The Haplotype-resolved Autotetraploid Genome Assembly Provides Insights into the genomic evolution and fruit divergence in Wax apple (Syzygium samarangense (BI.) Merr.et Perry)

Abstract

The wax apple (Syzygium samarangense) is an economically important fruit crop with great potential value to human health because it has rich antioxidant substances. Here, we presented one haplotype-resolved autotetraploid genome assembly of the wax apple with size of 1.59 Gb. Comparative genomic analysis revealed three rounds of whole-genome duplication (WGD) events, including two independent WGDs after WGT-{gamma}. Resequencing analysis of 35 accessions partitioned these individuals into two distinct groups, including 28 landraces and seven cultivated species, and several selectively swept genes possibly contributed to fruit growth, including KRP1-like, IAA17-like, GME-like, and FLACCA-like genes. Transcriptome analysis in three different varieties during flower and fruit development identified key genes related to fruit size, sugar content, and male sterility. We found AP2 also affects the fruit size by regulating the sepal development in wax apples. The expression of sugar transport-related genes (SWEETs and SUTs) was high in ZY, likely contributing to a high level of sugar content. Male sterility in Tub was associated with tapetal abnormalities due to the decreased expression of DYT1, TDF1, and AMS, which affects the early tapetum development. The chromosome-scale genome and large-scale transcriptome data presented in this study offer new valuable resources for biological research on S. samarangense, and sheds new light on fruit size control, sugar metabolism, and male sterility regulatory metabolism in wax apple.