Supporting data for "De novo genome assembly of the endangered Acer yangbiense, a plant species with extremely small populations endemic to Yunnan of China"

<i>Acer yangbiense</i> is a newly described critically endangered endemic maple tree confined to the Yangbi County in Yunnan Province in Southwest China. It was included in a programme for rescuing the most threatened species in China, focusing on plant species with extremely small populations (PSESP). <br>We generated 64 Gb, 94 Gb and 110 Gb of raw DNA sequences and obtained chromosome-level genome assembly of <i>A. yangbiense</i> through a combination of Pacific Biosciences (PacBio) Single-molecule Real-time (SMRT), Illumina HiSeq X, and Hi-C mapping, respectively. The final genome assembly is approximately 666 Mb, with 13 chromosomes covering ~97% of the genome and scaffold N50 sizes of 45 Mb. Further, Benchmarking Universal Single-Copy Orthologs analysis recovered 95.5% complete BUSCO genes. The total number of repetitive elements account for 68.0% of the <i>A. yangbiense</i> genome. Genome annotation generated 28,320 protein-coding genes, assisted by a combination of prediction and transcriptome sequencing. In addition, nearly 1:1 orthology ratio of dot plots of longer syntenic blocks revealed a similar evolution history between <i>A. yangbiense</i> and grape, indicating that the genome has not undergone a whole genome duplication (WGD) event after the core-eudicotcommon hexaploidization (ECH).<br> Here, we report a high quality de novo genome assembly of<i> A. yangbiense</i>, the first genome for the genus Acer and the family Aceraceae. This will provide a fundamental conservation genomics resources as well as representing a new high-quality reference genome for the economically important Acer lineage and the wider order of Sapindales.