Chromosome-level genome assembly of Phoebe chekiangensis, an endemic and endangered tree in east Asia.

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Learn more: PMC Disclaimer | PMC Copyright Notice Sci Data . 2026 Apr 7;13:831. doi: 10.1038/s41597-026-07211-5 Chromosome-level genome assembly of Phoebe chekiangensis , an endemic and endangered tree in east Asia Ying-Feng Hu 1, ✉ , Ju Tang 1 , Xiao-Hong Li 1 , Zhi-Zhong Li 2 , Jian-Wen Shao 1, 3, ✉ Author information Article notes Copyright and License information 1 College of Life Sciences, Anhui Normal University, Wuhu, 241000 Anhui China 2 Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin, Anhui Normal University, Wuhu, 241002 China 3 The Anhui Provincial Key Laboratory of Biodiversity Conservation and Ecological Security in the Yangtze River Basin, Anhui Normal University, Wuhu, 241002 China ✉ Corresponding author. Received 2025 Sep 1; Accepted 2026 Apr 1; Collection date 2026. © The Author(s) 2026 Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution 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 modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. The 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/ . PMC Copyright notice PMCID: PMC13233860  PMID: 41946731 Abstract Phoebe chekiangensis is a rare nanmu species endemic to southeastern China that provides high-quality timber and has ecological and economic importance. Genomic resources for this genus are limited, constraining research on its genetic diversity, adaptive evolution, and conservation. Here we report a chromosome-level reference genome of P. chekiangensis generated using PacBio HiFi long reads, MGI short reads, and Hi-C sequencing. The assembled genome spans 918.59 Mb with a scaffold N50 of 68.99 Mb, and 98.88% of sequences were anchored to 12 pseudochromosomes. Repetitive elements account for 49.45% of the genome. A total of 34,381 protein-coding genes were predicted, of which 91.91% were functionally annotated. Genome quality was supported by a QV of 44.96 (99.99% base accuracy), a BUSCO completeness of 98.4%, and an LAI score of 14.32, meeting reference-quality standards. This high-quality genome provides a valuable resource for conservation genomics, evolutionary biology, and molecular breeding within Phoebe and the Lauraceae family. Subject terms: Plant genetics, Genetics Background & Summary The genus Phoebe (Lauraceae) comprises more than 55 recognized species, mainly distributed across tropical and subtropical regions of Asia 1 . Members of this genus produce hard, fine-textured, and aromatic timber that has long been valued for construction, furniture making, and artisanal carving 2 , 3 . In addition, volatile aromatic compounds and diverse secondary metabolites derived from Phoebe species have been reported to exhibit pharmacological activities, underscoring their economic and medicinal value 4 , 5 . Despite this importance, genomic studies of Phoebe remain scarce, with only the genome of P. bournei currently available 2 , 6 . The lack of genomic resources has limited both basic research and applied studies within this genus. Phoebe chekiangensis C. B. Shang is a rare species endemic to southeastern China and a key source of high-value nanmu timber. Historically, it was widely employed in the construction and furnishing of imperial palaces, while its distinctive morphology also makes it suitable for ornamental planting 7 , 8 . However, natural populations have declined sharply due to environmental change, human disturbance, and poor natural regeneration 9 , leading to its designation as a Grade II species in the List of National Key Protected Wild Plants in China and Vulnerable in the IUCN Red list of threatened species 10 , 11 . Previous studies have primarily focused on its physiology, ecology, and population dynamics, whereas conservation genetics efforts have largely relied on conventional molecular markers, including simple sequence repeats (SSRs), inter-simple sequence repeats (ISSRs), and chloroplast DNA fragments 10 , 12 , 13 . Although plastome 14 and transcriptome 15 data are available, the absence of a reference genome has hindered systematic investigations of its genetic diversity, adaptive evolution, and conservation management. Here, we present a chromosome-level reference genome of P. chekiangensis constructed using PacBio HiFi long reads, MGI short reads, and Hi-C sequencing. The assembled genome spans 918.58 Mb with a contig N50 of 10.38 Mb (Table 1 ). Hi-C scaffolding anchored 98.88% of sequences to 12 pseudochromosomes, yielding a scaffold N50 of 68.99 Mb (Figs. 1A , 2 ). This assembly shows markedly improved contiguity compared with the published P. bournei genome 2 (contig N50 = 5.64 Mb). Repetitive sequences account for 50.88% of the genome, with transposable elements comprising ~95.11% of the