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Generation and analysis of expressed sequence tags from a normalized cDNA library of young leaf from Ma bamboo (Dendrocalamus latiflorus Munro)

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Abstract

Ma bamboo (Dendrocalamus latiflorus Munro) belongs to Dendrocalamus genus, Bambusease tribe, Bambusoideae subfamily, Poaceae family. It is a representative species of clumping bamboo, and a principal commercial species for various construction purposes using mature culms and for human consumption using young shoots. A normalized cDNA library was constructed from young leaves of Ma bamboo and 9,574 high-quality ESTs were generated, from which 5,317 unigenes including 1,502 contigs and 3,815 singletons were assembled. The unigenes were assigned into different gene ontology (GO) categories and summarized into 13 broad biologically functional groups according to similar functional characteristics or cellular roles by BLAST search against public databases. Eight hundred and ninety-one unigenes were assigned by KO identifiers and mapped to six KEGG biochemical pathways. The transcripts involved in biosynthesis of secondary metabolites such as cytochrome 450, flavonol synthase/flavanone 3-hydroxylase, and dihydroflavonol-4-reductase were well represented by 14 unigenes in the unigene set. The candidate genes involved in phytohormone metabolism, signal transduction and encoding cell wall-associated receptor kinases were also identified. Sixty-seven unigenes related to plant resistance (R) genes, including RPP genes, RGAs and RDL/RF genes, were discovered. These results will provide genome-wide knowledge about the molecular physiology of Ma bamboo young leaves and tools for advanced studies of molecular mechanism underlying leaf growth and development.

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Abbreviations

AGL:

Agamous like

BLAST:

Basic local alignment search tool

CAP3:

Sequence assembly program 3

cDNA:

Complementary deoxyribonucleic acid

CYP450:

Cytochrome P450-dependent monooxygenase

ESTs:

Expressed sequence tags

GA:

Gibberellin

GO:

Gene ontology

KEGG:

Kyoto Encyclopedia of Genes and Genomes

MADS:

Initial letter of MCM1

Agamous:

Deficiens and SRF

NCBI:

National Center for Biotechnology Information

PCR:

Polymerase chain reaction

RPP:

Recognition of Phytophthora parasitica

RGA:

Resistance gene analogs

RDL/RF:

Resistance to dieldrin/resistant factor

RPM:

Resistance to Pseudomonas syringae pv. maculicola

SSRs:

Simple sequence repeats

TIGR:

The Institute of Genomic Research Database

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Acknowledgments

This work was supported by the Special Funds for Scientific Research on Forestry Public Causes of the State Forestry Administration of the People’s Republic of China (Grant No. 201004005) and the National Science Foundation of China (Grant No. 30972328). The authors thank Dr. Hongbin Zhang from Texas A&M University, USA, for his kind help on the correction of the manuscript.

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Authors and Affiliations

  1. International Center for Bamboo and Rattan, State Forestry Administration Key Open Laboratory on Bamboo and Rattan Science and Technology, Beijing, 100102, People’s Republic of China

    Z. M. Gao, C. L. Li & Z. H. Peng

  2. Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, People’s Republic of China

    Z. H. Peng

Authors
  1. Z. M. Gao
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  2. C. L. Li
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  3. Z. H. Peng
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Corresponding authors

Correspondence to Z. M. Gao or Z. H. Peng.

Additional information

Communicated by B. Li.

Electronic supplementary material

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299_2011_1112_MOESM1_ESM.xls

ESM_1 Overview of all data obtained for assembled unignes. All information obtained for each unigene during this analysis is included in this table (e.g. number of ESTs per unigene, superunigene, blast hits, domains, signal peptides, SSRs). (XLS 2857 kb)

ESM_2 (DOC 43 kb)

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Gao, Z.M., Li, C.L. & Peng, Z.H. Generation and analysis of expressed sequence tags from a normalized cDNA library of young leaf from Ma bamboo (Dendrocalamus latiflorus Munro). Plant Cell Rep 30, 2045–2057 (2011). https://doi.org/10.1007/s00299-011-1112-0

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  • DOI: https://doi.org/10.1007/s00299-011-1112-0

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