The telomere-to-telomere genome of flowering cherry (Prunus campanulata) reveals genomic evolution of the subgenus Cerasus.

IF 11.8 2区生物学 Q1 MULTIDISCIPLINARY SCIENCES

GigaScience Pub Date : 2025-01-06 DOI:10.1093/gigascience/giaf009

Dongyue Jiang, Yingang Li, Fei Zhuge, Qi Zhou, Wenjin Zong, Xinhong Liu, Xin Shen

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引用次数: 0

Abstract

Background: Prunus campanulata, a species of ornamental cherry, holds significant genetic and horticultural value. Despite the availability of various cherry genomes, a fully resolved telomere-to-telomere (T2T) assembly for this species has been lacking. Recent advancements in long-read sequencing technologies have made it possible to generate gap-free genome assemblies, providing comprehensive insights into genomic structures that were previously inaccessible.

Findings: We present the first T2T genome assembly for P. campanulata "Lianmeiren" (v2.0), achieved through the integration of PacBio HiFi, ultra-long Oxford Nanopore Technologies, Illumina, and Hi-C sequencing. The assembly resulted in a highly contiguous genome with a total size of 266.23 Mb and a contig N50 of 31.6 Mb. The genome exhibits remarkable completeness (98.9% BUSCO) and high accuracy (quality value of 48.75). Additionally, 13 telomeres and putative centromere regions were successfully identified across the 8 pseudochromosomes. Comparative analysis with the previous v1.0 assembly revealed 336,943 single nucleotide polymorphisms, 107,521 indels, and 1,413 structural variations, along with the annotation of 1,402 new genes.

Conclusions: This T2T genome assembly of P. campanulata "Lianmeiren" provides a critical reference for understanding the genetic architecture of the species. It enhances our ability to study structural variations, gene function, and evolutionary biology within the Prunus genus.

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开花樱桃（Prunus campanulata）的端粒到端粒基因组揭示了樱花亚属的基因组进化。

背景：钟樱是观赏樱桃的一种，具有重要的遗传和园艺价值。尽管有各种各样的樱桃基因组，但这个物种缺乏完全解决的端粒到端粒（T2T）组装。长读测序技术的最新进展使得产生无间隙基因组组装成为可能，为以前无法获得的基因组结构提供了全面的见解。研究结果：通过PacBio HiFi、超长牛津纳米孔技术、Illumina和Hi-C测序，我们首次获得了P. campanulata“Lianmeiren”（v2.0）的T2T基因组组装。该基因组高度连续，总大小为266.23 Mb，序列N50为31.6 Mb。该基因组具有显著的完整性（98.9% BUSCO）和高准确性（48.75质量值）。此外，在8条假染色体上成功鉴定了13个端粒和假定的着丝粒区域。与之前的v1.0版本进行比较分析，发现336,943个单核苷酸多态性，107,521个索引，1,413个结构变异，并注释了1,402个新基因。结论：这一T2T基因组组装为了解该物种的遗传结构提供了重要参考。它增强了我们研究李属结构变异、基因功能和进化生物学的能力。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

GigaScience MULTIDISCIPLINARY SCIENCES-

CiteScore

15.50

自引率

1.10%

发文量

119

审稿时长

1 weeks

期刊介绍： GigaScience seeks to transform data dissemination and utilization in the life and biomedical sciences. As an online open-access open-data journal, it specializes in publishing "big-data" studies encompassing various fields. Its scope includes not only "omic" type data and the fields of high-throughput biology currently serviced by large public repositories, but also the growing range of more difficult-to-access data, such as imaging, neuroscience, ecology, cohort data, systems biology and other new types of large-scale shareable data.