repeats (Table 1 ). A total of 34,381 protein-coding genes (PCGs) were predicted, of which 31,598 (91.91%) received functional annotations. This reference genome provides an essential resource for the conservation and sustainable utilization of P. chekiangensis and serves as a valuable foundation for evolutionary studies and molecular improvement within the genus Phoebe . Table 1. Summary of the Phoebe chekiangensis genome assembly and annotation. Genome assembly Total scaffold length (bp) 918,593,100 Number of chromosome-level scaffolds 12 Longest scaffold (bp) 141,852,477 N50 of scaffold (bp) 68,986,285 Total contig length (bp) 918,578,000 Number of contigs 166 N50 of contig (bp) 10,378,288 GC content (%) 40.05 BUSCO completeness (genome mode) (%) 98.40% LAI vaule 14.32 QV vaule 44.96 mapping rate(%) 98.07% Genome annotation Number of protein-coding genes 34,381 Repeats in genome (%) 49.45% TEs in genome (%) 47.81% Open in a new tab Fig. 1. Open in a new tab The circus map ( A ) and habitat ( B ) of Phoebe chekiangensis . The circles, from innermost to outermost, show track the syntenic regions within each pseudochromosomes (a), track the LTR- Copia density (b), track the LTR- Gypsy density (c), track the gene density (d), track the GC content (e), and track the length of pseudochromosomes (f), respectively. Fig. 2. Open in a new tab Hi-C heat map of the finally assembled genome of Phoebe chekiangensis . There were strong interactive signals within the 12 chromosomes around the diagonal based on the spatial positional relationship of chromatin DNA. The strength of the interaction was shown by different colors from white (low) to dark red (high). Methods Sample collection In 2024, a healthy and wild individual of P. chekiangensis was collected from the type locality at West Lake, Hangzhou, Zhejiang, China (30.19°N, 120.09°E) for genome sequencing (Fig. 1B ; Figure S1 ). Young leaves, mature leaves, stems, and fruits were sampled, immediately flash-frozen in liquid nitrogen, and transported on dry ice to Novogene Corporation (Tianjin, China) for sequencing. A voucher specimen was deposited in the Herbarium of Anhui Normal University (ANUB) under accession number ANUB100117 (Figure S2 ). Library construction and genome sequencing High-quality genomic DNA was extracted from frozen young leaves of P. chekiangensis using a modified CTAB method 16 , and DNA concentration and purity were assessed with a NanoDrop spectrophotometer. Three sequencing libraries were prepared. First, a short-read library with an insert size of 300–500 bp was constructed using the MGIEasy FS DNA Library Prep Set and sequenced on the DNBSEQ-T7 platform, yielding ~118.37 Gb of clean data (Table S1 ). Second, a PacBio HiFi library was generated by randomly shearing high-molecular-weight DNA into 15–18 kb fragments, followed by SMRTbell library preparation and Circular Consensus Sequencing (CCS) on the PacBio Revio platform, producing ~45.53 Gb of HiFi reads with an N50 of 18.36 kb (Table S1 ). Third, a Hi-C library was constructed using the restriction enzyme DpnIII (GATC). After crosslink reversal, DNA was fragmented into 300–700 bp, and interacting fragments were enriched and sequenced on the DNBSEQ-T7 platform (PE150), generating ~96.74 Gb of data for chromosome-scale scaffolding (Table S1 ). In addition, total RNA was extracted from flash-frozen tissues of young leaves, mature leaves, stems, and fruits using the Plant Total RNA Isolation Kit (Sangon Biotech Co., China) following the manufacturer’s protocol. RNA-seq libraries were prepared with the NEBNext Ultra™ RNA Library Prep Kit for Illumina (NEB) and sequenced on the Illumina NovaSeq. 6000 platform, generating ~48.96 Gb of paired-end (PE150) clean data in total (Table S2 ). Genome survey The genome size of P. chekiangensis was estimated using flow cytometry, with Zea mays (2.3 Gb) serving as the internal reference. Relative fluorescence intensity suggested that the genome size of P. chekiangensis was ~0.39 × that of maize (~0.90 Gb, Figure S3 ). In addition, ~118.37 Gb of short-read sequencing data were analyzed using Jellyfish v2.3.0 17 with k-mer = 19 to generate the k-mer frequency distribution, and genome characteristics were inferred with GCE v1.0.2 18 , yielding an estimated genome size of 907 Mb, a heterozygosity rate of 2.33%, and a repeat content of 52.19% (Figure S4 ). Ploidy analysis performed with Smudgeplot v0.4.0 19 indicated that P. chekiangensis is diploid, with the most frequent haplotype structure being ab (frequency = 0.82, Figure S5 ). Genome assembly A total of 45.53 Gb (~50.59 × coverage) of PacBio HiFi reads were assembled using Hifiasm v0.25.0-r726 20 with default parameters. Redundant and heterozygous regions were removed with Purge_Dups v1.2.6 21 , in which short reads were aligned to the assembly using BWA v0.7.17-r1188 22 to