Previous assemblies of the donkey genome remain with gaps and structural errors, and a complete donkey genome will greatly facilitate genetic research related to donkeys. In the present study, a 2. 78-Gb telomere-to-telomere gap-free donkey genome (CAUT2Tdonkey) was assembled, including a 29. 78-Mb Y chromosome, aided by ONT and trio-binning approach. CAUT2Tdonkey corrected the structural errors of previous assemblies and added a total of 153. 8-Mb previously unresolved regions and 354 genes to the reference genome EquAss-T2Tᵥ2. We identified a 1. 9-Mb PAR on CAUT2Tdonkey- chromosome Y, and added 17. 1Mb regions and 75 new genes to the chromosome Y of the previous reference genome ASM1607732v2. Multi-copy genes, such as TSPY, L1RE, ETY, HSFY, and ETSTY were also identified in CAUT2Tdonkey- chromosome Y. Totally 6 types of repetitive sequences in centromeric regions were identified, and the features of the centromeric regions were revealed, and satellite-free centromeres were identified. We aligned HiFi long-read sequences of donkeys from six breeds against CAUT2Tdonkey and identified SVs in previously unresolved regions, and some of the novel SVs were located in functional genes, such as AOX1 (Chr4: DEL61), ASIC2 (Chr13: INS954), and Twist2 (Chr19: DEL98).
Yang et al. (Wed,) studied this question.