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Chromosome-level genome assembly and annotation of the loquat (Eriobotrya japonica) genome

文献类型： 外文期刊

作者： Jiang, Shuang 1 ; An, Haishan 1 ; Xu, Fangjie 1 ; Zhang, Xueying 1 ;

作者机构： 1.Shanghai Acad Agr Sci, Forestry & Pomol Res Inst, Shanghai Key Lab Protected Hort Technol, Shanghai 201403, Peoples R China

关键词： loquat; genome assembly; Nanopore; Hi-C

期刊名称：GIGASCIENCE （ 影响因子：6.524； 五年影响因子：8.702 ）

ISSN： 2047-217X

年卷期： 2020 年 9 卷 3 期

页码：

收录情况： SCI

摘要： 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.

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