Draft genome sequence of ramie, Boehmeria nivea (L.) Gaudich

Abstract

Ramie, Boehmeria nivea (L.) Gaudich, family Urticaceae, is a plant native to eastern Asia, and one of the world's oldest fibre crops. It is also used as animal feed and for the phytoremediation of heavy metal-contaminated farmlands. Thus, the genome sequence of ramie was determined to explore the molecular basis of its fibre quality, protein content and phytoremediation. For further understanding ramie genome, different paired-end and mate-pair libraries were combined to generate 134.31 Gb of raw DNA sequences using the Illumina whole-genome shotgun sequencing approach. The highly heterozygous B. nivea genome was assembled using the Platanus Genome Assembler, which is an effective tool for the assembly of highly heterozygous genome sequences. The final length of the draft genome of this species was approximately 341.9 Mb (contig N50 = 22.62 kb, scaffold N50 = 1,126.36 kb). Based on ramie genome annotations, 30,237 protein-coding genes were predicted, and the repetitive element content was 46.3%. The completeness of the final assembly was evaluated by benchmarking universal single-copy orthologous genes (BUSCO); 90.5% of the 1,440 expected embryophytic genes were identified as complete, and 4.9% were identified as fragmented. Phylogenetic analysis based on single-copy gene families and one-to-one orthologous genes placed ramie with mulberry and cannabis, within the clade of urticalean rosids. Genome information of ramie will be a valuable resource for the conservation of endangered Boehmeria species and for future studies on the biogeography and characteristic evolution of members of Urticaceae.

Comparative transcriptomics of stem bark reveals genes associated with bast fiber development in Boehmeria nivea L. gaud (ramie)

“…The genome size of Zhongzhu No. 1 is approximately 340 Mb [3,4]. Therefore, the depth of the RNA-seq data used in this study is sufficient for a high quality de novo assembly of transcriptome for the expressed genes from the top bud and stem bark tissues.…”

“…These results suggest that a higher accumulation of active GAs in FER than in ER. We subsequently determined 10 types of GA molecules, including GA 1,3,4,7,9,15,19,20,24 and 53, in TB, ER and FER samples by LC-MS-MS. All the GAs but GA4 were detected in ramie samples. The active form GA7 had a very low concentration, while GA1 was the most abundant active GA. GA9 was the most abundant precursor.…”

“…Besides ramie, the well-known bast fiber crops include flax (Linum usitatissimum) and hemp (Cannabis sativa). By using genomic and transcriptomic analysis, significant progress has been made on bast fiber study in flax, hemp and ramie in recent years [1][2][3][4][5][6][7]. Through transcriptomic profiling, several secondary cell wall synthesis related proteins such as cellulose synthase, expansin and xyloglucan endotransglucosylase/hydrolase (XTH) were identified to be likely involved in fiber development in ramie [7].…”

Comparative transcriptomics of stem bark reveals genes associated with bast fiber development in Boehmeria nivea L. Gaud (ramie)

“…Besides ramie, the well-known bast fiber crops include flax (Linum usitatissimum) and hemp (Cannabis sativa). By using genomic and transcriptomic analysis, significant progress has been made on bast fiber study in flax, hemp and ramie in recent years [1][2][3][4][5][6][7]. Through transcriptomic profiling, several secondary cell wall synthesis related proteins such as cellulose synthase, expansin and xyloglucan endotransglucosylase/hydrolase (XTH) were identified to be likely involved in fiber development in ramie [7].…”

Analysis of BnMTL, a novel metallothionein‐like protein in the bast fiber crop Ramie (Boehmeria nivea)

“…Some wild genotypes were dominant in the smelter tailings, highlighting their hyperaccumulation properties. Ramie genome and genome‐wide expression profiles will aid the identification, quantification and annotation of key genes related to heavy metal tolerance. This will also be helpful for target discovery and pathway studies.…”