Rambutan genome revealed gene networks for spine formation and aril development

Wenping Zhang, Jishan Lin, Jianguo Li, Shaoquan Zheng, Xingtan Zhang, Shuai Chen, Xiaokai Ma, Fei Dong, Haifeng Jia, Xiuming Xu, Ziqin Yang, Panpan Ma, Fang Deng, Ban Deng, Yongji Huang, Zhanjie Li, Xiaozhou Lv, Yaying Ma, Zhenyang Liao, Zhicong LinJing Lin, Shengcheng Zhang, Tracie Matsumoto, Rui Xia, Jisen Zhang, Ray Ming

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish (US)
Pages (from-to)1037-1052
Number of pages16
JournalPlant Journal
Issue number4
StatePublished - Nov 2021


  • Nephelium lappaceum L.
  • Sapindaceae
  • aril development
  • chromosome fusion
  • domestication
  • selective sweeps

ASJC Scopus subject areas

  • Genetics
  • Plant Science
  • Cell Biology


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