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Research article - Peer-reviewed, 2022

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

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

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.

Keywords

Acer pseudosieboldianum; PacBio SMRT; HiFi; genome assembly; Hi-C; TCPs

Published in

Frontiers in Plant Science
2022, volume: 13, article number: 850054
Publisher: FRONTIERS MEDIA SA

Authors' information

Li, Xiang
Jilin Agricultural University
Li, Xiang
Northeast Forestry University - China
Cai, Kewei
Northeast Forestry University - China
Han, Zhiming
Northeast Forestry University - China
Zhang, Shikai
Northeast Forestry University - China
Sun, Anran
Northeast Forestry University - China
Xie, Ying
Northeast Forestry University - China
Han, Rui
Jilin Agricultural University
Guo, Ruixue
Jilin Agricultural University
Swedish University of Agricultural Sciences, Southern Swedish Forest Research Centre
Sederoff, Ronald
North Carolina State University (NC State)
Pei, Xiaona
Jilin Agricultural University
Zhao, Chunli
Jilin Agricultural University
Zhao, Xiyang
Jilin Agricultural University
Zhao, Xiyang
Northeast Forestry University - China

UKÄ Subject classification

Forest Science
Bioinformatics and Systems Biology

Publication Identifiers

DOI: https://doi.org/10.3389/fpls.2022.850054

URI (permanent link to this page)

https://res.slu.se/id/publ/116843