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To date, little is known about the evolution of fern genomes, with only two small genomes published from the heterosporous Salviniales. Here we assembled the genome of Alsophila spinulosa, known as the flying spider-monkey tree fern, onto 69 pseudochromosomes. The remarkable preservation of synteny, despite resulting from an ancient whole-genome duplication over 100 million years ago, is unprecedented in plants and probably speaks to the uniqueness of tree ferns. Our detailed investigations into stem anatomy and lignin biosynthesis shed new light on the evolution of stem formation in tree ferns. We identified a phenolic compound, alsophilin, that is abundant in xylem, and we provided the molecular basis for its biosynthesis. Finally, analysis of demographic history revealed two genetic bottlenecks, resulting in rapid demographic declines of A. spinulosa. The A. spinulosa genome fills a crucial gap in the plant genomic landscape and helps elucidate many unique aspects of tree fern biology.

Bamboo, the fast-growing grass plant, and rattan, the spiky climbing palm, are both essential forest resources that have been closely linked with human lives, livelihoods and material culture since ancient times. To promote genetic and genomic research in bamboo and rattan, a comprehensive and coordinated international project, the Genome Atlas of Bamboo and Rattan (GABR), was launched in 2017. GABR achieved great success during Phase I (2017-2022). We will focus on investigating and protecting bamboo and rattan germplasm resources in Phase II ( 2022-2027). Here, we briefly review the achievements of Phase I and introduce the goals of Phase II.

PePIP2;7, a leaf-specific aquaporin gene in bamboo, is upregulated under abiotic stresses. Overexpressing PePIP2;7 confers abiotic stresses tolerance in transgenic Arabidopsis plant and yeast. Aquaporins (AQPs) participate in the regulation of water balance in plants. However, the function of AQPs in bamboo remains unclear. Here, PePIP2;7 was identified as a leaf-specific aquaporin gene in moso bamboo based on the expression analysis of transcriptome data and PCR. In situ hybridization further indicated that PePIP2;7 was mainly expressed in mesophyll cells of mature leaves, while in immature leaves it was dominant in blade edge cells followed by mesophyll cells. Interestingly, PePIP2;7 was strongly expressed in the mesophyll cells near bulliform cells of immature leaves, suggesting that PePIP2;7 might function in water transport and contribute to leaf unfolding. The transient expression assay showed that PePIP2;7 was a plasma membrane intrinsic protein. Furthermore, PePIP2;7 was upregulated under abiotic stresses such as high light, drought, and NaCl. Compared with Col-0, transgenic Arabidopsis plants overexpressing PePIP2;7 had better seed germination rate, longer taproot length, higher SOD activity, and lower MDA content under abiotic stresses. Besides, yeasts expressing PePIP2;7 also had higher tolerance to stress compared to the control. Taken together, our results show that PePIP2;7 is leaf-specific and involved in stress response, which provides new insights into aquaporin function in bamboo.

Background LncRNAs are extensively involved in plant biological processes. However, the lack of a comprehensive lncRNA landscape in moso bamboo has hindered the molecular study of lncRNAs. Moreover, the role of lncRNAs in secondary cell wall (SCW) biosynthesis of moso bamboo is elusive. Results For comprehensively identifying lncRNA throughout moso bamboo genome, we collected 231 RNA-Seq datasets, 1 Iso-Seq dataset, and 1 full-length cDNA dataset. We used a machine learning approach to improve the pipeline of lncRNA identification and functional annotation based on previous studies and identified 37,009 lncRNAs in moso bamboo. Then, we established a network of potential lncRNA-coding gene for SCW biosynthesis and identified SCW-related lncRNAs. We also proposed that a mechanism exists in bamboo to direct phenylpropanoid intermediates to lignin or flavonoids biosynthesis through the PAL/4CL/C4H genes. In addition, we identified 4 flavonoids and 1 lignin-preferred genes in the PAL/4CL/C4H gene families, which gained implications in molecular breeding. Conclusions We provided a comprehensive landscape of lncRNAs in moso bamboo. Through analyses, we identified SCW-related lncRNAs and improved our understanding of lignin and flavonoids biosynthesis.

Brassinosteroids (BRs) are a group of plant steroid hormones that play crucial roles in a range of plant growth and development processes. BR action includes active BR formation by a complex biosynthesis process and driving BR biological function through signal transduction. Although the characterization of several BR action-related genes has been conducted in a few model plants, systematic information about these genes in bamboo is still lacking. We identified 64 genes related to BR action from the genome of moso bamboo (Phyllostachys edulis), including twenty that participated in BR biosynthesis and forty-four involved in BR signal transduction. The characteristics of all these candidate genes were identified by bioinformatics methods, including the gene structures, basic physical and chemical properties of proteins, conserved domains and evolutionary relationships. Based on the transcriptome data, the candidate genes demonstrated different expression patterns, which were further validated by qRT-PCR using templates from bamboo shoots with different heights. Thirty-four positive and three negative co-expression modules were identified by 44 candidate genes in the newly emerging bamboo shoot. The gene expression patterns and co-expression modules of BR action-related genes in bamboo shoots indicated that they might function to promote bamboo growth through BR biosynthesis and signal transduction processes. This study provides the first step towards the cloning and functional dissection of the role of BR action-related genes in moso bamboo, which also presents an excellent opportunity for genetic engineering using the candidate genes to improve bamboo quantity and quality.

