Transcriptome Analysis of Dendrobium officinale and its Application to the Identification of Genes Associated with Polysaccharide Synthesis

被引：86

作者：

Zhang, Jianxia ^{[1
]}

He, Chunmei ^{[1
]}

Wu, Kunlin ^{[1
]}

Teixeira da Silva, Jaime A.

Zeng, Songjun ^{[1
]}

Zhang, Xinhua ^{[1
]}

Yu, Zhenming ^{[1
]}

Xia, Haoqiang ^{[2
]}

Duan, Jun ^{[1
]}

机构：

[1] Chinese Acad Sci, Key Lab South China Agr Plant Mol Anal & Gene Imp, South China Bot Garden, Guangzhou, Guangdong, Peoples R China

[2] Guangzhou Genedenovo Biotechnol Co Ltd, Guangzhou, Guangdong, Peoples R China

来源：

FRONTIERS IN PLANT SCIENCE | 2016年 / 7卷

基金：

美国国家科学基金会;

关键词：

D; officinale; glycosyltransferase; secondary metabolism; polysaccharide synthesis; transcriptome; SYNTHASE-LIKE GENES; ALKALOID BIOSYNTHESIS; EXPRESSION; REGULATOR; BARLEY; (1,3/1,4)-BETA-D-GLUCAN; METABOLISM; REVEALS; CELLS; STEMS;

D O I：

10.3389/fpls.2016.00005

中图分类号：

Q94 [植物学];

学科分类号：

071001 ;

摘要：

Dendrobiurn officinale is one of the most important Chinese medicinal herbs. Polysaccharides are one of the main active ingredients of D. officinale. To identify the genes that maybe related to polysaccharides synthesis, two cDNA libraries were prepared from juvenile and adult D. officinale, and were named Dendrobium-1 and Dendrobium-2, respectively. Illumina sequencing for Dendrobium-1 generated 102 million high quality reads that were assembled into 93,881 unigenes with an average sequence length of 790 base pairs. The sequencing for Dendrobium-2 generated 86 million reads that were assembled into 114,098 unigenes with an average sequence length of 695 base pairs. Two transcriptome databases were integrated and assembled into a total of 145,791 unigenes. Among them, 17,281 unigenes were assigned to 126 KEGG pathways while 135 unigenes were involved in fructose and mannose metabolism. Gene Ontology analysis revealed that the majority of genes were associated with metabolic and cellular processes. Furthermore, 430 glycosyltransferase and 89 cellulose synthase genes were identified. Comparative analysis of both transcriptome databases revealed a total of 32,794 differential expression genes (DEGs), including 22,051 up-regulated and 10,743 down-regulated genes in Dendrobium-2 compared to Dendrobium-1. Furthermore, a total of 1142 and 7918 unigenes showed unique expression in Dendrobium-1 and Dendrobium-2, respectively. These DEGs were mainly correlated with metabolic pathways and the biosynthesis of secondary metabolites. In addition, 170 DEGs belonged to glycosyltransferase genes, 37 DEGs were related to cellulose synthase genes and 627 DEGs encoded transcription factors. This study substantially expands the transcriptome information for D. officinale and provides valuable clues for identifying candidate genes involved in polysaccharide biosynthesis and elucidating the mechanism of polysaccharide biosynthesis.

引用

页数：14

共 48 条

[1] Glucomannan, a promising polysaccharide for biopharmaceutical purposes [J].

Alonso-Sande, M. ;

Teijeiro-Osorio, D. ;

Remunan-Lopez, C. ;

Alonso, M. J. .

EUROPEAN JOURNAL OF PHARMACEUTICS AND BIOPHARMACEUTICS, 2009, 72 (02) :453-462

[2] The significance of digital gene expression profiles [J].

Audic, S ;

Claverie, JM .

GENOME RESEARCH, 1997, 7 (10) :986-995

[3] MYB75 Functions in Regulation of Secondary Cell Wall Formation in the Arabidopsis Inflorescence Stem [J].

Bhargava, Apurva ;

Mansfield, Shawn D. ;

Hall, Hardy C. ;

Douglas, Carl J. ;

Ellis, Brian E. .

PLANT PHYSIOLOGY, 2010, 154 (03) :1428-1438

[4] Activation tagging identifies a conserved MYB regulator of phenylpropanoid biosynthesis [J].

Borevitz, JO ;

Xia, YJ ;

Blount, J ;

Dixon, RA ;

Lamb, C .

PLANT CELL, 2000, 12 (12) :2383-2393

[5] Over-expression of specific HvCslF cellulose synthase-like genes in transgenic barley increases the levels of cell wall (1,3;1,4)-β-D-glucans and alters their fine structure [J].

Burton, Rachel A. ;

Collins, Helen M. ;

Kibble, Natalie A. J. ;

Smith, Jessica A. ;

Shirley, Neil J. ;

Jobling, Stephen A. ;

Henderson, Marilyn ;

Singh, Rohan R. ;

Pettolino, Filomena ;

Wilson, Sarah M. ;

Bird, Anthony R. ;

Topping, David L. ;

Bacic, Antony ;

Fincher, Geoffrey B. .

PLANT BIOTECHNOLOGY JOURNAL, 2011, 9 (02) :117-135

[6] A gene from the cellulose synthase-like C family encodes a β-1,4 glucan synthase [J].

Cocuron, Jean-Christophe ;

Lerouxel, Olivier ;

Drakakaki, Georgia ;

Alonso, Ana P. ;

Liepman, Aaron H. ;

Keegstra, Kenneth ;

Raikhel, Natasha ;

Wilkerson, Curtis G. .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2007, 104 (20) :8550-8555

[7] Blast2GO:: a universal tool for annotation, visualization and analysis in functional genomics research [J].

Conesa, A ;

Götz, S ;

García-Gómez, JM ;

Terol, J ;

Talón, M ;

Robles, M .

BIOINFORMATICS, 2005, 21 (18) :3674-3676

[8] Composition analysis and antioxidant activity of polysaccharide from Dendrobium denneanum [J].

Fan, Yijun ;

He, XingJin ;

Zhou, Songdong ;

Luo, Aoxue ;

He, Tao ;

Chun, Ze .

INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES, 2009, 45 (02) :169-173

[9] Full-length transcriptome assembly from RNA-Seq data without a reference genome [J].

Grabherr, Manfred G. ;

Haas, Brian J. ;

Yassour, Moran ;

Levin, Joshua Z. ;

Thompson, Dawn A. ;

Amit, Ido ;

Adiconis, Xian ;

Fan, Lin ;

Raychowdhury, Raktima ;

Zeng, Qiandong ;

Chen, Zehua ;

Mauceli, Evan ;

Hacohen, Nir ;

Gnirke, Andreas ;

Rhind, Nicholas ;

di Palma, Federica ;

Birren, Bruce W. ;

Nusbaum, Chad ;

Lindblad-Toh, Kerstin ;

Friedman, Nir ;

Regev, Aviv .

NATURE BIOTECHNOLOGY, 2011, 29 (07) :644-U130

[10] Engineering secondary metabolism in maize cells by ectopic expression of transcription factors [J].

Grotewold, E ;

Chamberlin, M ;

Snook, M ;

Siame, B ;

Butler, L ;

Swenson, J ;

Maddock, S ;

Clair, GS ;

Bowen, B .

PLANT CELL, 1998, 10 (05) :721-740

← 1 2 3 4 5 →