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.
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Acknowledgments
This research was supported by the National Natural Science Foundation of China (31200514, 31270651 and 30960310), Fundamental Research Funds for Rubber Research Institute, CATAS (1630022015003), and National Program on Key Basic Research Project of China (2012CB723005). We would like to thank Beijing Genomics Institute (Shenzhen) for assistance with the raw data processing and bioinformatics analyses.
Data Archiving Statement
The assembled sequences and sequence reads were separately submitted to the NCBI Transcriptome Shotgun Assembly (TSA) and Sequence Read Archive (SRA) database, and the accession numbers of TSA and SRA were GBHP00000000 and SRP044081, respectively.
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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.
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Li, D., Hao, L., Liu, H. et al. Next-generation sequencing, assembly, and comparative analyses of the latex transcriptomes from two elite Hevea brasiliensis varieties. Tree Genetics & Genomes 11, 98 (2015). https://doi.org/10.1007/s11295-015-0928-0
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DOI: https://doi.org/10.1007/s11295-015-0928-0