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An ordered EST catalogue and gene expression profiles of cassava (Manihot esculenta) at key growth stages

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Abstract

A cDNA library was constructed from the root tissues of cassava variety Huanan 124 at the root bulking stage. A total of 9,600 cDNA clones from the library were sequenced with single-pass from the 5′-terminus to establish a catalogue of expressed sequence tags (ESTs). Assembly of the resulting EST sequences resulted in 2,878 putative unigenes. Blastn analysis showed that 62.6% of the unigenes matched with known cassava ESTs and the rest had no ‘hits’ against the cassava database in the integrative PlantGDB database. Blastx analysis showed that 1,715 (59.59%) of the unigenes matched with one or more GenBank protein entries and 1,163 (40.41%) had no ‘hits’. A cDNA microarray with 2,878 unigenes was developed and used to analyze gene expression profiling of Huanan 124 at key growth stages including seedling, formation of root system, root bulking, and starch maturity. Array data analysis revealed that (1) the higher ratio of up-regulated ribosome-related genes was accompanied by a high ratio of up-regulated ubiquitin, proteasome-related and protease genes in cassava roots; (2) starch formation and degradation simultaneously occur at the early stages of root development but starch degradation is declined partially due to decrease in UDP-glucose dehydrogenase activity with root maturity; (3) starch may also be synthesized in situ in roots; (4) starch synthesis, translocation, and accumulation are also associated probably with signaling pathways that parallel Wnt, LAM, TCS and ErbB signaling pathways in animals; (5) constitutive expression of stress-responsive genes may be due to the adaptation of cassava to harsh environments during long-term evolution.

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Abbreviations

ADPGPase:

ADP glucose pyrophosphorylase

Ar.:

Arachis

DAP:

Days after planting

dbEST:

Database of EST

ErbB:

Epidermal growth factor family of receptor tyrosine kinase

EST:

Expressed sequence tag

GBSS:

Granule-bound SS

GO:

Gene ontology

Hy.:

Hyacinthus

JAK-STAT:

Janus kinase-signal transducer and activator of transcription

KEGG:

Kyoto encyclopedia of genes and genomes

LAM:

Linoleic acid metabolism

ln:

Natural logarithm

MAPK:

Mitogen-activated protein kinase

Mer.:

Mercurialis

mTOR:

Mammalian target of rapamycin

nARVOL:

Normalized AR volume

Pis.:

Pisum

qRT-PCR:

Quantitative real-time PCR

rpm:

Revolutions per minute

SBE:

Starch branching enzyme

Sp.:

Spinacia

SS:

Starch synthase

sV:

Subtracted value

TCS:

Two-component system

TGF beta:

Transforming growth factor beta

VEGF:

Vascular endothelial growth factor

Wnt:

Wingless

YT:

Yeast trypton

Z.:

Zea

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Acknowledgments

This work was supported by The Pilot Project of the China National Key Program for Fundamental Research (2004CCA00600) and The Project of the China National Key Program for Fundamental Research (2010CB126601).

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Authors and Affiliations

  1. Guangxi Key Laboratory of Subtropical Bioresource Conservation and Utilization, College of Life Science and Technology, Guangxi University, 530004, Nanning, Guangxi, People’s Republic of China

    You-Zhi Li, Chang-Bin Sun, Zhi-Qiang Wang, Ji-Liang Tang & Baoshan Chen

  2. Agricultural College, Guangxi University, 530004, Nanning, Guangxi, People’s Republic of China

    Ying-Hua Pan & Xing-Lu Luo

  3. Institute of Biotechnology, Zhejiang University, 310029, Hangzhou, Zhejiang, People’s Republic of China

    Hai-Tao Dong

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  1. You-Zhi Li
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Corresponding authors

Correspondence to Ji-Liang Tang or Baoshan Chen.

Additional information

DNA sequences of all ESTs used in this study have been deposited at http://www.ncbi.nlm.nih.gov/dbEST with accession number from FG804688 to FG807563.

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Li, YZ., Pan, YH., Sun, CB. et al. An ordered EST catalogue and gene expression profiles of cassava (Manihot esculenta) at key growth stages. Plant Mol Biol 74, 573–590 (2010). https://doi.org/10.1007/s11103-010-9698-0

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