The haplotype-resolved autotetraploid genome assembly provides insights into the genomic evolution and fruit divergence in wax apple (Syzygium samarangense (Blume) Merr. and Perry)

Abstract

Wax apple (Syzygium samarangense) is an economically important fruit crop with great potential value to human health because of its richness in antioxidant substances. Here, we present a haplotype-resolved autotetraploid genome assembly of the wax apple with a size of 1.59 Gb. Comparative genomic analysis revealed three rounds of whole-genome duplication (WGD) events, including two independent WGDs after WGT- γ. Resequencing analysis of 35 accessions partitioned these individuals into two distinct groups, including 28 landraces and seven cultivated species, and several genes subject to selective sweeps possibly contributed to fruit growth, including the KRP1- like, IAA17-like, GME-like, and FLACCA-like genes. Transcriptome analysis of three different varieties during flower and fruit development identified key genes related to fruit size, sugar content, and male sterility. We found that AP2 also affected fruit size by regulating sepal development in wax apples. The expression of sugar transport-related genes (SWEETs and SUTs) was high in ‘ZY’, likely contributing to its high sugar content. Male sterility in ‘Tub’ was associated with tapetal abnormalities due to the decreased expression of DYT1, TDF1, and AMS, which affected 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 shed new light on fruit size control, sugar metabolism, and male sterility regulatory metabolism in wax apple.

Acknowledgements

This work was supported by the Natural Science Foundation of Fujian Province (2020 J011361), and the High-quality Development beyond the ‘5511’ Collaborative Innovation Project in Fujian Province (XTCXGC2021016-4). We thank Ping Zhou (Fujian Academy of Agricultural Sciences) for the data analysis program.

Author contributions

J.X. and L.Z. designed the experiments; X.W. performed the most of the experiments; M.C. performed the genome assembly, annotation and the transcriptome data analysis; X.Z. and L.X. performed phenotype analysis; L.L. collected the materials for sequencing; H.W. and C.W. analysed the resequenced data; M.J. conducted comparative genomic analysis. Y.W. filled the gaps in the wax apple genome.

Data availability

The raw sequencing reads used for de novo whole-genome assembly and the final genome and annotation files have been deposited in the Genome Warehouse in National Genomics Data Center, under accession number GWHDUEN00000000 and GWHDVFZ00000000 which are publicly accessible at https://ngdc.cncb.ac.cn/gwh. Raw resequencing data were uploaded to the National Genomics Data Center (NGDC, https://ngdc.cncb.ac.cn/), submission ID: WGS034963; BioProject access number: PRJCA011822; BioSample access number: SAMC1129200; GSA access number: CRA010157.

Conflict of interest statement

The authors declare no competing interests.

Supplementary data

Supplementary data is available at Horticulture Research Journal online.

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