Genome-wide analysis and transcriptomic profiling of the auxin biosynthesis, transport and signaling family genes in moso bamboo (Phyllostachys heterocycla)

Wenjia Wang,Yubang Gao,Hangxiao Zhang,Qiang Zhu,Mengqi Xiang,Chentao Lin,Qin Wang,Shanwen Ye,Changyang Cai,Lianfeng Gu

doi:10.1186/s12864-017-4250-0

Wenjia Wang, Yubang Gao + Show 8 more

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https://doi.org/10.1186/s12864-017-4250-0

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Abstract

BackgroundAuxin is essential for plant growth and development. Although substantial progress has been made in understanding auxin pathways in model plants such as Arabidopsis and rice, little is known in moso bamboo which is famous for its fast growth resulting from the rapid cell elongation and division.ResultsHere we showed that exogenous auxin has strong effects on crown and primary roots. Genes involved in auxin action, including 13 YUCCA (YUC) genes involved in auxin synthesis, 14 PIN-FORMED/PIN-like (PIN/PILS) and 7 AUXIN1/LIKE-AUX1 (AUX1/LAX) members involved in auxin transport, 10 auxin receptors (AFB) involved in auxin perception, 43 auxin/indole-3-aceticacid (AUX/IAA) genes, and 41 auxin response factors (ARF) involved in auxin signaling were identified through genome-wide analysis. Phylogenetic analysis of these genes from Arabidopsis, Oryza sativa and bamboo revealed that auxin biosynthesis, transport, and signaling pathways are conserved in these species. A comprehensive study of auxin-responsive genes using RNA sequencing technology was performed, and the results also supported that moso bamboo shared a conserved regulatory mechanism for the expression of auxin pathway genes; meanwhile it harbors its own specific properties.ConclusionsIn summary, we generated an overview of the auxin pathway in bamboo, which provides information for uncovering the precise roles of auxin pathway in this important species in the future.

Highlights

Auxin is essential for plant growth and development
A total of 13 YUC genes involved in auxin biosynthesis, 13 PIN/PILS and 7 AUX1/ LAX family members involved in auxin transport, 10 putative auxin receptors involved in auxin perception, and 43 AUX/indole-3-acetic acid (IAA) and 41 Auxin response factors (ARFs) involved in auxin signaling were identified from the moso bamboo genome
Our results showed that bamboo root is sensitive to the exogenous Naphthaleneacetic acid (NAA) treatment, and NAA affects the root architecture in a dose-dependent manner, low concentration (100 nM and 500 nM) of NAA promoted the formation and growth of crown roots, while an inhibition of primary root and lateral root growth was observed at a higher concentration of auxin (5 μM) (Fig. 1a and b)

Summary

Introduction

Auxin is essential for plant growth and development. substantial progress has been made in understanding auxin pathways in model plants such as Arabidopsis and rice, little is known in moso bamboo which is famous for its fast growth resulting from the rapid cell elongation and division. Auxin action can be achieved through different levels, mainly auxin concentration pathways including auxin biosynthesis and directional auxin transport, and auxin signaling pathways including auxin perception and signal transduction [3,4,5]. In Arabidopsis, 4 amino acid permease-like family members (AtAUX1/ LAX1–3) regulate auxin uptake from the apoplast [10], whereas 8 PIN proteins (AtPIN1-PIN8) and 7 PILS members (AtPILS1–7) are responsible for the polar pump-off of auxin and determine the direction of auxin flow through tissues [5]. As AtPIN proteins, AtPILS proteins contain the so-called InterPro auxin carrier domain, which is predicted to have auxin transport function in silico. The proper concentration of auxin throughout the plant body is achieved by auxin biosynthesis and polar auxin transport

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