Telomere-to-telomere and haplotype-resolved genome assembly of the Chinese cork oak (Quercus variabilis)

Longxin Wang; Lei-Lei Li; Li Chen; Ren-Gang Zhang; Shi-Wei Zhao; Han Yan; Jie Gao; Xue Chen; Yu-Jun Si; Zhe Chen; Haibo Liu; Xiao-Man Xie; Wei Zhao; Biao Han; Xiaochun Qin; Kai-Hua Jia

Telomere-to-telomere and haplotype-resolved genome assembly of the Chinese cork oak (Quercus variabilis)

2023

The Quercus variabilis, a deciduous broadleaved tree species, holds significant ecological and economical value. While a chromosome-level genome for this species has been made available, it remains riddled with unanchored sequences and gaps. In this study, we present a nearly complete comprehensive telomere-to-telomere (T2T) and haplotype-resolved reference genome for Q. variabilis. This was achieved through the integration of ONT ultra-long reads, PacBio HiFi long reads, and Hi-C data. The resultant two haplotype genomes measure 789 Mb and 768 Mb in length, with a contig N50 of 65 Mb and 56 Mb, and were anchored to 12 allelic chromosomes. Within this T2T haplotype-resolved assembly, we predicted 36,830 and 36,370 protein-coding genes, with 95.9% and 96.0% functional annotation for each haplotype genome. The availability of the T2T and haplotype-resolved reference genome lays a solid foundation, not only for illustrating genome structure and functional genomics studies but also to inform and facilitate genetic breeding and improvement of cultivated Quercus species.

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