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 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. 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.

Telomere Length in Plants Estimated with Long Read Sequencing

“…Inodorus (Wei et al, 2023)), Mangifera indica 'Irwin' (Henry et al preprint), Musa acuminata Wild type (Liu et al, 2023) and Cavendish , Oryza sativa ZS97RS3 and MH63RS3 (Song et al, 2021), Mycrica rubra (Zhang et al, 2024) (Supplemental Table S1). However, assembled telomere sequence is often used as a means to an end in confirming a complete assembly; their details are often relegated to supplemental materials or in many cases not clearly reported at all (Belser et al, 2021;Bao et al, 2023;Sato et al, 2023;Sun et al, 2023;Wang et al, 2023;Bi et al, 2024;Z. Wang et al, 2024).…”

Comparative population genomics reveals convergent and divergent selection in the apricot–peach–plum–mei complex

“…By remapping the HiFi and Hi-C reads to their respective PS_T2T assemblies, we achieved a mapping ratio of >98.5%, emphasizing the accuracy and completeness of our genome assembly (Supplementary Data Table S1 ). In comparison, the quality of PS_T2T is similar to those of published complete genomes, including maize [ 46 ], rice [ 47 ], grapes [ 48 , 49 ], pear [ 50 ], and kiwifruit [ 51 ]. These high-quality genomes provide the opportunity to study the evolutionary genomics among Prunus species.…”