identify and eliminate duplicated sequences. Hi-C data were subsequently used to anchor the primary contigs onto 12 pseudochromosomes with HapHiC v1.0.7 23 under default settings, and potential assembly or scaffolding errors were manually corrected with Juicebox v2.20.0 24 (Fig. 2 ). Assembly quality was assessed with Merqury v1.3 25 to estimate the QV value, while BUSCO v6.0.0 26 and the LTR Assembly Index (LAI) were employed to evaluate genome completeness 27 . The final chromosome-level assembly of P. chekiangensis was 918.59 Mb in size with a GC content of 40.05%, comprising 12 pseudochromosome scaffolds and 20 unanchored scaffolds, and achieved a scaffold N50 of 68.99 Mb (Table 1 ). Gene prediction and functional annotation For genome annotation, repetitive elements were first identified using both homology-based and de novo approaches. In the homology-based analysis, RepeatMasker v4.1.9 ( http://www.repeatmasker.org ) with the Repbase database 28 was used to detect known repeats under default parameters. For the de novo prediction, RepeatModeler v2.0.1 29 was employed to generate a species-specific repeat library, which was subsequently used by RepeatMasker for genome-wide repeat annotation. Unclassified repeat elements were further classified using DeepTE with the plant model 30 . In total, ~454.33 Mb of repetitive sequences were identified (Table 2 ), representing 49.55% of the genome, including DNA transposons (17.82%), LTR retrotransposons (24.12%), LINEs (1.95%), rolling-circle elements (0.17%), unclassified repeats (4.26%), and other elements (2.49%). Table 2. Repeat annotation of the Phoebe chekiangensis genome. Type Number Length (bp) Percentage of the genome (%) DNA transposons 360,296 22,315,883 2.42% LTR 126,177 221,572,083 24.12% LINE 20,607 17,933,450 1.95% Rolling-circles 474 1,645,810 0.17% Unclassifed 107,019 39,203,031 4.26% Non-interspersed Repeats(Simple repeat, Low complexity and rRNA) 521,228 22,874,499 2.49% Open in a new tab We next annotated non-coding RNAs, including miRNAs, tRNAs, rRNAs, and snRNAs, across the genome. tRNAs were identified using tRNAscan-SE v1.3.1 31 , while rRNAs were predicted with RNAmmer v1.2 32 under default parameters. Other ncRNAs, including miRNAs and snRNAs, were annotated using Infernal v1.1.3 33 with recommended settings. In total, 201 miRNAs, 551 tRNAs, 3,229 rRNAs, and 750 snRNAs were identified in the P. chekiangensis genome (Table S3 ). For PCG annotation, we employed an integrative strategy combining ab initio prediction, homology-based annotation, and RNA-seq–assisted annotation. Ab initio and homology-based predictions were conducted using BRAKER v2.1.5 34 and GeMoMa v1.9 35 , respectively, with PCGs from Oryza sativa , Arabidopsis thaliana , Phoebe bournei , Cinnamomum camphora , Lindera megaphylla , and Chimonanthus salicifolius serving as homologous references 2 , 36 – 39 . For the RNA-seq–based approach, transcriptomic reads were aligned to the genome with HISAT v2.1.0 40 , and transcripts were assembled with TRINITY v2.4.0 41 in both genome-guided and de novo modes. The assembled transcripts were further processed with the PASA v2.4.1 pipeline 42 to predict gene structures. Results from the three approaches were integrated using EVM v1.1.1 43 , with weighting ratios of PASA:GeMoMa:BRAKER set at 10:5:1, and PASA was subsequently applied to refine the consensus models by adjusting exon–intron boundaries. The final annotation yielded 34,381 PCGs (Table 1 ) in the genome of P. chekiangensis , with mean gene models spanning 7,953.43 bp and containing an average of 4.68 coding sequences (CDSs). Functional annotation was performed by aligning the predicted protein sequences against six public databases (NR, KEGG, Swiss-Prot, InterPro, KOG, and eggNOG) using DIAMOND v4.0.515 44 with an E-value cutoff of 1E-05. In total, 31,598 PCGs (91.91%) were annotated in at least one database (Table 3 ). Table 3. Functional annotation of protein coding genes in Phoebe chekiangensis . Type Count % of all protein coding genes Annotation NR 30,234 87.94 Swiss-Prot 20,701 60.21 KOG 10,791 31.39 InterPro 29,197 84.92 eggNOG 28,624 83.26 KEGG 8711 25.34 Total Annotated 31,598 91.91 Protein coding genes 34,381 — Open in a new tab Comparative genomic analysis To further compare the assembly quality of P. chekiangensis with that of the previously reported P. bournei , we performed interspecific synteny analysis using JCVI v1.5.3 45 with default parameters. The results revealed a very high degree of collinearity between the two genomes, with 20,898 syntenic gene pairs identified (Fig. 3 ). Moreover, the syntenic depth exhibited a clear 1:1 relationship, indicating high assembly accuracy and strong genomic consistency between the two species (Figure S6 ). In addition, assembly quality of P. bournei was further assessed using BUSCO v6.0.0 46 in