Transcriptome Assembly of the Bast Fiber Crop, Ramie, Boehmeria nivea (L.) Gaud. (Urticaceae)

Abstract

Ramie (Boehmeria nivea) is a perennial crop valued for its strong bast fibers. Unlike other major bast fiber crops, ramie fiber processing does not include retting, but does require degumming, suggesting distinctive features in pectin and the development and composition of fibers. A comprehensive transcriptome assembly of ramie has not been made available, to date. We obtained the sequence of RNA transcripts (RNA Seq) from the apical region of developing ramie stems and combined these with reads from public databases for a total of 157,621,051 paired-end reads (30.3 billion base pairs Gbp) used as input for de novo assembly, resulting in 70,721 scaffolds (≥200 base pairs (bp); N 50 = 1798 bp). As evidence of the quality of the assembly, 36,535 scaffolds aligned to at least one Arabidopsis protein (BLASTP e-value ≤ 10 −10 ). The resource described here for B. nivea will facilitate an improved understanding of bast fibers, cell wall, and middle lamella development in this and other comparative species.

A genomic resource derived from the integration of genome sequences, expressed transcripts and genetic markers in ramie

“…In this study, PacBio transcriptome sequencing resulted in the identification of 30,591 transcripts in ramie, with an average length of 2629 bp, and 91.1% of the transcripts were functionally annotated. Obviously, this was a significant improvement in both transcript length and the number of annotated transcripts as compared with previous studies [3, 5–15]. In addition, 72.0 and 91.0% of the transcripts had 5′ UTR and 3′ UTR sequences, respectively, which was far higher than in previous studies [7].…”

“…The ramie transcriptome has been characterized in many previous studies, which have remarkably improved our knowledge about the growth and development of this crop [3, 5–15]. However, although a large number of transcripts were identified, in these studies, they were not always suitable for use in further research.. First, all the assembled transcriptomes were of low quality.…”

“…In model plants, these genetic and genomic resources are generally integrated into a platform, which makes them easier to use in basic and applied research [26, 27]. However, in ramie, although the complete genomic sequence has been obtained [21, 22] and large numbers of expressed sequences and SSRs have been identified from the transcriptome [3, 5–15], these resources are still difficult for researchers to use owing to the absence of positional connections among these resources. Taking a study on QTL cloning as an example, although a QTL was mapped into an interval flanked by two SSRs, the genomic sequences of this QTL region were unavailable because the positions of the SSRs were unknown in the genome.…”

“…Because of the significant economic importance of ramie, its agronomic traits have been widely targeted for genetic and molecular studies. To understand the expression profiling of ramie and identify important genes, the transcriptome of this crop has been de novo assembled in many studies [3, 5–15], resulting in the identification of millions of expressed transcripts. In addition, to characterize the genetic basis of traits, a total of 1827 and 2431 simple sequence repeat markers (SSRs) were developed in two previous studies [16, 17].…”

“…Although plentiful genetic and genomic resources have been obtained from ramie, these resources are still inconvenient for researchers to use because there is considerable redundancy. Two sets of ramie SSRs were developed from the transcriptome by two independent studies [16, 17], causing potential redundancy of markers; undoubtedly, there were large numbers of redundant sequences among the transcripts identified from these transcriptomes [3, 5–15]. Furthermore, the absence of positional connections among the genome sequences, expressed transcripts, and molecular markers made them difficult to apply to other studies.…”