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

doi:10.15302/J-FASE-2016126

Front. Agr. Sci. Eng.

2016, Vol. 3

Issue (4) : 295-307 https://doi.org/10.15302/J-FASE-2016126

RESEARCH ARTICLE

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

Zhiqiang XIA^1,²,Xin CHEN^1,²,Cheng LU^1,²,Meiling ZOU^1,²,Shujuan WANG^1,²,Yang ZHANG^1,²,Kun PAN^1,²,Xincheng ZHOU^1,²,Haiyan WANG^1,²,Wenquan WANG^1,²(

)

¹. The Institute of Tropical Bioscience and Biotechnology (ITBB), Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China
². Key Laboratory of Biology and Genetic Resources for Tropical Crops, Ministry of Agriculture, Haikou 571101, China

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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

Corresponding Author(s): Wenquan WANG

Just Accepted Date: 26 December 2016 Online First Date: 17 January 2017 Issue Date: 22 January 2017

Cite this article:

Zhiqiang XIA,Xin CHEN,Cheng LU, et al. Comparative transcriptomics revealed enhanced light responses, energy transport and storage in domestication of cassava (Manihot esculenta)[J]. Front. Agr. Sci. Eng. , 2016, 3(4): 295-307.

URL:

https://academic.hep.com.cn/fase/EN/10.15302/J-FASE-2016126
https://academic.hep.com.cn/fase/EN/Y2016/V3/I4/295

Tab.1 Summary transcripts from eight developing organs of Arg7 (Manihot esculenta ssp. flabellifolia) and W14 (M. esculenta ssp. esculenta)

Fig.1 Gene Ontology (GO) assignments for the transcriptome in leaves and storage roots of Arg7 and W14. Summarized are the enriched genes in three main GO categories: biological process, cellular component, and molecular function. The left y-axis indicates the percentage of a specific category of genes in each main category. The right y-axis indicates the number of genes in the same category.

Fig.2 Number of genes expressed differentially in leaves, stems, and storage roots between Arg7 and W14. (a–c) Distribution of the genes expressed differentially in leaf, stem, and storage root between Arg7 and W14; AR90, AR150, and AR210 refer to Arg7 storage roots at three growth stages compared with WR150; (d) the numbers of species-specific genes and genes shared between Arg7 compared to W14.

Fig.3 Genes predominantly expressed in light reactions, Calvin cycle but not in photorespiration pathways in leave of cultivated Arg7 compared to n wild W14. Colored rectangles correspond to the value of log2 (the FPKM of WL/AL): blue means that a gene expressed folds in Arg7 compared to W14, but red is converse.

Fig.4 Validation of expression level of part of genes in leaves of cassava plant, as ATPase III, Rubisco small subunit, and PEPCase by RT-PCR, the expression level 148-, 68- to 3-fold in Arg7 compared to W14

Fig.5 Genes involved in transport predominantly expressed in developing stems of cultivated Arg7 compared to W14. Colored rectangles correspond to the value of log2 (the FPKM of WS/AS): blue means that a gene expressed folds in W14 compared to Arg7, but red is converse.

Fig.6 Genes for sucrose degradation mostly expressed in developing stems of cultivated Arg7 compared to W14. Colored rectangles correspond to the value of log2 (the FPKM of WS/AS): blue means that a gene expressed folds in W14 compared to Arg7, but red is converse.

Fig.7 Confirmation of the high expression of GBSS and SBE2.2 genes in the storage roots of Arg7 compared to W14 by RT-PCR. The GBSS and SBE2.2 6- to 12-folds expressed in Arg7 compared to W14 respectively.

Fig.8 Differentially expressed genes in the pathways of sucrose and starch metabolism with three development stage of storage root. Colored rectangles correspond to the value of log2 (the FPKM of a gene in W14/that in Arg7): blue means that a gene expressed folds in W14 compared to Arg7, whereas red is converse

Fig.9 Genes involved in transport predominantly expressed in storage roots of cultivated Arg7 compared to W14. Colored rectangles correspond to the value of log2 (the FPKM of WR150/AR150): blue means that a gene expressed folds in W14 compared to Arg7, but red is converse.

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