genome mode, which provided a reference for subsequent comparisons with the P. chekiangensis assembly. Fig. 3. Open in a new tab The BUSCO assessments of Phoebe chekiangensis ( A ) and synteny analysis result between P. chekiangensis and P. bournei ( B, C ). Data Records The sequencing datasets generated in this study are available from the National Center for Biotechnology Information (NCBI) under project accession PRJNA1440944. These datasets comprise genome survey (SRX32595579) 47 , PacBio HiFi (SRX32595574) 48 , Hi-C (SRX32595573) 49 , and RNA-seq (SRX32595575–SRX32595578) 50 – 53 reads. The assembled genome sequence has been deposited in the National Center for Biotechnology Information (NCBI) under accession JBQMFG000000000 54 , and the associated genome annotation files are accessible via Figshare (10.6084/m9.figshare.29644925.v1) 55 . Technical Validation The quality of the P. chekiangensis genome assembly was evaluated using BUSCO v6.0.0 46 with the embryophyta_odb12 dataset (2,026 core embryophyte genes), which identified 98.4% complete BUSCOs (91.2% single-copy and 7.2% duplicated, Fig. 3 ). This value exceeds the 97.1% completeness reported for the closely related species P. bournei (86.9% single-copy and 10.2% duplicated), reflecting an improvement in assembly quality. The QV estimated with Merqury v1.3 56 was 44.96, corresponding to a base-level accuracy of 99.99% (Table 1 ). Additionally, resequencing reads mapped to the assembly with a rate of 98.40% and an average coverage of >99.88%, further supporting its completeness and accuracy (Table 1 ). The LTR Assembly Index (LAI) score was 14.32, confirming that the P. chekiangensis assembly meets the reference-quality standard (Figure S7 ). Supplementary information Supplementary figures and tables (1.7MB, docx) Acknowledgements This study was supported by grants from the National Natural Science Foundation of China (No. 32470380) and the Peak Discipline Construction Project of Anhui Province (No. 2025GFXK057). Author contributions Ying-Feng Hu: Methodology, Formal analysis, Writing-original draft. Ju Tang, Xiao-Hong Li: Formal analysis. Zhi-Zhong Li: Investigation, Funding acquisition, Writing-review & editing. Jian-Wen Shao: Conceptualization, Writing-review & editing, Supervision. Data availability The data that support the findings of this study are available on the Genbank under accession JBQMFG000000000 (assembled genome sequence, https://identifiers.org/ncbi/insdc:JBQMFG000000000 ), and the Figshare (associated genome annotation files, 10.6084/m9.figshare.29644925.v1), and the NCBI under project accession PRJNA1440944 (sequencing datasets, https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1440944 ). Code availability No custom scripts were used in this study. All analyses were performed with standard bioinformatics tools following the recommended parameters and protocols. Competing interests The authors declare no competing interests. Footnotes Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Contributor Information Ying-Feng Hu, Email: huyf@ahnu.edu.cn. Jian-Wen Shao, Email: shaojw@ahnu.edu.cn. Supplementary information The online version contains supplementary material available at 10.1038/s41597-026-07211-5. References 1. Xiao, T. W. et al . Plastid phylogenomics of tribe Perseeae (Lauraceae) yields insights into the evolution of East Asian subtropical evergreen broad-leaved forests. BMC Plant Biol. 22 (1), 32, 10.1186/s12870-021-03413-8 (2022). [ DOI ] [ PMC free article ] [ PubMed ] [ Google Scholar ] 2. Han, X. et al . 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NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRR37718288 (2026). NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRR37718283 (2026). NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRR37718284 (2026). NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRR37718285 (2026). NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRR37718286 (2026). Li, Z. Z. Chromosome-level genome assembly of the endemic and endangered plant Phoebe chekiangensis . figshare 10.6084/m9.figshare.29644925.v1 (2025). Supplementary Materials Supplementary figures and tables (1.7MB, docx) Data Availability Statement The data that support the findings of this study are available on the Genbank under accession JBQMFG000000000 (assembled genome sequence, https://identifiers.org/ncbi/insdc:JBQMFG000000000 ), and the Figshare (associated genome annotation files, 10.6084/m9.figshare.29644925.v1), and the NCBI under project accession PRJNA1440944 (sequencing datasets, https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1440944 ). No custom scripts were used in this study. All analyses were performed with standard bioinformatics tools following the recommended parameters and protocols. 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