Comparative transcriptomics revealed enhanced light responses, energy transport and storage in domestication of cassava (Manihot esculenta)

Abstract

Cassava is a staple food, feed and bioenergy crop important to the world especially in the tropics. Domesticated cassava is characterized by powerful carbohydrate accumulation but its wild progenitor is not. Here, we investigated the transcriptional differences of eight cDNA libraries derived from developing leaf, stem and storage root of cassava cv. Arg7 and an ancestor line, W14, using next generation sequencing system. A total of 41302 assembled transcripts were obtained and from these, 25961 transcripts with FPKM≥3 in at least one library were named the expressed genes. A total of 2117, 1963 and 3584 transcripts were found to be differentially expressed in leaf, stem and storage root (150 d after planting), respectively, between Arg7 and W14 and ascribed to 103, 93 and 119 important pathways in leaf, stem and storage root, respectively. The highlight of this work is that the genes involved in light response, such as those for photosystem I (PSA) and photosystem II (PSB), other genes involved in light harvesting, and some of the genes in the Calvin cycle of carbon fixation were specially upregulated in leaf. Genes for transport and also for key rate-limiting enzymes (PFK, PGK and PK, GAPDH) coupling ATP consumption in glycolysis pathway were predominantly expressed in stem, and genes for sucrose degradation (INVs), amylose synthesis (GBSS) and hydrolysis (RCP1, AMYs), the three key steps of starch metabolism, and transport associated with energy translocation (ABC, AVPs and ATPase) and their upstream transcription factors had enhanced expression in storage root in domesticated cassava. Co-expression networks among the pathways in each organs revealed the relationship of the genes involved, and uncovered some of the important hub genes and transcription factors targeting genes for photosynthesis, transportation and starch biosynthesis.

Keywords

cassava / comparative transcriptomics / energy transport / photosynthesis / starch synthesis

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Acknowledgements

This work was supported by the National Natural Science Foundation of China (31261140363, 31171230), the National Basic Research and Development Program (2010CB126601), China Agriculture Research System (CARS-12wwq), and the Hainan Province Innovative Research Team Foundation (2016CXTD013).

Supplementary materials

The RNA-seq reads are deposited in the GenBank/SRR sequence read archive under the accession codes: SRR1298999, SRR1298998, SRR1298996, SRR1299008, SRR1299009, SRR1299005, SRR1299006 and SRR1299007. The online version of this article at http://dx.doi.org/10.15302/J-FASE-2016045 contains supplementary materials (Appendixes A–E).

Compliance with ethics guidelines

Zhiqiang Xia, Xin Chen, Cheng Lu, Meiling Zou, ShujuanWang, Yang Zhang, Kun Pan, Xincheng Zhou, Haiyan Wang, and Wenquan Wang declare that they have no conflict of interest or financial conflicts to disclose.

This article does not contain any studies with human or animal subjects performed by any of the authors.

RIGHTS & PERMISSIONS

The Author(s) 2016. Published by Higher Education Press. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0)