pyrifolia_Yunhong No.1
Common Name
Yunhong No.1

Previously released pear genomes contain a plethora 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’). 1,531 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.


Sequencing Platforms               Illumina, PacBio HiFi, ONT ultra-long, and Hi-C.

 Assembly Level                       Chromosome

Estimated Genome Size           506.65Mb

Assembled Genome Size         501.20Mb

Contig N50                              29.26Mb

Gene Number                          41969

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