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

Manyi Sun; Chenjie Yao; Qun Shu; Yingyun He; Guosong Chen; Guangyan Yang; Shaozhuo Xu; Yueyuan Liu; Zhaolong Xue; Jun Wu

doi:10.1093/hr/uhad201

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

Hortic Res. 2023 Oct 12;10(11):uhad201. doi: 10.1093/hr/uhad201. eCollection 2023 Nov.

Authors

Manyi Sun^{1

2}, Chenjie Yao^{1

2}, Qun Shu³, Yingyun He³, Guosong Chen^{1

2}, Guangyan Yang^{1

2}, Shaozhuo Xu^{1

2}, Yueyuan Liu^{1

2}, Zhaolong Xue^{1

2}, Jun Wu^{1

2}

Affiliations

¹ College of Horticulture, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China.
² Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, Jiangsu 210014, China.
³ Institute of Horticulture, Yunnan Academy of Agricultural Sciences, Kunming 650205, China.

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.