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.FindingsWe 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.ConclusionsWe 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.

Chromosome-level reference genome and alternative splicing atlas of moso bamboo (Phyllostachys edulis)

“…We used standard methods for the RNA isolation, purity and concentration determination, reverse transcription, and cDNA library construction, as described in a previous study [ 41 ]. All cDNA libraries were constructed and normalized as described in the Additional Files.…”

“…Then, these known genes were used as query sequences for further gene identification. We identified lignin biosynthetic genes using a Basic Local Alignment Search Tool (BLAST) search (National Center for Biotechnology Information [NCBI] BLAST, RRID:SCR_004870 ) and domain analysis as described previously [ 41 , 58 ]. Briefly, we performed standard protein BLAST searches (version 2.2.26) against the six genome sequences including moso bamboo using the coding sequences of known genes with the following cutoff values: E-value <1e-10, identity >40%, and coverage rate >95% of the query sequence.…”

Genetics and genomics of moso bamboo (Phyllostachys edulis): Current status, future challenges, and biotechnological opportunities toward a sustainable bamboo industry

“…Besides several other subprojects, GABR includes two core subprojects, Bamboo‐T1K (Transcriptomes of 1,000 bamboos) and Rattan‐G5 (genomes of five Rattans) (Zhao et al., 2017). Under this program, in 2018, chromosome‐level assemblies of moso bamboo (Zhao, Gao, et al, 2018) and two rattan species (Zhao, Wang, et al, 2018) were released.…”

Coexpression Analysis Reveals Dynamic Modules Regulating the Growth and Development of Cirri in the Rattans (Calamus simplicifolius and Daemonorops jenkinsiana)

“…Trimmomatic v0.36 (Bolger et al, 2014) was used to filter the adapters and low-quality sequences using the following parameters: LEADING:3, TRAILING:3, SLIDINGWINDOWS 4:15, MINLEN:50, and TOPPHRED64. For data mapping, clean data from Trimmomatic were mapped to the respective reference genomes (Zhao et al, 2018) using HISAT2 v2.1.0 (Kim et al, 2015) software, with the following modifications from the default parameters: -min-intronlen 20, -max-intronlen 4000, and -rna-strandness RF. All datasets from HISAT2 were reserved (Supplementary Table S2) for transcript assembly.…”

“…Gene function annotations have significant implications in molecular biological studies and help researchers gain novel insights into the biological characteristics of organisms. In 2018, our team published two representative rattan genomes (Calamus simplicifolius and Daemonorops jenkinsiana) and their corresponding annotations as part of the Genome Atlas of Bamboo and Rattan (GABR) project (Zhao et al, 2017b(Zhao et al, , 2018. However, a transcriptome-level analysis of gene function has not been reported for rattans.…”