AUTHOR=Ren Weichao , Liu Chi , Yan Song , Jiang Zhehui , Wang Tianhao , Wang Zhen , Zhang Meiqi , Liu Meiqi , Sun Jiaying , Gao Jinhui , Ma Wei 

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

JOURNAL=Frontiers in Genetics

VOLUME=13

YEAR=2022

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2022.849182

DOI=10.3389/fgene.2022.849182

ISSN=1664-8021

ABSTRACT=<p><italic>Acer ukurunduense</italic> 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 <italic>A. ukurunduense</italic> 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 <italic>A. ukurunduense</italic>. Four hotspot regions (<italic>trnK-UUU/rps16</italic>, <italic>ndhF/rpl32</italic>, <italic>rpl32/trnL-UAG</italic>, and <italic>ycf1</italic>) were detected among the five analyzed <italic>Acer</italic> species. Those hotspot regions may be useful molecular markers and contribute to future population genetics studies. The phylogenetic analysis demonstrated that <italic>A. ukurunduense</italic> is most closely associated with the species of Sect. <italic>Palmata</italic>. <italic>A. ukurunduense</italic> and <italic>A. pubipetiolatum</italic> var. <italic>pingpienense</italic> diverged in 22.11 Mya. We selected one of the hypervariable regions (<italic>trnK-UUU/rps16</italic>) to develop a new molecular marker and designed primers and confirmed that the molecular markers could accurately discriminate five <italic>Acer</italic> species through Sanger sequencing. By sequencing the cp genome of <italic>A. ukurunduense</italic> and comparing it with the relative species of <italic>Acer</italic>, we can effectively address the phylogenetic problems of <italic>Acer</italic> at the species level and provide insights into future research on population genetics and genetic diversity.</p>