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. 2022 Mar 3:13:850054.
doi: 10.3389/fpls.2022.850054. eCollection 2022.

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

Xiang Li  1   2 , Kewei Cai  2 , Zhiming Han  2 , Shikai Zhang  2 , Anran Sun  2 , Ying Xie  2 , Rui Han  1 , Ruixue Guo  1 , Mulualem Tigabu  3 , Ronald Sederoff  4 , Xiaona Pei  1 , Chunli Zhao  1 , Xiyang Zhao  1   2
Affiliations

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

Xiang Li et al. Front Plant Sci. .

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; Hi-C; HiFi; PacBio SMRT; TCPs; genome assembly.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

FIGURE 1
FIGURE 1
Photographs of Acer pseudosieboldianum. (A) Adult tree, (B) flower, (C) fruit, (D) leaf, and (E) seed.
FIGURE 2
FIGURE 2
Distribution of A. pseudosieboldianum genomic features. (A) Circular representation of the chromosome, (B) gene density, (C) repeat density, (D) rRNA, (E) tRNA, and (F) GC content.
FIGURE 3
FIGURE 3
Gene family, phylogenetic analysis, and 4dTV and Ks distribution of A. pseudosieboldianum and Acer species. (A) Number of genes in various plant species, showing a high gene number for A. pseudosieboldianum compared with other species. (B) Venn diagram of the gene family between A. pseudosieboldianum, A. yangbiense, A. truncatum, A. thaliana, Populus trichocarpa, and O. sativa. (C) Distribution of Ks. (D) Species tree on the basis of 347 single-copy orthologs from 16 plant species.
FIGURE 4
FIGURE 4
Synteny analysis of A. pseudosieboldianum, A. yangbiense and A. truncatum. (A) Dot plots of syntenic blocks between A. pseudosieboldianum and A. yangbiense. (B) Dot plots of syntenic blocks between A. pseudosieboldianum and A. truncatum. The red line represents sequence forward matching, and the blue line represents reverse complementary matching. (C) Blocks with syntenic genes among A. pseudosieboldianum, A. yangbiense, and A. truncatum. The blue line shows an example of two syntenic blocks.
FIGURE 5
FIGURE 5
Comparative transcriptomic analysis of genes involved in anthocyanin biosynthesis during leaf color change. (A) Photographs of different leaf colors of A. pseudosieboldianum. GL, green leaf; HRL, half-red leaf; RL, red leaf. (B) The biosynthesis pathways of flavonoids, anthocyanin and flavonoid and the expression analysis of differentially expressed genes and differentially expressed metabolites. (C) Correlation network of metabolite-related genes involved in anthocyanin biosynthetic pathways. r represents the Pearson correlation coefficient; relation represents the correlation, including positive (r > 0.8) and negative correlations (r < –0.8). (D) Heatmap showing the differential expression of MYB and bHLH transcription factors according to the transcriptome data from leaves of different colors.
FIGURE 6
FIGURE 6
Teosinte branched1, cycloidea, and proliferating cell factors (TCP) gene family in A. pseudosieboldianum, A. yangbiense, and A. truncatum. and expression analysis of TCP genes in different tissues. (A) Photographs of leaf shape in A. yangbiense, A. truncatum, and A. pseudosieboldianum. L1 represents the mature leaf in A. yangbiense; L2 represents the mature leaf in A. truncatum; L3 represents the mature leaf in A. pseudosieboldianum. (B) Phylogenetic tree of TCP genes from A. pseudosieboldianum (24 genes), A. yangbiense (22 genes), and A. truncatum (21 genes). (C) Synteny analysis of TCP genes in A. pseudosieboldianum, A. yangbiense, and A. truncatum. Gray lines in the background indicate collinear blocks between A. pseudosieboldianum, A. yangbiense, and A. truncatum, whereas red lines highlight syntenic ApTCP gene pairs, blue lines highlight syntenic AtruTCP gene pairs, and green lines highlight syntenic AyTCP gene pairs. Expression analysis of TCP genes in different tissues of A. truncatum. (D) Heatmap showing the expression level of TCP family in different tissues in A. truncatum. (E) Heatmap showing the expression level of TCP family in different tissues in A. yangbiense. (F) Heatmap showing the expression level of TCP family in different tissues in A. pseudosieboldianum.
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