Trihelix proteins, which are a plant-specific family of transcription factors (TFs), play important roles in plant growth and development, as well as in the plant response to biotic and abiotic stressors. The DNA-binding domain of trihelix proteins is a tryptophan-enriched tandem repeat, forming a helix–loop–helix–loop–helix structure. Here, we identified and characterized 24 full-length trihelix genes from Phyllostachys edulis and classified these genes into 6 previously described subfamilies. Within a given subfamily, the trihelix genes shared similar conserved motifs and structures. Most of the promoters of the trihelix genes in P. edulis contained stress-related cis-elements. Our tissue-specific and gene expression analysis using quantitative real-time PCR indicated that the trihelix genes were expressed primarily in the stems, followed by leaves and roots, and were regulated by cold, drought, and salt stresses. This study delivers novel insights into the phylogenetic relationships and functions of the trihelix TFs of P. edulis. Our results provide a framework for further functional studies investigating the diverse roles of trihelix genes in other bamboo species.

Additional file 2: Figure S2. A phylogenetic tree constructed by 567 complete chloroplast genomes. These species span the phylogenetic diversity of 7 major clades including 40 order and 57 family. The details were provided in Supplementary Table S2.

Rattan is regarded as one of the major non-timber forest products, second only to wood and bamboo, worldwide. Although the published genomes of Calamus simplicifolius and Daemonorops jenkinsiana have facilitated genome-wide gene functional analyses, coexpression networks (CENs) provide more comprehensive and complete annotations of gene function at the transcriptome level. Thus, we analyzed the CENs of the two rattans, C. simplicifolius and D. jenkinsiana, by integrating the genome sequences and analyzing in-house transcriptome data from different development stages of their cirri using a well-developed strategy. A total of 3,504 and 3,027 functional modules were identified in C. simplicifolius and D. jenkinsiana, respectively, based on a combination of CENs, gene family classification, and function enrichment tools. These modules covered the major developmental processes, including photosynthesis, lignin biosynthesis, flavonoid biosynthesis, and phenylpropanoid biosynthesis. Reference annotations were refined using CENs and functional modules. Moreover, we obtained novel insights into the regulation of cirrus growth and development in rattans. Furthermore, Rattan-NET (http://rattan.bamboogdb.org/), an online database with analysis tools for gene set enrichment analysis, module enrichment, network comparison analysis, and cis-element analysis, was constructed for the easy analysis of gene function and regulation modules involved in the growth and development of cirri in rattans.

In order to make better use of bamboo resources in industrial processes, it is necessary to understand its recalcitrant morphological stem structure and unique chemical composition. In the present work, microspectroscopic imaging approaches were used to reveal the heterogeneous distribution of lignin at cellular and subcellular level. Results showed the higher lignin concentration in the narrow layer of fiber and parenchyma secondary cell walls. Furthermore, ethanol organosolv lignin, isolated from different zones of the bamboo vascular tissue [outer (green), middle (timber) and inner (yellow)], was subjected to extensive structural characterization, including chemical component analysis, Fourier-transform infrared spectroscopy (FT-IR), thermogravimetric/differential thermal analysis (TGA/DTA), and nuclear magnetic resonance (NMR). Main chemical differences among the green, timber and yellow zone were sugar content and S/G/H ratios. Since bamboo green had higher density, hardness and lignin content than bamboo timber and bamboo yellow, the mass transfer during the organosolv process was limited and resulted in the reduced removal/dissolution of polysaccharides at the same acidic conditions. Because bamboo green exhibited the highest content of G units in the vascular tissue, it was more condensed and thus had increased thermal stability compared to bamboo timber and bamboo yellow.

