Abstract
BackgroundJute fiber, extracted from stem bast, is called golden fiber. It is essential for fiber improvement to discover the genes associated with jute development at the vegetative growth stage. However, only 858 EST sequences of jute were deposited in the GenBank database. Obviously, the public available data is far from sufficient to understand the molecular mechanism of the fiber biosynthesis. It is imperative to conduct transcriptomic sequence for jute, which can be used for the discovery of a number of new genes, especially genes involved in cellulose biosynthesis.ResultsA total of 79,754,600 clean reads (7.98 Gb) were generated using Illumina paired-end sequencing. De novo assembly yielded 48,914 unigenes with an average length of 903 bp. By sequence similarity searching for known proteins, 27,962 (57.16 %) unigenes were annotated for their function. Out of these annotated unigenes, 21,856 and 11,190 unigenes were assigned to gene ontology (GO) and euKaryotic Ortholog Groups (KOG), respectively. Searching against the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG) indicated that 14,216 unigenes were mapped to 268 KEGG pathways. Moreover, 5 Susy, 3 UGPase, 9 CesA, 18 CSL, 2 Kor (Korrigan), and 12 Cobra unigenes involving in cellulose biosynthesis were identified. Among these unigenes, the unigenes of comp11264_c0 (SuSy), comp24568_c0 (UGPase), comp11363_c0 (CesA), comp11363_c1 (CesA), comp24217_c0 (CesA), and comp23531_c0 (CesA), displayed relatively high expression level in stem bast using FPKM and RT-qPCR, indicating that they may have potential value of dissecting mechanism on cellulose biosynthesis in jute. In addition, a total of 12,518 putative gene-associate SNPs were called from these assembled uingenes.ConclusionWe characterized the transcriptome of jute, discovered a broad survey of unigenes associated with vegetative growth and development, developed large-scale SNPs, and analyzed the expression patterns of genes involved in cellulose biosynthesis for bast fiber. All these provides a valuable genomics resource, which will accelerate the understanding of the mechanism of fiber development in jute.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2256-z) contains supplementary material, which is available to authorized users.
Highlights
Jute fiber, extracted from stem bast, is called golden fiber
De novo assembly of 48,914 unigenes based on transcriptome sequence of jute Recently, to accelerate the research of functional genomics and mine the genes involved in important agricultural traits, transcriptomic sequences of some minor crops have been characterized with next generation sequencing (NGS) [4,5,6,7,8,9,10,11]
The RNA of this study isolated from different tissues of leaves, roots, stem bast, and stem stick at a vigorous vegetative stage; while the RNA of Chakraborty et al [8] extracted from the bast fiber tissues excluding the inner core tissues
Summary
Jute fiber, extracted from stem bast, is called golden fiber. Jute fiber is second to cotton in its importance of natural fiber production in the world, which belongs to a member of the Corchorus genus in the Tiliaceae family. Jute fiber is a bast fiber and isolated from the stem. White jute (C. capsularis) and dark jute (C. olitorius) are cultivated as crops and both are diploid species (2n = 14). Kundu et al [2] recently reported that the two cultivated species of jute originated in Africa using nuclear and chloroplast simple sequence repeats (SSRs) or microsatellites. As one of the most important crops for natural fiber production, jute is mainly distributed in Bangladesh, India, China and east-central Africa.
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