Structural Characterization of the Acer ukurunduense Chloroplast Genome Relative to Related Species in the Acer Genus

Abstract

Acer ukurunduense refers to a deciduous tree distributed in Northeast Asia and is a widely used landscaping tree species. Although several studies have been conducted on the species' ecological and economic significance, limited information is available on its phylo-genomics. Our study newly constitutes the complete chloroplast genome of A. ukurunduense into a 156,645-bp circular DNA, which displayed a typical quadripartite structure. In addition, 133 genes were identified, containing 88 protein-coding genes, 37 tRNA genes, and eight rRNA genes. In total, 107 simple sequence repeats and 49 repetitive sequences were observed. Thirty-two codons indicated that biased usages were estimated across 20 protein-coding genes (CDS) in A. ukurunduense. Four hotspot regions (trnK-UUU/rps16, ndhF/rpl32, rpl32/trnL-UAG, and ycf1) were detected among the five analyzed Acer species. Those hotspot regions may be useful molecular markers and contribute to future population genetics studies. The phylogenetic analysis demonstrated that A. ukurunduense is most closely associated with the species of Sect. Palmata. A. ukurunduense and A. pubipetiolatum var. pingpienense diverged in 22.11 Mya. We selected one of the hypervariable regions (trnK-UUU/rps16) to develop a new molecular marker and designed primers and confirmed that the molecular markers could accurately discriminate five Acer species through Sanger sequencing. By sequencing the cp genome of A. ukurunduense and comparing it with the relative species of Acer, we can effectively address the phylogenetic problems of Acer at the species level and provide insights into future research on population genetics and genetic diversity.

Keywords: Acer ukurunduense; Aceraceae; chloroplast genome; phylogenetic analysis; species identification.

FIGURE 1

Gene map of the A. ukurunduense complete cp genome. Genes drawn within and out of the circle are transcribed in the clockwise and anticlockwise directions, respectively. Genes are color-filled, which represents different functions.

FIGURE 2

Codon content of twenty amino acids in all protein-coding genes of five Acer species cp genomes. The histogram of each amino acid indicated codon usage within Acer (from left to right: A. mandshuricum, A. pictum, A. tataricum, A. tegmentosum, and A. ukurunduense).

FIGURE 3

Repeated sequences in five Acer cp genomes.

FIGURE 4

Number of different types of SSRs from five Acer species cp genomes. (A) Number of different SSR types detected in five cp genomes. (B) Number of SSRs in LSC, SSC, and IR regions. (C) Number of SSRs in the intergenic regions, genes, and introns.

FIGURE 5

Comparison of the junctions of LSC, SSC, and IR regions among five cp genomes.

FIGURE 6

Nucleotide variability across the cp genomes of the five Acer species studied. The highest values were annotated based on the localization of predicted genes of the A. ukurunduense cp genome.

FIGURE 7

Comparison of the genome structure of five Acer species using the MAUVE program.

FIGURE 8

Visualized alignments of five cp genomes of Acer using mVISTA, with A. mandshuricum as the reference. The horizontal axis indicates the five species’ cp genome of the alignment. The vertical scale represents the percentage identity, ranging from 50 to 100%.

FIGURE 9

Phylogenetic trees based on 107 species of the whole-cp genome sequences using maximum likelihood (ML) (A) and Bayesian inference (BI) (B) analyses. Numbers at nodes are values for bootstrap support. Sequences from Sapindus mukorossi and Arabidopsis thaliana served as outgroups. The position of A. ukurunduense is indicated by a yellow star.

FIGURE 10

Alignment of the sequences of the PCR products amplified using the primer of AcerTS and the reference sequences. The red arrows indicate SNPs, Indel loci, and their corresponding peaks. Acuk: A. ukurunduense; Acma: A. mandshuricum; Acte: A. tegmentosum; Acta: A. tataricum; Acpi: A. pictum.