Next-generation sequencing, assembly, and comparative analyses of the latex transcriptomes from two elite Hevea brasiliensis varietiesby Dejun Li, Lili Hao, Hui Liu, Manman Zhao, Zhi Deng, Yu Li, Rizhong Zeng, Weimin Tian

Tree Genetics & Genomes

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Year
2015
DOI
10.1007/s11295-015-0928-0
Subject
Forestry / Genetics / Molecular Biology / Horticulture

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ORIGINAL ARTICLE

Next-generation sequencing, assembly, and comparative analyses of the latex transcriptomes from two elite Hevea brasiliensis varieties

Dejun Li1 & Lili Hao2 & Hui Liu1 & Manman Zhao1,3 &

Zhi Deng1 & Yu Li1 & Rizhong Zeng1 & Weimin Tian1

Received: 21 November 2014 /Revised: 21 July 2015 /Accepted: 1 September 2015 # Springer-Verlag Berlin Heidelberg 2015

Abstract The great progress has been made in rubber tree breeding, but the molecular mechanisms underlying high yield are not well understood. Here, we reported the sequencing, assembly, and comparative analyses of latex transcriptome from two rubber tree varieties. In total, 33,852 unigenes were generated with de novo assembly. The blastx results indicated that 27,886 and 15,704 unigenes showed significant similarities to known proteins from NCBI nr and

Swissprot databases, respectively. Among these annotated unigenes, 21,841 and 9010 ones were separately assigned to

Gene Ontology (GO) functional categories and Clusters of

Orthologous Groups (COGs). Of 126 KEGG pathways, metabolic pathway was the biggest one, suggesting that active metabolic processes happen in rubber tree latex. In contrast to RRIM 600, 2513 and 1391 genes were separately up- and downregulated in RY 7-20-59. The expression profiles of 25 unigenes were further confirmed by real-time RT-PCR, suggesting that the differently expressed genes (DEGs) identified by RNA-seq were accurate and reliable in this study. The

DEGs between RRIM 600 and RY 7-20-59 were significantly enriched in plant-pathogen interactions, phenylpropanoid biosynthesis, phenylalanine metabolism, ubiquinone and other terpenoid-quinone biosynthesis, biosynthesis of secondary metabolites, and photosynthesis. Interestingly, the genes involved in rubber biosynthesis pathway, such as CPT, GPPS,

HMGR, HMGS, FPPS and DXS, were differently expressed between RRIM 600 and RY 7-20-59. It was the first time that the latex transcriptomes of two rubber tree varieties have been compared and analyzed on a transcriptome-wide scale. Our results not only enrich the transcriptome data of rubber tree but also provide new insights into understanding latex transcriptome and molecular mechanisms underlying high yielding in rubber tree.

Keywords Expression analysis . Latex transcriptome .

Next-generation sequencing . High yielding . Rubber biosynthesis . Rubber tree

Introduction

Natural rubber (NR) is an important raw material, and it is used for more than 40,000 products and cannot be replaced by synthetic alternatives due to its unique properties including resilience, elasticity, impact and abrasion resistance, efficient heat dispersion, and malleability at cold temperatures (Cataldo 2000; Cornish 2001). Hevea brasiliensis (rubber tree) is the only species cultivated commercially for harvesting NR. With the rapid development of the world economy, NR yields need to be increased to meet the market demands. Great progress has been made in rubber tree breeding, which resulted in a

Communicated by J. L. Wegrzyn

This article is part of the Topical Collection on Gene Expression

Dejun Li and Lili Hao contributed equally to this work.

Electronic supplementary material The online version of this article (doi:10.1007/s11295-015-0928-0) contains supplementary material, which is available to authorized users. * Dejun Li djli.rricatas@gmail.com 1 Key Laboratory of Biology and Genetic Resources of Rubber Tree,

Ministry of Agriculture, Rubber Research Institute, Chinese

Academy of Tropical Agricultural Sciences, Danzhou 571737, China 2 CAS Key Laboratory of Genome Sciences and Information, Beijing

Institute of Genomics, Chinese Academy of Sciences,

Beijing 100101, China 3 College of Horticulture & Forestry Sciences, Huazhong Agricultural

University, Wuhan 430070, China

Tree Genetics & Genomes (2015) 11:98

DOI 10.1007/s11295-015-0928-0 gradual increase in NR yields from 650 kg/ha in unselected seedlings to 1600 kg/ha in optimized varieties. Some elite rubber tree varieties, such as RRIM 501, RRIM 600, RRIM 712, PB 217, PB 235, PB 260, RRII 105, RRIC 100, IRCA 18, IRCA 230, IRCA 331, BPM 24, IAC 35, and IAC 40, were bred and planted (Priyadarshan et al. 2009). China belongs to nontraditional rubber growing areas, where rubber tree is often subjected to serious damage caused by typhoons and cold snaps (Huang and Pan 1992). Therefore, the NR yield in China is normally lower than in traditional rubbergrowing areas. Following multiple successive breeding programs, several rubber tree varieties including RY 7-20-59, RY 7-33-97, and RY 8–79 have been successfully bred and cultivated in China (Huang 2005).

In contrast to the progress made in rubber tree breeding, the molecular mechanisms underlying high yield are not well understood. NR consists of high molecular weight cis-polyisoprene (rubber), which is produced via the isoprenoid pathway (Chappell 1995). Furthermore, the rubber biosynthesis (RB) pathway has been elucidated in the rubber tree (d’Auzac et al. 1997), and the genes involved in this pathway have been identified (Sando et al. 2008; Xia et al. 2011; Li et al. 2012). Some genes, such as cis-prenyltransferase (CPT), rubber elongation factor (REF), small rubber particle protein (SRPP), and hydroxymethylglutaryl coenzymeA reductase (HMGR), have been cloned and further characterized (Hepper and Audley 1969; Dennis and Light 1989; Chye et al. 1992; Oh et al. 1999; Asawatreratanakul et al. 2003; Priya et al. 2007; Post et al. 2012). The cytosolic mevalonate (MVA) pathway is a conventionally accepted pathway providing isopentenyl diphosphate (IPP) for rubber biosynthesis. Recently, Chow et al. (2012) reported that the plastidic 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway might be an alternative source of

IPP in rubber tree. By analyzing differentially expressed transcript-derived fragments between PR 107 and a superhigh-yield PR 107 variety (SY 107), Tang et al. (2013) suggested that the molecular basis for super-high yields in SY 107 might result from an improved sucrose loading capability, rubber biosynthesis-preferred sugar utilization, enhanced general metabolism, and timely stress alleviation. It is important for rubber tree researchers to study the molecular mechanisms underlying high yield. Once the molecular mechanisms are well elucidated, high-yield varieties can be generated via transgenic technology in rubber tree.