The chromosome-level rambutan genome reveals a significant role of segmental duplication in the expansion of resistance genes

Authors: ZHENG, JINFANG - University Of Nebraska; Meinhardt, Lyndel; Goenaga, Ricardo; Matsumoto Brower, Tracie; Zhang, Dapeng; YIN, YANBIN - University Of Nebraska

Submitted to: Horticulture Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/23/2021
Publication Date: 2/11/2022
Citation: Zheng, J., Meinhardt, L.W., Goenaga, R.J., Matsumoto Brower, T.K., Zhang, D., Yin, Y. 2022. The chromosome-level rambutan genome reveals a significant role of segmental duplication in the expansion of resistance genes. Horticulture Research. 9:uhac014. https://doi.org/10.1093/hr/uhac014.
DOI: https://doi.org/10.1093/hr/uhac014

Interpretive Summary: Rambutan (Nephelium lappaceum) is a member of the Sapindaceae family and is a close relative of lychee. This fruit tree is native to Malaysia and Indonesia but is now cultivated in humid tropical lowlands in southeast Asia, Australia, Hawaii and tropical America. Rambutan fruit is primarily consumed fresh. The annual production was estimated approximately 2.0 million tons globally. Cutting edge genetic tools are needed to support the conservation and use of rambutan genetic resources. This study aims to develop the first draft genome of rambutan tree and comparatively analyze disease resistance genes in rambutan and the related species. The result significantly increased our research capacity for understanding the genetic factors influencing the important horticultural traits of rambutan. It’s an indispensable resource for breeding new varieties with improved yield, fruit quality and disease-resistance. In addition, the rambutan draft genome is highly useful for studying genetic diversity in other related species in the family of Sapindaceae. This information will be used by researchers, plant breeders, and collection curators around the world, to study and improve rambutan and advance its production and utilization.

Technical Abstract: Rambutan is one of the most important tropical fruits widely cultivated in Southeast Asia, Australia, Hawaii and tropical America. However, rambutan has lagged on crop improvement partially due to the lack of genomic and genetic research tools. Here we report the first draft genome of rambutan using hybrid de novo assembly approach. The draft genome contains scaffolds of 16 chromosomes. Genome annotation led to the identification of 49,959 protein-coding genes, approximately 10,000 more than the longan fruit (Dimocarpus longan), a species closely related to rambutan. Whole genome duplication (WDG) analysis of rambutan revealed the WDG event shared with other dicot plants but no recent WGD was detected. However, local gene duplications were found prevalent in the rambutan genome. The time of divergence between longan and rambutan was estimated to be 15.5 MYA. Functional analysis of orthologous gene clusters (OGCs) revealed that plant resistance genes are enriched in significantly expanded OGCs. In fact, rambutan has the most disease resistance gene analogs (RGAs) among the 11-sequenced genome of Spindale’s species. The rambutan draft genome also enabled the discovery of genes for anthocyanin biosynthesis pathway, which are enriched in differentially expressed genes (DGEs). The rambutan draft genome shall facilitate in gene discovery for crop improvement and disease resistance, marker-assisted breeding, as well as serve as an indispensable source for studying other related species in the family of Sapindaceae.