Telomere-to-telomere pear (Pyrus pyrifolia) reference genome reveals segmental and whole genome duplication driving genome evolution

Abstract

Previously released pear genomes contain a plethora of gaps and unanchored genetic regions. Here, we report a telomere-to-telomere (T2T) gap-free genome for the red-skinned pear, ‘Yunhong No. 1’ (YH1; Pyrus pyrifolia), which is mainly cultivated in Yunnan Province (southwest China), the pear’s primary region of origin. The YH1 genome is 501.20 Mb long with a contig N50 length of 29.26 Mb. All 17 chromosomes were assembled to the T2T level with 34 characterized telomeres. The 17 centromeres were predicted and mainly consist of centromeric-specific monomers (CEN198) and long terminal repeat (LTR) Gypsy elements (≥74.73%). By filling all unclosed gaps, the integrity of YH1 is markedly improved over previous P. pyrifolia genomes (‘Cuiguan’ and ‘Nijisseiki’). A total of 1531 segmental duplication (SD) driven duplicated genes were identified and enriched in stress response pathways. Intrachromosomal SDs drove the expansion of disease resistance genes, suggesting the potential of SDs in adaptive pear evolution. A large proportion of duplicated gene pairs exhibit dosage effects or sub-/neo-functionalization, which may affect agronomic traits like stone cell content, sugar content, and fruit skin russet. Furthermore, as core regulators of anthocyanin biosynthesis, we found that MYB10 and MYB114 underwent various gene duplication events. Multiple copies of MYB10 and MYB114 displayed obvious dosage effects, indicating role differentiation in the formation of red-skinned pear fruit. In summary, the T2T gap-free pear genome provides invaluable resources for genome evolution and functional genomics.

Acknowledgements

This study was supported by the National Science Foundation of China (31820103012), National Key Research and Development Program (2022YFD1200503), Earmarked Fund for China Agriculture Research System (CARS-28), and Earmarked Fund for Jiangsu Agricultural Industry Technology System, China (JATS[2022]454). We thank the high-performance computing platforms of the Bioinformatics Center of Nanjing Agricultural University for supporting this project.

Author contributions

J.W. designed this project and coordinated research activities; M.S. contributed to major data analysis; C.Y. performed the RNA-seq and WGCNA analysis. Q.S. and Y.H. collected and provided plant materials; G.C. and Z.X. performed the experiments. G.Y., and Y.L. provided valuable suggestions for analysis and manuscript writing. M.S. and J.W. interpreted data and contributed to writing the manuscript.

Data availability

The raw reads generated in this study have been deposited in the CNCB genome sequence archive (GSA) with the accession number PRJCA019842 (https://ngdc.cncb.ac.cn/). The genome assembly and gene annotation data are available at database (http:// pyrusgdb.sdau.edu.cn/).

Conflict of interest statement

The authors declare no competing interests.

Supplementary data

Supplementary data is available at Horticulture Research online.

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