BACKGROUND The loquat (Eriobotrya japonica) is a species of flowering plant in the family Rosaceae that is widely cultivated in Asian, European, and African countries. It blossoms in the winter and ripens in the early summer. The genome of loquat has to date not been published, which limits the study of molecular biology in this cultivated species. Here, we used the third-generation sequencing technology of Nanopore and Hi-C technology to sequence the genome of Eriobotrya. FINDINGS We generated 100.10 Gb of long reads using Oxford Nanopore sequencing technologies. Three types of Illumina high-throughput sequencing data, including genome short reads (47.42 Gb), transcriptome short reads (11.06 Gb), and Hi-C short reads (67.25 Gb), were also generated to help construct the loquat genome. All data were assembled into a 760.1-Mb genome assembly. The contigs were mapped to chromosomes by using Hi-C technology based on the contacts between contigs, and then a genome was assembled exhibiting 17 chromosomes and a scaffold N50 length of 39.7 Mb. A total of 45,743 protein-coding genes were annotated in the Eriobotrya genome, and we investigated the phylogenetic relationships between the Eriobotrya and 6 other Rosaceae species. Eriobotrya shows a close relationship with Malus and Pyrus, with the divergence time of Eriobotrya and Malus being 6.76 million years ago. Furthermore, chromosome rearrangement was found in Eriobotrya and Malus. CONCLUSIONS We constructed the first high-quality chromosome-level Eriobotrya genome using Illumina, Nanopore, and Hi-C technologies. This work provides a valuable reference genome for molecular studies of the loquat and provides new insight into chromosome evolution in this species.

中文翻译：

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枇杷（Eriobotrya japonica）基因组的染色体水平基因组组装和注释。

背景技术枇杷（Eriobotrya japonica）是蔷薇科的一种开花植物，在亚洲、欧洲和非洲国家广泛种植。它在冬天开花，在初夏成熟。迄今为止，枇杷的基因组尚未发表，这限制了对该栽培物种的分子生物学研究。在这里，我们利用Nanopore第三代测序技术和Hi-C技术对枇杷属基因组进行了测序。研究结果 我们使用 Oxford Nanopore 测序技术生成了 100.10 Gb 的长读长。还生成了三种类型的Illumina高通量测序数据，包括基因组短读长（47.42 Gb）、转录组短读长（11.06 Gb）和Hi-C短读长（67.25 Gb），以帮助构建枇杷基因组。所有数据均被组装成 760.1 Mb 的基因组组件。根据重叠群之间的接触，使用 Hi-C 技术将重叠群映射到染色体，然后组装出具有 17 条染色体和支架 N50 长度为 39.7 Mb 的基因组。枇杷基因组中总共注释了 45,743 个蛋白质编码基因，我们研究了枇杷属与其他 6 个蔷薇科物种之间的系统发育关系。枇杷属与海棠属和梨属关系密切，其分歧时间为676万年前。此外，在枇杷属和苹果属中发现了染色体重排。结论 我们使用 Illumina、Nanopore 和 Hi-C 技术构建了第一个高质量染色体水平的枇杷基因组。这项工作为枇杷的分子研究提供了有价值的参考基因组，并为该物种的染色体进化提供了新的见解。