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. 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. 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.

The triploid loquat (Eriobotrya japonica) is a new germplasm with a high edible fruit rate. Under natural conditions, the triploid loquat has a low fruit setting ratio (not more than ten fruits in a tree), reflecting fertilization failure. To unravel the molecular mechanism of GA treatment to induce parthenocarpy in triploid loquats, a transcriptome analysis of fruit setting induced by GA3 was analyzed using RNA-seq at four different stages during the development of young fruit. Approximately 344 million high quality reads in seven libraries were de novo assembled, yielding 153,900 unique transcripts with more than 79.9% functionally annotated transcripts. A total of 2,220, 2,974 and 1,614 differentially expressed genes (DEGs) were observed at 3, 7 and 14 days after GA treatment, respectively. The weighted gene co-expression network and Venn diagram analysis of DEGs revealed that sixteen candidate genes may play critical roles in the fruit setting after GA treatment. Five genes were related to auxin, in which one auxin synthesis gene of yucca was upregulated, suggesting that auxin may act as a signal for fruit setting. Furthermore, ABA 8'-hydroxylase was upregulated, while ethylene-forming enzyme was downregulated, suggesting that multiple hormones may be involved in GA signaling. Four transcription factors, NAC7, NAC23, bHLH35 and HD16, were potentially negatively regulated in fruit setting, and two cell division-related genes, arr9 and CYCA3, were upregulated. In addition, the expression of the GA receptor gid1 was downregulated by GA treatment, suggesting that the negative feedback mechanism in GA signaling may be regulated by gid1. Altogether, the results of the present study provide information from a comprehensive gene expression analysis and insight into the molecular mechanism underlying fruit setting under GA treatment in E. japonica.