Genome-wide identification and transcriptional profiling analysis of auxin response-related gene families in cucumberReport as inadecuate

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BMC Research Notes

, 7:218

First Online: 08 April 2014Received: 18 March 2013Accepted: 28 March 2014DOI: 10.1186-1756-0500-7-218

Cite this article as: Wu, J., Liu, S., Guan, X. et al. BMC Res Notes 2014 7: 218. doi:10.1186-1756-0500-7-218


BackgroundAuxin signaling has a vital function in the regulation of plant growth and development, both which are known to be mediated by auxin-responsive genes. So far, significant progress has been made toward the identification and characterization of auxin-response genes in several model plants, while no systematic analysis for these families was reported in cucumber Cucumis sativus L., a reference species for Cucurbitaceae crops. The comprehensive analyses will help design experiments for functional validation of their precise roles in plant development and stress responses.

ResultsA genome-wide search for auxin-response gene homologues identified 16 auxin-response factors ARFs, 27 auxin-indole acetic acids Aux-IAAs, 10 Gretchen Hagen 3 GH3s, 61 small auxin-up mRNAs SAURs, and 39 lateral organ boundaries LBDs in cucumber. Sequence analysis together with the organization of putative motifs indicated the potential diverse functions of these five auxin-related family members. The distribution and density of auxin response-related genes on chromosomes were not uniform. Evolutionary analysis showed that the chromosomal segment duplications mainly contributed to the expansion of the CsARF, CsIAA, CsGH3, and CsLBD gene families. Quantitative real-time RT-PCR analysis demonstrated that many ARFs, AUX-IAAs, GH3s, SAURs, and LBD genes were expressed in diverse patterns within different organs-tissues and during different development stages. They were also implicated in IAA, methyl jasmonic acid, or salicylic acid response, which is consistent with the finding that a great number of diverse cis-elements are present in their promoter regions involving a variety of signaling transduction pathways.

ConclusionGenome-wide comparative analysis of auxin response-related family genes and their expression analysis provide new evidence for the potential role of auxin in development and hormone response of plants. Our data imply that the auxin response genes may be involved in various vegetative and reproductive developmental processes. Furthermore, they will be involved in different signal pathways and may mediate the crosstalk between various hormone responses.

AbbreviationsARFAuxin response factors

Aux-IAAAuxin-indole-3-acetic acid

AuxREAuxinresponsive cis-element

DBDDNA-binding domain

GH3Gretchen Hagen 3

LBDLateral organ boundaries

MEMEMultiple Expectation Maximization for Motif Elicitation

NLSNuclear localization signal

QRT–PCRQuantitative reverse transcription–PCR

SAURSmall auxin up mRNA

SGNSolanaceae Genomics Network

TAIRThe Arabidopsis Information Resource.

Electronic supplementary materialThe online version of this article doi:10.1186-1756-0500-7-218 contains supplementary material, which is available to authorized users.

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Author: Jian Wu - Songyu Liu - Xiaoyan Guan - Lifei Chen - Yanjun He - Jie Wang - Gang Lu


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