黄麻（Corchorus capsularis L.）中参与纤维素生物合成的主要韧皮部相关基因的从头转录组测序与鉴定。
De novo transcriptome sequence and identification of major bast-related genes involved in cellulose biosynthesis in jute (Corchorus capsularis L.).
作者信息
Zhang Liwu, Ming Ray, Zhang Jisen, Tao Aifen, Fang Pingping, Qi Jianmin
机构信息
Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education / College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
Department of Plant Biology, University of Illlinois at Urbana-Champaign, Urbana, IL, 61801, USA.
出版信息
BMC Genomics. 2015 Dec 15;16:1062. doi: 10.1186/s12864-015-2256-z.
BACKGROUND
Jute 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.
RESULTS
A 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.
CONCLUSION
We 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.
背景
从茎皮中提取的黄麻纤维被称为金色纤维。在营养生长阶段发现与黄麻发育相关的基因对于纤维改良至关重要。然而，在GenBank数据库中仅存入了858条黄麻的EST序列。显然，公开可用的数据远远不足以理解纤维生物合成的分子机制。对黄麻进行转录组测序势在必行，这可用于发现许多新基因，尤其是参与纤维素生物合成的基因。
结果
使用Illumina双末端测序共产生了79,754,600条clean reads（7.98 Gb）。从头组装产生了48,914个单基因，平均长度为903 bp。通过对已知蛋白质进行序列相似性搜索，27,962个（57.16%）单基因被注释了功能。在这些注释的单基因中，分别有21,856个和11,190个单基因被分配到基因本体论（GO）和真核直系同源组（KOG）。与京都基因与基因组百科全书通路数据库（KEGG）进行比对表明，14,216个单基因被映射到268条KEGG通路。此外，鉴定出了5个Susy、3个UGPase、9个CesA、18个CSL、2个Kor（Korrigan）和12个Cobra参与纤维素生物合成的单基因。在这些单基因中，comp11264_c0（SuSy）、comp24568_c0（UGPase）、comp11363_c0（CesA）、comp11363_c1（CesA）、comp24217_c0（CesA）和comp23531_c0（CesA）的单基因在茎皮中使用FPKM和RT-qPCR显示出相对较高的表达水平，表明它们可能具有剖析黄麻纤维素生物合成机制的潜在价值。此外，从这些组装的单基因中共鉴定出12,518个推定的基因关联SNP。
结论
我们对黄麻的转录组进行了表征，发现了与营养生长和发育相关的大量单基因，开发了大规模SNP，并分析了韧皮纤维中参与纤维素生物合成的基因的表达模式。所有这些都提供了宝贵的基因组资源，这将加速对黄麻纤维发育机制的理解。
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