Rambutan genome revealed gene networks for spine formation and aril development

Abstract

Rambutan is a popular tropical fruit known for its exotic appearance, has long flexible spines on shells, extraordinary aril growth, desirable nutrition, and a favorable taste. The genome of an elite rambutan cultivar Baoyan 7 was assembled into 328 Mb in 16 pseudo-chromosomes. Comparative genomics analysis between rambutan and lychee revealed that rambutan chromosomes 8 and 12 are collinear with lychee chromosome 1, which resulted in a chromosome fission event in rambutan (n = 16) or a fusion event in lychee (n = 15) after their divergence from a common ancestor 15.7 million years ago. Root development genes played a crucial role in spine development, such as endoplasmic reticulum pathway genes, jasmonic acid response genes, vascular bundle development genes, and K + transport genes. Aril development was regulated by D-class genes (STK and SHP1), plant hormone and phenylpropanoid biosynthesis genes, and sugar metabolism genes. The lower rate of male sterility of hermaphroditic flowers appears to be regulated by MYB24. Population genomic analyses revealed genes in selective sweeps during domestication that are related to fruit morphology and environment stress response. These findings enhance our understanding of spine and aril development and provide genomic resources for rambutan improvement.

Attenuation of Postharvest Browning in Rambutan Fruit by Melatonin Is Associated With Inhibition of Phenolics Oxidation and Reinforcement of Antioxidative Process

“…Rambutan ( Nephelium lappaceum L.) is a Sapindaceae plant native to Malaysia and is now extensively cultivated in tropical and subtropical regions and countries, such as China, Thailand, Philippines, Vietnam, Malaysia, Indonesia, India, Australia, and South Africa ( 1 , 2 ). Rambutan fruit has been accepted and loved by a vast number of consumers in the global market for its superior taste, high nutritional value, and unique appearance ( 2 , 3 ).…”

“…Rambutan ( Nephelium lappaceum L.) is a Sapindaceae plant native to Malaysia and is now extensively cultivated in tropical and subtropical regions and countries, such as China, Thailand, Philippines, Vietnam, Malaysia, Indonesia, India, Australia, and South Africa ( 1 , 2 ). Rambutan fruit has been accepted and loved by a vast number of consumers in the global market for its superior taste, high nutritional value, and unique appearance ( 2 , 3 ). Nevertheless, as a typical non-climacteric fruit with a peculiar tissue structure, the rambutan fruit after harvest is perishable and highly susceptible to pericarp (comprising soft spines) browning during storage and transportation, which leads to rapid deterioration of fruit quality and serious loss of commercial value ( 3 ).…”

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

“…At present, only three Sapindaceae genomes are publicly available: Xanthoceras sorbifolium [ 2 ], Dimocarpus longan (longan) [ 3 ], and Acer yangbiense [ 4 ]. During the process of submitting this manuscript, the genome paper for the rambutan cultivar Baoyan7 became available online, but its genome sequence has not yet been released [ 5 ].…”

SapBase (Sapinaceae Genomic DataBase): a central portal for functional and comparative genomics of Sapindaceae species

“…Many Sapindaceae species possess great economic value; some furnish delicious fruits, like lychee ( Litchi chinensis ), longan ( Dimocarpus longan ), rambutan ( Nephelium lappaceum ); and ackee ( Blighia sapida ) - the national fruit of Jamaica; some produce abundance secondary metabolites, like saponin from soapberry ( Sapindus mukorossi ), and seed oil from yellowhorn ( Xanthoceras sorbifolium ); some yield valuable timber including maple ( Acer spp .) and buckeye ( Aesculus glabra ); and some are of great herbal medicinal value, like balloon-vine ( Cardiospermum halicacabum ). In the last decade, with the rocketing of next generation sequencing (NGS) and genomic technologies, the full genome sequences of several Sapindaceae plants have been resolved (Lin et al, 2017; Liang et al, 2019; Yang et al, 2019; Zhang et al, 2021; Hu et al, 2022; Xue et al, 2022). Among them, our recent publication of the lychee genome attracted broad attention (Edger, 2022; Hu et al, 2022; Lyu, 2022).…”

“…In the last decade, with the rocketing of next generation sequencing (NGS) and genomic technologies, the full genome sequences of several Sapindaceae plants have been resolved (Lin et al, 2017; Liang et al, 2019; Yang et al, 2019; Zhang et al, 2021; Hu et al, 2022; Xue et al, 2022). Among them, our recent publication of the lychee genome attracted broad attention (Edger, 2022; Hu et al, 2022; Lyu, 2022).…”