Higher plants have an array of photoprotection mechanisms alleviating the harmful effects of light. Non-photochemical quenching (NPQ) is one of the photoprotective mechanisms, which dissipates the excess of light energy absorbed in the light-harvesting complexes (LHCs) into thermal energy. The photosystem II subunit S (PsbS), a member of the LHC family thought to be present exclusively in higher plants, is supposed to activate NPQ through interactions with antenna proteins. However, the roles of PsbS in bamboo remain unclear. Here, two genes of bamboo (Phyllostachys edulis), PePsbS1 and PePsbS2, are investigated and functionally analyzed. PePsbS1 and PePsbS2 have a similar gene structure with three introns separated by two exons, which encode 269 and 268 amino acid residues, respectively. Tissue-specific analysis showed that PePsbS1 and PePsbS2 are highly expressed in leaf blade. Besides, they are both upregulated in the leaf blade when plantlets are submitted to an increased and prolonged light intensity, suggesting that they are light-induced. Western blot analysis indicated that the accumulation level of total PePsbSs is consistent with what obtained by quantitative real-time polymerase chain reaction for PePsbS1 and PePsbS2. Transgenic Arabidopsis plants overexpressing PePsbS1 and PePsbS2 both displayed an enhanced photoprotection. Moreover, the expression of PePsbS1 and PePsbS2 could both rescue the NPQ of Arabidopsis npq4 mutant, indicating that the PsbSs are functionally conserved between monocots and dicots. These results indicated that both PePsbS1 and PePsbS2 could circumvent photoinhibition and enhance photoprotection, which are key factors for bamboo's adaptation to different light environment.

Zeaxanthin epoxidase (ZEP) plays important roles in plant response to various environmental stresses by involving in abscisic acid (ABA) biosynthesis and xanthophyll cycle. A full-length cDNA of PeZEP was isolated from moso bamboo (Phyllostachys edulis), which comprised of a 138-bp 5′-untranslated region (UTR), a 381-bp 3′-UTR, and a 2013-bp open reading frame (ORF) encoding a putative protein of 670 amino acids. PeZEP was mainly expressed in leaf blades and leaf sheaths, and less in roots and culms. The transcript level of PeZEP in bamboo leaf was elevated with the increasing light intensity. PeZEP was significantly upregulated in response to high light (HL: 1200 μmol·m−2·s−1) and reached to a higher level after 1 h treatment, and kept higher levels in the following hours. Besides, PeZEP was upregulated under high temperature (42°C), and downregulated under low temperature (4°C) and exogenous ABA treatment. The expression vector of PeZEP driven by CaMV 35S was constructed and transformed into Arabidopsis...

Bamboo and rattan are widely grown for manufacturing, horticulture, and agroforestry. Bamboo and rattan production might help reduce poverty, boost economic growth, mitigate climate change, and protect the natural environment. Despite progress in research, sufficient molecular and genomic resources to study these species are lacking. We launched the Genome Atlas of Bamboo and Rattan (GABR) project, a comprehensive, coordinated international effort to accelerate understanding of bamboo and rattan genetics through genome analysis. GABR includes 2 core subprojects: Bamboo-T1K (Transcriptomes of 1000 Bamboos) and Rattan-G5 (Genomes of 5 Rattans), and several other subprojects. Here we describe the organization, directions, and status of GABR.

PeTIP4;1–1, an aquaporin gene involved in bamboo shoot growth, is regulated by abiotic stresses. Overexpression of PeTIP4;1–1 confers drought and salinity tolerance in transgenic Arabidopsis. Aquaporins play a central role in numerous physiological processes throughout plant growth and development. PeTIP4;1–1, an aquaporin gene isolated from moso bamboo (Phyllostachys edulis), comprises an open reading frame (ORF) of 756 bp encoding a peptide of 251 amino acids. The genomic sequence corresponding to the ORF of PeTIP4;1–1 was 1777 bp and contained three exons separated by two introns. PeTIP4;1–1 was constitutively expressed at the highest level in culms, and the expression level was elevated with increasing height of the bamboo shoot. PeTIP4;1–1 was significantly up-regulated in response to drought and salinity stresses in bamboo roots and leaves. To investigate the role of PeTIP4;1–1 in response to drought and salinity stresses, transgenic Arabidopsis plants overexpressing PeTIP4;1–1 under the control of CaMV 35S promoter were generated and subjected to morphological and physiological assays. Compared with Col-0, the transgenic plants showed enhanced tolerance to drought and salinity stresses and produced longer taproots, which had more green leaves, higher F v/F m and NPQ values, higher activities of SOD, POD and CAT, lower MDA concentration and higher water content. Transcript levels of three stress-related genes (AtP5CS, AtNHX1 and AtLEA) were enhanced. These results indicated that PeTIP4;1–1 might play an important function in response to drought and salinity stresses, and is a candidate gene for breeding of stress tolerance in other crops through genetic engineering.

