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

Abstract

Background: Fargesia macclureana (Poaceae) is a woody bamboo species found on the Qinghai–Tibet Plateau (QTP) approximately 2,000 ~ 3,800 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. Results: Illumina 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 9,296 simple sequence repeats (SSRs) that may be useful for further molecular marker-assisted breeding. Conclusions: F. 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.

Morphological Characteristics and Transcriptome Comparisons of the Shoot Buds from Flowering and Non-Flowering Pleioblastus pygmaeus

“…With the population of high-throughput sequencing and the release of the genome resource of Phyllostachys edulis (Carrière) J.Houz., 1906 in 2013, more and more studies have shifted to the molecular mechanism of bamboo flowering by transcriptome analysis in recent years [9,10]. For example, the transcriptome of Fargesia macclureana (Bor) Stapleton, 1983 inflorescences was firstly profiled to investigate the putative mechanisms underlying flowering time [11]. The transcriptome data of flowering tissues of P. edulis was analyzed to screen key genes involved in the flowering process [12].…”

Identification and functional characterization of two bamboo FD gene homologs having contrasting effects on shoot growth and flowering

“…Non targeted transcriptome sequencing has been undertaken to identify floral tissue specifically expressed sequence tags (ESTs) of short lengths from many temperate/tropical, woody/herbaceous bamboo species such as Dendrocalamus latiflorus 12 , 13 , Phyllostachys edulis 14 – 16 , P. violascens 17 , P . aurea, Guadua inermis, Otatea acuminata, Lithachne pauciflora 18 and Fargesia macclureana 19 . In addition, identification and expression analyses of a group of floral pathway genes or gene families have been undertaken.…”