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

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 chromos...

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Autores principales: Zhao, Hansheng, Wang, Songbo, Wang, Jiongliang, Chen, Chunhai, Hao, Shijie, Chen, Lianfu, Fei, Benhua, Han, Kai, Li, Rongsheng, Shi, Chengcheng, Sun, Huayu, Wang, Sining, Xu, Hao, Yang, Kebin, Xu, Xiurong, Shan, Xuemeng, Shi, Jingjing, Feng, Aiqin, Fan, Guangyi, Liu, Xin, Zhao, Shancen, Zhang, Chi, Gao, Qiang, Gao, Zhimin, Jiang, Zehui
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6117794/
https://www.ncbi.nlm.nih.gov/pubmed/30101322
http://dx.doi.org/10.1093/gigascience/giy097
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author Zhao, Hansheng
Wang, Songbo
Wang, Jiongliang
Chen, Chunhai
Hao, Shijie
Chen, Lianfu
Fei, Benhua
Han, Kai
Li, Rongsheng
Shi, Chengcheng
Sun, Huayu
Wang, Sining
Xu, Hao
Yang, Kebin
Xu, Xiurong
Shan, Xuemeng
Shi, Jingjing
Feng, Aiqin
Fan, Guangyi
Liu, Xin
Zhao, Shancen
Zhang, Chi
Gao, Qiang
Gao, Zhimin
Jiang, Zehui
author_facet Zhao, Hansheng
Wang, Songbo
Wang, Jiongliang
Chen, Chunhai
Hao, Shijie
Chen, Lianfu
Fei, Benhua
Han, Kai
Li, Rongsheng
Shi, Chengcheng
Sun, Huayu
Wang, Sining
Xu, Hao
Yang, Kebin
Xu, Xiurong
Shan, Xuemeng
Shi, Jingjing
Feng, Aiqin
Fan, Guangyi
Liu, Xin
Zhao, Shancen
Zhang, Chi
Gao, Qiang
Gao, Zhimin
Jiang, Zehui
author_sort Zhao, Hansheng
collection PubMed
description 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.
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spelling pubmed-61177942018-09-05 The chromosome-level genome assemblies of two rattans (Calamus simplicifolius and Daemonorops jenkinsiana) Zhao, Hansheng Wang, Songbo Wang, Jiongliang Chen, Chunhai Hao, Shijie Chen, Lianfu Fei, Benhua Han, Kai Li, Rongsheng Shi, Chengcheng Sun, Huayu Wang, Sining Xu, Hao Yang, Kebin Xu, Xiurong Shan, Xuemeng Shi, Jingjing Feng, Aiqin Fan, Guangyi Liu, Xin Zhao, Shancen Zhang, Chi Gao, Qiang Gao, Zhimin Jiang, Zehui Gigascience Data Note 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. Oxford University Press 2018-08-07 /pmc/articles/PMC6117794/ /pubmed/30101322 http://dx.doi.org/10.1093/gigascience/giy097 Text en © The Author(s) 2018. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Data Note
Zhao, Hansheng
Wang, Songbo
Wang, Jiongliang
Chen, Chunhai
Hao, Shijie
Chen, Lianfu
Fei, Benhua
Han, Kai
Li, Rongsheng
Shi, Chengcheng
Sun, Huayu
Wang, Sining
Xu, Hao
Yang, Kebin
Xu, Xiurong
Shan, Xuemeng
Shi, Jingjing
Feng, Aiqin
Fan, Guangyi
Liu, Xin
Zhao, Shancen
Zhang, Chi
Gao, Qiang
Gao, Zhimin
Jiang, Zehui
The chromosome-level genome assemblies of two rattans (Calamus simplicifolius and Daemonorops jenkinsiana)
title The chromosome-level genome assemblies of two rattans (Calamus simplicifolius and Daemonorops jenkinsiana)
title_full The chromosome-level genome assemblies of two rattans (Calamus simplicifolius and Daemonorops jenkinsiana)
title_fullStr The chromosome-level genome assemblies of two rattans (Calamus simplicifolius and Daemonorops jenkinsiana)
title_full_unstemmed The chromosome-level genome assemblies of two rattans (Calamus simplicifolius and Daemonorops jenkinsiana)
title_short The chromosome-level genome assemblies of two rattans (Calamus simplicifolius and Daemonorops jenkinsiana)
title_sort chromosome-level genome assemblies of two rattans (calamus simplicifolius and daemonorops jenkinsiana)
topic Data Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6117794/
https://www.ncbi.nlm.nih.gov/pubmed/30101322
http://dx.doi.org/10.1093/gigascience/giy097
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