Chromosome-scale and haplotype-resolved genome assembly of Populus trichocarpa

Abstract

Populus trichocarpa, a pivotal model organism for woody transgenic research, not only garners substantial scientific interest but plays an integral role in forestry economics. Previous genomic assemblies of P. trichocarpa predominantly treated its heterozygous genome as homozygous, thereby neglecting crucial haplotypic diversity. Leveraging the high-fidelity (HiFi) sequencing capabilities of PacBio sequencing and the chromosome conformation capture insights provided by Illumina's Hi-C technique, this study is the first to achieve a near telomere-to-telomere assembly of both paternal and maternal haplotypes in P. trichocarpa. Comparative genomic analysis between these haplotypes has uncovered several allelic variants and pathways critical for trait determination through allele-specific expression. Furthermore, utilizing RNA-seq data from multiple tissues, this investigation has detailed the tissue-specific expression patterns of the leucine-rich repeat gene family, which are essential in mediating plant signal transduction and developmental regulation. Our results not only illuminate the functional genomics landscape of P. trichocarpa but also provide invaluable theoretical underpinnings for the genetic improvement of woody plants and a robust framework for exploring genetic variability and allelic expression disparities in arboreal species.

Acknowledgments

This work was supported by National Natural Science Foundation of China (Nos 62225109, 62072095) and the Fundamental Research Funds for the Central Universities (Nos 2572022BD04，HIT.BRET.2022003).

Author Contributions

G.H.W. and S.W. initiated and designed the research. W.T.G., G.H.W, S.W., T.J., H.H., R.T.G. and M.R.Z performed the data processing and experiment. W.T.G. wrote the paper. G.H.W, S.W., T.J. were involved in finalizing the manuscript.

Data availability

The whole genome sequence data reported in this paper have been deposited in the Genome Warehouse in National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, under accession number GWHERCM00000000 and GWHERCL00000000 that is publicly accessible at https://ngdc.cncb.ac.cn/gwh. The raw sequences are available at https://bigd.big.ac.cn/gsa/browse/CRA015670. The supplemental files can be downloaded at: http://www.wangsui.net.cn/resource/database/public/plant/Populus/trichocarpa/Supplemental_Files.zip

Conflict of interest statement

The authors declare no competing interest.

Supplementary Data

Supplementary data is available at Horticulture Research online.

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