1Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China 2Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Henan Zhengzhou 450001, China *Corresponding author. E-mail: firstname.lastname@example.org,email@example.com †Both authors contributed equally to the study.
Received: 20 May 2022 Accepted: 08 Jul 2022 Published online: 01 Aug 2022
For any species, a high-quality reference genome is the basis for almost all kinds of genomic analysis . However, for decades the reference sequences of important eukaryotic genomes were incomplete due to the missing repetitive genomic regions including both tandem repeats such as centromere, telomere, and ribosomal DNA, and interspersed repeats like transposons and segmental duplications. The incomplete reference genomes not only cause data analytical mistakes like false-positive variant calls but also impede the studies of repeat-related diseases such as cancer and infertility [2, 3]. Fortunately, the generation of Pacbio high-fidelity (HiFi) long sequences and Oxford Nanopore Technology (ONT) ultra-long (UL) sequences provides the opportunity of solving repeat assembly problems because of their advantages in accuracy and length, respectively, and a list of complete (T2T, or Telomere to Telomere) or near-complete reference genomes of important eukaryotic species like human , Arabidopsis , rice  and tomato  have been built recently.