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

Jing Yang; Hafiz Muhammad Wariss; Lidan Tao; Rengang Zhang; Quanzheng Yun; Peter Hollingsworth; Zhiling Dao; Guifen Luo; Huijun Guo; Yongpeng Ma; Weibang Sun

doi:10.1093/gigascience/giz085

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

Gigascience. 2019 Jul 1;8(7):giz085. doi: 10.1093/gigascience/giz085.

Authors

Jing Yang^{1

2}, Hafiz Muhammad Wariss^{1

2

3}, Lidan Tao^{1

2}, Rengang Zhang⁴, Quanzheng Yun⁴, Peter Hollingsworth⁵, Zhiling Dao^{1

2}, Guifen Luo^{1

2}, Huijun Guo⁶, Yongpeng Ma^{1

2}, Weibang Sun^{1

2

7}

Affiliations

¹ Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
² Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
³ University of Chinese Academy of Sciences, Beijing, 100049, China.
⁴ Beijing Ori-Gene Science and Technology Co. Ltd, Beijing, 102206, China.
⁵ Royal Botanic Garden Edinburgh, 20a Inverleith Row, Edinburgh, UK.
⁶ Southwest Forestry University, Kunming, 650224, Yunnan, China.
⁷ Kunming Botanical Garden, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.

Abstract

Background: Acer yangbiense is a newly described critically endangered endemic maple tree confined to 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)".

Findings: We generated 64, 94, and 110 Gb of raw DNA sequences and obtained a chromosome-level genome assembly of A. yangbiense through a combination of Pacific Biosciences Single-molecule Real-time, Illumina HiSeq X, and Hi-C mapping, respectively. The final genome assembly is ∼666 Mb, with 13 chromosomes covering ∼97% of the genome and scaffold N50 sizes of 45 Mb. Further, BUSCO analysis recovered 95.5% complete BUSCO genes. The total number of repetitive elements account for 68.0% of the A. yangbiense genome. Genome annotation generated 28,320 protein-coding genes, assisted by a combination of prediction and transcriptome sequencing. In addition, a nearly 1:1 orthology ratio of dot plots of longer syntenic blocks revealed a similar evolutionary history between A. yangbiense and grape, indicating that the genome has not undergone a whole-genome duplication event after the core eudicot common hexaploidization.

Conclusion: Here, we report a high-quality de novo genome assembly of A. yangbiense, the first genome for the genus Acer and the family Aceraceae. This will provide 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.

Keywords: Acer yangbiense; PSESP; PacBio sequencing; genome annotation; genome assembly.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Acer / genetics*
China
Chromosomes, Plant / genetics*
Contig Mapping
Endangered Species*
Genome, Plant*
Molecular Sequence Annotation
Whole Genome Sequencing