文献类型：期刊文献

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

作者：Zhao, Hansheng[1] Wang, Songbo[2,5] Wang, Jiongliang[1] Chen, Chunhai[2] Hao, Shijie[3] Chen, Lianfu[1] Fei, Benhua[1] Han, Kai[3] Li, Rongsheng[4] Shi, Chengcheng[3] Sun, Huayu[1] Wang, Sining[1] Xu, Hao[1] Yang, Kebin[1] Xu, Xiurong[1] Shan, Xuemeng[1] Shi, Jingjing[1] Feng, Aiqin[2] Fan, Guangyi[3] Liu, Xin[3,6] Zhao, Shancen[2,5] Zhang, Chi[2,5] Gao, Qiang[2] Gao, Zhimin[1] Jiang, Zehui[1]

第一作者：Zhao, Hansheng

通信作者：Gao, ZM[1];Jiang, ZH[1];Gao, Q[2]

机构：[1]Int Ctr Bamboo & Rattan, Inst Gene Sci Bamboo & Rattan Resources, State Forestry Adm, Key Open Lab Sci & Technol Bamboo & Rattan, Futongdong Rd, Beijing 100102, Peoples R China;[2]BGI Shenzhen, BGI Genom, Bldg 7,BGI Pk,21 Hongan 3rd St, Shenzhen 518083, Peoples R China;[3]BGI Qingdao, 2877,Tuanjie Rd,Sinogerman Ecopk, Qingdao 266555, Shandong, Peoples R China;[4]Chinese Acad Forestry, Res Inst Trop Forestry, Guangshanyi Rd, Guangzhou 510000, Guangdong, Peoples R China;[5]BGI Shenzhen, State Key Lab Agr Genom, 7 Pengfei Rd, Shenzhen 518120, Peoples R China;[6]BGI Fuyang, Floor 3,Jinshan Bldg,Qinghe East Rd, Fuyang 236009, Peoples R China

年份：2018

卷号：7

期号：9

外文期刊名：GIGASCIENCE

收录：;WOS:【SCI-EXPANDED(收录号:WOS:000450160500001)】；

基金：This work was supported by the Sub-Project of the National Science and Technology Support Plan of the Twelfth Five-Year Plan in China (2015BAD04B03 and 2015BAD04B01), Fundamental Research Funds for the International Center for Bamboo and Rattan (1632017018), and the Science Technology and Innovation Committee of Shenzhen Municipality (JCYJ20160331190123578).

语种：英文

外文关键词：rattan; Calamus simplicifolius; Daemonorops jenkinsiana; whole-genome sequencing; genome assembly; annotation

摘要：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 similar to 730 Gb and similar to 682 Gb of raw data covered the predicted genome lengths (similar to 1.98 Gb of C. simplicifolius and similar to 1.61 Gb of D. jenkinsiana) to similar to 372 x and similar to 426 x read depths, respectively. The two de novo genome assemblies, similar to 1.94 Gb and similar to 1.58 Gb, were generated with scaffold N50s of similar to 160 Mb and similar to 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 similar to 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.