Format

Send to

Choose Destination
Gigascience. 2018 Sep 1;7(9). doi: 10.1093/gigascience/giy097.

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

Author information

1
State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, Institute of Gene Science for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Futongdong Rd, WangJing, Chaoyang District, Beijing 100102, China.
2
BGI Genomics, BGI-Shenzhen, Building No. 7, BGI Park, No. 21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China.
3
State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, No. 7, Pengfei Road, Dapeng District, Shenzhen 518120, China.
4
BGI-Qingdao, No. 2877, Tuanjie Road, Sino-German Ecopark, Qingdao, Shandong 266555, China.
5
Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangshanyi Rd, Tianhe District, Guangzhou 510000, China.
6
BGI-Fuyang, Floor 3, Jinshan Building, Qinghe East Road, Yingzhou District, Fuyang 236009, China.

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.

PMID:
30101322
PMCID:
PMC6117794
DOI:
10.1093/gigascience/giy097
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for Silverchair Information Systems Icon for PubMed Central
Loading ...
Support Center