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

文献类型： 外文期刊

作者： Li, Fangping 1 ; Xu, Shiqiang 1 ; Xiao, Zitong 1 ; Wang, Jingming 1 ; Mei, Yu 1 ; Hu, Haifei 3 ; Li, Jingyu 1 ; Liu, Jieying 1 ; Hou, Zhuangwei 2 ; Zhao, Junliang 3 ; Yang, Shaohai 1 ; Wang, Jihua 1 ;

作者机构： 1.Guangdong Acad Agr Sci, Crop Res Inst, Guangdong Prov Key Lab Crops Genet & Improvement, Guangzhou 510640, Peoples R China

2.South China Agr Univ, Guangdong Prov Key Lab Plant Mol Breeding, State Key Lab Conservat & Utilizat Subtrop Agrobio, Guangzhou 510642, Peoples R China

3.Guangdong Acad Agr Sci, Rice Res Inst, Guangzhou 510640, Peoples R China

4.Guangdong Acad Agr Sci, Guangdong Key Lab New Technol Rice Breeding, Guangzhou 510640, Peoples R China

5.Guangdong Acad Agr Sci, Guangdong Rice Engn Lab, Guangzhou 510640, Peoples R China

期刊名称：HORTICULTURE RESEARCH （ 影响因子：8.7； 五年影响因子：9.0 ）

ISSN： 2662-6810

年卷期： 2023 年 10 卷 3 期

页码：

收录情况： SCI

摘要： 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 similar to 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.

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