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


ABSTRACT: 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.

SUBMITTER: Wang L 

PROVIDER: S-EPMC10652414 | biostudies-literature | 2023

REPOSITORIES: biostudies-literature

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Telomere-to-telomere and haplotype-resolved genome assembly of the Chinese cork oak (<i>Quercus variabilis</i>).

Wang Longxin L   Wang Longxin L   Li Lei-Lei LL   Chen Li L   Zhang Ren-Gang RG   Zhao Shi-Wei SW   Yan Han H   Gao Jie J   Chen Xue X   Si Yu-Jun YJ   Chen Zhe Z   Liu Haibo H   Xie Xiao-Man XM   Zhao Wei W   Han Biao B   Qin Xiaochun X   Jia Kai-Hua KH  

Frontiers in plant science 20231102


The <i>Quercus variabilis</i>, 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 <i>Q. variabilis</i>. This was achieved through the integration of ONT ultra-long reads, PacBio HiFi long reads, and Hi-C  ...[more]

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