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

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 �owered 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 �owering, and no studies of �owering have been conducted on wild bamboo plants growing in extreme environments. Here, we report the �rst de novo transcriptome sequence for F. macclureana to investigate the putative mechanisms underlying the �owering 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, speci�cally 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-�owering and �owering 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 speci�c reproductive strategies for �owering-related pathways in response to photoperiodic cues to ensure long vegetation growing period. Our �ndings will provide new insights to future investigations into the mechanisms of �owering time control and adaptive evolution in plants growing at high altitudes. to its high radiation and pathogen-speci�c environment on the QTP. We identi�ed both similarities and differences in adaptive mechanisms (e.g., disease-resistance and DNA repair pathways) and stress-induced �owering mechanisms (e.g., carbohydrate metabolism and signal transduction pathways) among plants that grow at high altitudes. Although further experimental veri�cation is needed, our results provide insight into the regulation of �owering time in highland bamboo as well as how this species adapts to harsh and extreme environments. BEUs: Broadly expressed unigenes; BP: Biological process; CC: Cellular component; COG: Clusters of orthologous groups; DEUs: Differentially expressed unigenes; F-branchlets: Branchlets of the �owering plants; F-leaves: Leaves of the �owering plants; FPKM: Fragments per kb per million fragments; GO: Gene ontology; I-spikelets: In�orescences in the initial �ower stage; KEGG: Kyoto Encyclopedia of Genes and Genomes; ME: Module eigengene; MF: Molecular function; NF-branchlets: Branchlets of the non-�owering plants; NF-leaves: Leaves of the non-�owering plants; Nr: NCBI non-redundant protein sequences; PCA: Principal component analysis; Pfam: Protein family; PPIs: Protein-protein interactions. P-spikelets: In�orescences at the peak �ower stage; QTP: Qinghai–Tibet Plateau; SEUs: Speci�cally expressed unigenes; SSRs: Simple sequence repeats; TOMs: topological overlap measures. WGCNA: Weighted gene co-expression network analysis.