September 22, 2019  |  

The chromosome-level genome assemblies of two rattans (Calamus simplicifolius and Daemonorops jenkinsiana).

Authors: Zhao, Hansheng and Wang, Songbo and Wang, Jiongliang and Chen, Chunhai and Hao, Shijie and Chen, Lianfu and Fei, Benhua and Han, Kai and Li, Rongsheng and Shi, Chengcheng and Sun, Huayu and Wang, Sining and Xu, Hao and Yang, Kebin and Xu, Xiurong and Shan, Xuemeng and Shi, Jingjing and Feng, Aiqin and Fan, Guangyi and Liu, Xin and Zhao, Shancen and Zhang, Chi and Gao, Qiang and Gao, Zhimin and Jiang, Zehui

Calamus simplicifolius and Daemonorops jenkinsiana are two representative rattans, the most significant material sources for the rattan industry. However, the lack of reference genome sequences is a major obstacle for basic and applied biology on rattan.We produced two chromosome-level genome assemblies of C. simplicifolius and D. jenkinsiana using Illumina, Pacific Biosciences, and Hi-C sequencing data. A total of ~730 Gb and ~682 Gb of raw data covered the predicted genome lengths (~1.98 Gb of C. simplicifolius and ~1.61 Gb of D. jenkinsiana) to ~372 × and ~426 × read depths, respectively. The two de novo genome assemblies, ~1.94 Gb and ~1.58 Gb, were generated with scaffold N50s of ~160 Mb and ~119 Mb in C. simplicifolius and D. jenkinsiana, respectively. The C. simplicifolius and D. jenkinsiana genomes were predicted to harbor ?51,235 and ?53,342 intact protein-coding gene models, respectively. Benchmarking Universal Single-Copy Orthologs evaluation demonstrated that genome completeness reached 96.4% and 91.3% in the C. simplicifolius and D. jenkinsiana genomes, respectively. Genome evolution showed that four Arecaceae plants clustered together, and the divergence time between the two rattans was ~19.3 million years ago. Additionally, we identified 193 and 172 genes involved in the lignin biosynthesis pathway in the C. simplicifolius and D. jenkinsiana genomes, respectively.We present the first de novo assemblies of two rattan genomes (C. simplicifolius and D. jenkinsiana). These data will not only provide a fundamental resource for functional genomics, particularly in promoting germplasm utilization for breeding, but also serve as reference genomes for comparative studies between and among different species.

Journal: GigaScience
DOI: 10.1093/gigascience/giy097
Year: 2018

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