Back to Search
Start Over
Draft genome sequence of ramie, Boehmeria nivea (L.) Gaudich
- Source :
- Molecular ecology resources. 18(3)
- Publication Year :
- 2017
-
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.
- Subjects :
- 0106 biological sciences
0301 basic medicine
Sequence assembly
Biology
01 natural sciences
Genome
DNA sequencing
Ramie
03 medical and health sciences
Genetics
Urticaceae
Ecology, Evolution, Behavior and Systematics
Phylogeny
Gene Library
Whole genome sequencing
Shotgun sequencing
Molecular Sequence Annotation
Sequence Analysis, DNA
biology.organism_classification
Boehmeria
Phylogeography
030104 developmental biology
Genome, Plant
010606 plant biology & botany
Biotechnology
Subjects
Details
- ISSN :
- 17550998
- Volume :
- 18
- Issue :
- 3
- Database :
- OpenAIRE
- Journal :
- Molecular ecology resources
- Accession number :
- edsair.doi.dedup.....c2358f9a3742c32aba9558ce5532eb98