Chromosome-Level Genome Assembly for Acer pseudosieboldianum and Highlights to Mechanisms for Leaf Color and Shape Change.

Xiang Li,Anran Sun,Zhiming Han,Chunli Zhao,Shikai Zhang,Ruixue Guo,Kewei Cai,Ronald Sederoff,Mulualem Tigabu,Xiaona Pei,Rui Han,Xiyang Zhao,Ying Xie

doi:10.3389/fpls.2022.850054

Abstract

Acer pseudosieboldianum (Pax) Komarov is an ornamental plant with prominent potential and is naturally distributed in Northeast China. Here, we obtained a chromosome-scale genome assembly of A. pseudosieboldianum combining HiFi and Hi-C data, and the final assembled genome size was 690.24 Mb and consisted of 287 contigs, with a contig N50 value of 5.7 Mb and a BUSCO complete gene percentage of 98.4%. Genome evolution analysis showed that an ancient duplication occurred in A. pseudosieboldianum. Phylogenetic analyses revealed that Aceraceae family could be incorporated into Sapindaceae, consistent with the present Angiosperm Phylogeny Group system. We further construct a gene-to-metabolite correlation network and identified key genes and metabolites that might be involved in anthocyanin biosynthesis pathways during leaf color change. Additionally, we identified crucial teosinte branched1, cycloidea, and proliferating cell factors (TCP) transcription factors that might be involved in leaf morphology regulation of A. pseudosieboldianum, Acer yangbiense and Acer truncatum. Overall, this reference genome is a valuable resource for evolutionary history studies of A. pseudosieboldianum and lays a fundamental foundation for its molecular breeding.

Highlights

Maple is a deciduous perennial tree or shrub belonging to the genus Acer of the Aceraceae family and is naturally distributed in Asia, Europe, North America, and the northern edge of Africa
Benchmarking Universal Single Copy Orthologs (BUSCO) results indicated that 1,588 complete conserved core plant genes (98.4% of the core genes) were found in the assembly genome (Supplementary Table 2), which was obviously higher than the values obtained in two recently released A. yangbiense and A. truncatum genomes sequenced by PacBio Sequel platforms
These results indicated that the genome assembly in the present study was accurate, and we obtained a chromosome-level reference genome of A. pseudosieboldianum

Summary

Introduction

Maple is a deciduous perennial tree or shrub belonging to the genus Acer of the Aceraceae family and is naturally distributed in Asia, Europe, North America, and the northern edge of Africa (van Gelderen et al, 1994; Yang et al, 2019; Grossman, 2021). Previous studies have shown that the root, leaf, bark, fruit and seed extracts of Acer species are rich in nutrient components, such as amino acids, fatty acids, mineral elements, and some key physiologically active substances, such as triterpene, chlorogenic acid and nervonic acids (He et al, 2021). In addition to medicinal value, many Acer species display varying leaf color types in the growth and development process, such as from green to yellow There is abundant phenotypic variation in leaf shape in Acer species, and simple leaves with trilobation, quinquepartite, and heptalobus can be found in Acer species, which lays the foundation for further genetic improvement of Acer species (Royer et al, 2009; Couturier et al, 2012; Zhu et al, 2015). Tsoong, are listed as endangered species by the Red List of Threatened Species of International Union for Conservation of Nature and Natural Resources (IUCN), and these Acer species are listed as national protected plants in China (Li et al, 2018; Wahlsteen, 2021)

Methods

Results

Conclusion