Gap-free genome assembly and comparative analysis reveal the evolution and anthocyanin accumulation mechanism of Rhodomyrtus tomentosa

Abstract

Rhodomyrtus tomentosa is an important fleshy-fruited tree and a well-known medicinal plant of the Myrtaceae family that is widely cultivated in tropical and subtropical areas of the world. However, studies on the evolution and genomic breeding of R. tomentosa were hindered by the lack of a reference genome. Here, we presented a chromosome-level gap-free T2T genome assembly of R. tomentosa using PacBio and ONT long read sequencing. We assembled the genome with size of 470.35 Mb and contig N50 of ∼43.80 Mb with 11 pseudochromosomes. A total of 33 382 genes and 239.31 Mb of repetitive sequences were annotated in this genome. Phylogenetic analysis elucidated the independent evolution of R. tomentosa starting from 14.37MYA and shared a recent WGD event with other Myrtaceae species. We identified four major compounds of anthocyanins and their synthetic pathways in R. tomentosa. Comparative genomic and gene expression analysis suggested the coloring and high anthocyanin accumulation in R. tomentosa tends to be determined by the activation of anthocyanin synthesis pathway. The positive selection and up-regulation of MYB transcription factors were the implicit factors in this process. The copy number increase of downstream anthocyanin transport-related OMT and GST gene were also detected in R. tomentosa. Expression analysis and pathway identification enriched the importance of starch degradation, response to stimuli, effect of hormones, and cell wall metabolism during the fleshy fruit development in Myrtaceae. Our genome assembly provided a foundation for investigating the origins and differentiation of Myrtaceae species and accelerated the genetic improvement of R. tomentosa.

Acknowledgements

This work was supported by the Natural Science Foundation of Crops Research Institute and Guangdong Academy of Agricultural (0145), the Scientific Innovation Strategy-Construction of High-Level Academy of Agriculture Science (R2019PY-JX003), Research and Development Program in Key Areas of the Guangdong Province (2021B0707010010). We would like to express our heartfelt thanks to Professor Zhou Xiaofan and Professor Wang Shaokui of South China Agricultural University for their support in this study.

Data availability

The genome assembly as well as the raw genomic data of Illumina sequences, PacBio sequences, ONT sequences and transcriptome data have been deposited in the NCBI Sequence Read Archive under accession number PRJNA893855.

Conflict of interest statement

The authors declare no conflict of interest.

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