Genome assembly of wild loquat (Eriobotrya japonica) and resequencing provide new insights into the genomic evolution and fruit domestication in loquat

Abstract

Wild loquats (Eriobotrya japonica Lindl.) provide remarkable genetic resources for studying domestication and breeding improved varieties. Herein, we generate the first high-quality chromosome-level genome assembly of wild loquat, with 45 791 predicted protein-coding genes. Analysis of comparative genomics indicated that loquat shares a common ancestor with apple and pear, and a recent whole-genome duplication event occurred in loquat prior to its divergence. Genome resequencing showed that the loquat germplasms can be distinctly classified into wild and cultivated groups, and the commercial cultivars have experienced allelic admixture. Compared with cultivated loquats, the wild loquat genome showed very few selected genomic regions and had higher levels of genetic diversity. However, whole-genome scans of selective sweeps were mainly related to fruit quality, size, and flesh color during the domestication process. Large-scale transcriptome and metabolome analyses were further performed to identify differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs) in wild and cultivated loquats at various fruit development stages. Unlike those in wild loquat, the key DEGs and DAMs involved in carbohydrate metabolism, plant hormone signal transduction, flavonoid biosynthesis, and carotenoid biosynthesis were significantly regulated in cultivated loquats during fruit development. These high-quality reference genome, resequencing, and large-scale transcriptome/metabolome data provide valuable resources for elucidating fruit domestication and molecular breeding in loquat.

Acknowledgements

This work was supported by the National Key R&D Program of China (No. 2019YFD1000200), the National Nature Science Foundation of China (No. 32102321), the Chongqing Science and Technology Commission (cstc2021jcyj-msxmX1156 and cstc2021jscx-gksbX0010), the Innovation Research Group Funds for Chongqing Universities (CXQT19005), and the Fundamental Research Funds for the Central Universities (SWU-KT22055). We thank Chao Nie (College of Horticulture and Landscape Architecture, Southwest University) for support during metabolite analysis. We also thank the BMKCloud (http://www.biocloud.net), which provided bioinformatics support in this project.

Author contributions

D.J., Q.H., Q.G., and G.L. conceived and designed the project. D.J., X.L. and Q.H. performed the data analysis. D.J., J.D., Y.X., D.W., C.Z., Q.G., and G.L. collected the samples of loquat germplasms. X.L., R.H., and Y.Y. collected the samples of fruits. S.W. and Y.Z. contributed to valuable discussions. D.J. and Q.X. analyzed the karyotype of wild loquat. D.J. wrote the manuscript. X.L., Q.G., and G.L. revised the manuscript. All authors read and approved the final manuscript.

Data availability

The raw genome sequence data have been deposited in the National Genomics Data Center (NGDC, https://ngdc.cncb.ac.cn/) under BioProject accession number PRJCA008992. The whole genome sequence of wild loquat has been deposited in the Genome Warehouse (https://ngdc.cncb.ac.cn/gwh/) under accession number GWHBOTF00000000.

Conflict of interest

The authors declare that they have no conflict of interest.

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