Berkeley, M.R., Seppey, M., et al., 2021. BUSCO update: novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes. Mol. Biol. Evol. 38, 4647-4654. https://doi.org/10.1093/molbev/msab199.
Marcais, G., Kingsford, C., 2011. A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics 27, 764-770. https://doi.org/10.1093/bioinformatics/btr011.
Meurman, O., 1929. Prunus laurocerasus L., a species showing high polyploidy. J. Genet. 21, 85-94. https://doi.org/10.1007/BF02983360.
Nguyen, L.T., Schmidt, H., Haeseler, A., et al., 2015. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol. 32, 268-274. https://doi.org/10.1093/molbev/msu300.
Ou, S., Chen, J., Jiang, N., 2018. Assessing genome assembly quality using the LTR Assembly Index (LAI). Nucleic Acids Res. 46, e126. https://doi.org/10.1093/nar/gky730.
Potter, D., Eriksson, T., Evans, R., et al., 2007. Phylogeny and classification of Rosaceae. Plant Syst. Evol. 266, 5-43. https://doi.org/10.1007/s00606-007-0539-9.
Ranallo-Benavidez, T.R., Jaron, K.S., Schatz, M.C., 2020. GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes. Nat. Commun. 11, 1432. https://doi.org/10.1038/s41467-020-14998-3.
Rehder, A., 1927. Manual of cultivated trees and shrubs hardy in North America, second ed. Macmillan, New York.
Shulaev, V., Sargent, D., Crowhurst, R., et al., 2011. The genome of woodland strawberry (Fragaria vesca). Nat. Genet. 43, 109-116. https://doi.org/10.1038/ng.740.
Stanke, M., Steinkamp, R., Waack, S., et al. 2004. AUGUSTUS: a web server for gene finding in eukaryotes. Nucleic Acids Res. 32, W309-W312. https://doi.org/10.1093/nar/gkh379.
Su, N., Hodel, R., Wang, X., et al., 2023. Molecular phylogeny and inflorescence evolution of Prunus (Rosaceae) based on RAD-seq and genome skimming analyses. Plant Divers. 45, 397-408. https://doi.org/10.1016/j.pld.2023.03.013.
Tarailo-Graovac, M., Chen, N., 2009. Using RepeatMasker to identify repetitive elements in genomic sequences. Curr. Protoc. Bioinformatics 4, 4.10.11-14.10.14. https://doi.org/10.1002/0471250953.bi0410s25.
Vurture, G.W., Sedlazeck, F.J., Nattestad, M., et al., 2017. GenomeScope: fast reference-free genome profiling from short reads. Bioinformatics 33, 2202-2204. https://doi.org/10.1093/bioinformatics/btx153.
Zeng, X., Yi, Z., Zhang, X., et al., 2024. Chromosome-level scaffolding of haplotype-resolved assemblies using Hi-C data without reference genomes. Nat. Plants 10, 1184-1200. https://doi.org/10.1038/s41477-024-01755-3.
Zhang, H., Zhang, Z., Yue, J., 1994. Summary of Chinese Materia Medical Resources, first ed. Science Press.
Zhao, L., Jiang, X., Zuo, Y., et al., 2016. Multiple events of allopolyploidy in the evolution of the racemose lineages in Prunus (Rosaceae) based on integrated evidence from nuclear and plastid data. PLoS One 11, e0157123. https://doi.org/10.1371/journal.pone.0157123.

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