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Mol Ecol Resour. 2018 May;18(3):639-645. doi: 10.1111/1755-0998.12766. Epub 2018 Mar 8.

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

Author information

1
Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-Fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Changsha, China.
2
BGI Genomics, BGI-Shenzhen, Shenzhen, China.

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.

KEYWORDS:

de novo assembly; evolution; genome sequence; highly heterozygous genome; ramie

PMID:
29423997
DOI:
10.1111/1755-0998.12766
[Indexed for MEDLINE]

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