De novo sequencing of the transcriptome reveals regulators of the floral transition in Fargesia macclureana (Poaceae)

Ying Li,Zhimin Gao,Jingjing Shi,Yulong Ding,Kebin Yang,Chunxia Zhang

doi:10.1186/s12864-019-6418-2

Ying Li, Zhimin Gao + Show 4 more

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https://doi.org/10.1186/s12864-019-6418-2

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Abstract

BackgroundFargesia macclureana (Poaceae) is a woody bamboo species found on the Qinghai–Tibet Plateau (QTP) approximately 2000 ~ 3800 m above sea level. It rarely blossoms in the QTP, but it flowered 20 days after growing in our lab, which is in a low-altitude area outside the QTP. To date, little is known regarding the molecular mechanism of bamboo flowering, and no studies of flowering have been conducted on wild bamboo plants growing in extreme environments. Here, we report the first de novo transcriptome sequence for F. macclureana to investigate the putative mechanisms underlying the flowering time control used by F. macclureana to adapt to its environment.ResultsIllumina deep sequencing of the F. macclureana transcriptome generated 140.94 Gb of data, assembled into 99,056 unigenes. A comprehensive analysis of the broadly, specifically and differentially expressed unigenes (BEUs, SEUs and DEUs) indicated that they were mostly involved in metabolism and signal transduction, as well as DNA repair and plant-pathogen interactions, which may be of adaptive importance. In addition, comparison analysis between non-flowering and flowering tissues revealed that expressions of FmFT and FmHd3a, two putative F. macclureana orthologs, were differently regulated in NF- vs F- leaves, and carbohydrate metabolism and signal transduction were two major KEGG pathways that DEUs were enriched in. Finally, we detected 9296 simple sequence repeats (SSRs) that may be useful for further molecular marker-assisted breeding.ConclusionsF. macclureana may have evolved specific reproductive strategies for flowering-related pathways in response to photoperiodic cues to ensure long vegetation growing period. Our findings will provide new insights to future investigations into the mechanisms of flowering time control and adaptive evolution in plants growing at high altitudes.

Highlights

Fargesia macclureana (Poaceae) is a woody bamboo species found on the Qinghai–Tibet Plateau (QTP) approximately 2000 ~ 3800 m above sea level
We found that 7027 (15.45%) unigenes showed similarity to genes found in rice, 11.33% were similar to those found in Brachypodium distachyon, and we found a significant proportion of the unigenes that were similar to those found in Setaria italica, Oryza brachyantha, and Zea mays (Fig. 2a)
The specifically expressed unigenes (SEUs) were mostly involved in carbohydrate metabolism, energy metabolism, and environmental adaptation As shown in Fig. 4a, we identified 10,653 unigenes that were expressed in spikelets, including 5528 and 5025 unigenes in I- and P-spikelets, respectively

Summary

Introduction

Fargesia macclureana (Poaceae) is a woody bamboo species found on the Qinghai–Tibet Plateau (QTP) approximately 2000 ~ 3800 m above sea level It rarely blossoms in the QTP, but it flowered 20 days after growing in our lab, which is in a low-altitude area outside the QTP. Little is known regarding the molecular mechanism of bamboo flowering, and no studies of flowering have been conducted on wild bamboo plants growing in extreme environments. Previous studies investigated flowering mainly by artificially altering the external signals (e.g. photoperiod and light intensity) and did not assess the impact of the original environment on the adaptive evolution of species-specific reproductive strategies

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