Whole transcriptome profiling of bast fibers of ramie

Ramie fibers extracted from the stem barks have been utilized for thousands years in China, and its biosynthetic mechanism is poorly understood. Here, we have characterized and compared the expression profiling of the barks from the top and middle part of stem where the secondary cellular walls (SCWs) of fiber cell have not initiated growth and was thickening, respectively; resulting in 4,520 differential expression (DE) protein-coding transcripts (PCTs), 1,287 DE long noncoding RNAs (lncRNAs), 88 DE miRNAs and 78 DE circular RNAs (circRNAs). Among the 4,520 DE PCTs, 75 were identified to be the homolog of the Arabidopsis SCW-biosynthetic genes. Overexpression of whole_GLEAN_10014861 (a homolog of SND1) in Arabidopsis caused a significant up-regulation in the expression of AtMYB46 and AtMYB83 that are two key regulators for SCW biosynthesis, thus conferring more fiber cells, along with a remarkable thickening in the SCWs of these cells. Bioinformatic prediction revealed 14 of the 75 homolog targeted by 16 noncoding RNAs (including 8 miRNAs and 8 lncRNAs), and two involved in the competing endogenous RNAs networks, indicating a complex regulatory network for the SCW biosynthesis of bast fiber in ramie. This study provides important insights into the bast fiber biosynthesis of ramie. Overall design: Experimental material, tissue sampling and RNA isolation: Elite cultivar Zhongzhu 1 was planted in the experimental farm of the Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Yuanjiang, China in June 2016. The TPS and MPS barks were separately collected from five individuals of Zhongzhu 1, immediately frozen in liquid nitrogen. Three replicates were sampled for TPS and MPS barks, respectively. Total RNA of this sample was extracted using an E.Z.N.A. Plant RNA Kit (OMEGA Bio-Tek, Norcross, GA, USA) according to the manufacturer's protocol. Libraries construction and sequencing: Total RNAs from six samples were used separately to construct the small RNAs, circRNAs and cDNA libraries, respectively. The small RNAs sequencing was performed using BGISEQ-500 platform (BGI, Shenzhen, China), and circRNAs and transcriptome were sequenced using the Illumina sequencing platform (HiSeq™ 2500; Illumina, San Diego, CA), according to the manufacturer's instructions of corresponding platform. Thereafter, the raw reads for each sample were filtered, generating clean reads used in next analysis.