Dataset Information

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

ABSTRACT: Background: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. Findings: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. Conclusions: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.

SUBMITTER: Zhao H

PROVIDER: S-EPMC6117794 | biostudies-literature | 2018 Sep

REPOSITORIES: biostudies-literature

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

Zhao Hansheng H Wang Songbo S Wang Jiongliang J Chen Chunhai C Hao Shijie S Chen Lianfu L Fei Benhua B Han Kai K Li Rongsheng R Shi Chengcheng C Sun Huayu H Wang Sining S Xu Hao H Yang Kebin K Xu Xiurong X Shan Xuemeng X Shi Jingjing J Feng Aiqin A Fan Guangyi G Liu Xin X Zhao Shancen S Zhang Chi C Gao Qiang Q Gao Zhimin Z Jiang Zehui Z

GigaScience 20180901 9

<h4>Background</h4>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.<h4>Findings</h4>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 p ...[more]

PMID: 30101322

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Dataset Information

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

Publications

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

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