UDP-galactose-4-epimerase (UGE) is a key enzyme involved in galactose metabolism by catalyzing the interconversion of UDP-glucose to UDP-galactose. The cDNA encoding UGE was isolated from Phyllostachys edulis by reverse transcription-polymerase chain reaction and by 5' and 3' rapid amplification of cDNA ends, and was designated as PeUGE. The full-length cDNA of PeUGE was 1778 bp, which contained an open reading frame (ORF) encoding a peptide of 420 amino acids, with a calculated molecular mass of 46.58 kDa and a theoretic isoelectric point of 9.07. The genomic sequence corresponding to the ORF of PeUGE was 2656 bp containing 10 exons separated by nine introns. Tissue-specific analysis showed that PeUGE was constitutively expressed with the highest level in shoots, which had an increasing trend with the growth of shoots. PeUGE was induced by abiotic stresses such as drought, salinity, and water stresses. Moreover, chlorophyll fluorescence parameters and lateral roots analysis of transgenic Arabidopsis thaliana plants overexpressing PeUGE systematically confirmed the crucial role of PeUGE in improving the tolerance to abiotic stresses. These results indicated that PeUGE might be one of the key genes involved in the biosynthesis of cell wall polysaccharides during the growth and development of bamboo and in response to stresses, which provided a candidate gene for molecular engineering to improve the quality of bamboo products.

Bamboo is one of the fastest-growing non-timber forest plants. Moso bamboo (Phyllostachys edulis) is the most economically valuable bamboo in Asia, especially in China. With the release of the whole-genome sequence of moso bamboo, there are increasing demands for refined annotation of bamboo genes. Recently, large amounts of bamboo transcriptome data have become available, including data on the multiple growth stages of tissues. It is now feasible for us to construct co-expression networks to improve bamboo gene annotation and reveal the relationships between gene expression and growth traits. We integrated the genome sequence of moso bamboo and 78 transcriptome data sets to build genome-wide global and conditional co-expression networks. We overlaid the gene expression results onto the network with multiple dimensions (different development stages). Through combining the co-expression network, module classification and function enrichment tools, we identified 1,896 functional modules related to bamboo development, which covered functions such as photosynthesis, hormone biosynthesis, signal transduction, and secondary cell wall biosynthesis. Furthermore, an online database (http://bioinformatics.cau.edu.cn/bamboo) was built for searching the moso bamboo co-expression network and module enrichment analysis. Our database also includes cis-element analysis, gene set enrichment analysis, and other tools. In summary, we integrated public and in-house bamboo transcriptome data sets and carried out co-expression network analysis and functional module identification. Through data mining, we have yielded some novel insights into the regulation of growth and development. Our established online database might be convenient for the bamboo research community to identify functional genes or modules with important traits.

Water supply is essential for maintaining normal physiological function during the rapid growth of bamboo. Aquaporins (AQPs) play crucial roles in water transport for plant growth and development. Although 26 PeAQPs in bamboo have been reported, the aquaporin-led mechanism of maintaining diurnal water balance in bamboo shoots remains unclear. In this study, a total of 63 PeAQPs were identified, based on the updated genome of moso bamboo (Phyllostachys edulis), including 22 PePIPs, 20 PeTIPs, 17 PeNIPs, and 4 PeSIPs. All of the PeAQPs were differently expressed in 26 different tissues of moso bamboo, based on RNA sequencing (RNA-seq) data. The root pressure in shoots showed circadian rhythm changes, with positive values at night and negative values in the daytime. The quantitative real-time PCR (qRT-PCR) result showed that 25 PeAQPs were detected in the base part of the shoots, and most of them demonstrated diurnal rhythm changes. The expression levels of some PeAQPs were significantly correlated with the root pressure. Of the 86 sugar transport genes, 33 had positive co-expression relationships with 27 PeAQPs. Two root pressure-correlated PeAQPs, PeTIP4, 1 and PeTIP4, 2, were confirmed to be highly expressed in the parenchyma and epidermal cells of bamboo culm, and in the epidermis, pith, and primary xylem of bamboo roots by in situ hybridization. The authors&rsquo, findings provide new insights and a possible aquaporin-led mechanism for bamboo fast growth.

PeSNAC1 , a stress-related NAC1 from Phyllostachys edulis , was characterized. Ectopic expression in Arabidopsis indicated that PeSNAC1 together with ped -miR164b participated in the regulation of organ boundaries and stress tolerance. NAC (NAM, ATAF1/2 and CUC2) participates in many different processes regulating plant growth, development, and stress response. A total of 125 NAC genes have been predicted in moso bamboo (Phyllostachys edulis), but their roles are poorly understood. PeSNAC1 targeted by ped-miR164b was focused for further study. The cleavage of PeSNAC1 mRNA guided by ped-miR164b was validated using RLM-5′ RACE. Tissue-specific expression analysis demonstrated that ped-miR164b had a declining trend from root, sheath, leaf, to that of stem, which was opposite to that of PeSNAC1. Transgenic Arabidopsis plants overexpressing either PeSNAC1 (OX-PeSNAC1) or, ped-miR164b (OX-ped-miR164b) driven by the CaMV35S promoter were generated. OX-ped-miR164b plants showed similar phenotype of cuc2 mutants whose growth was seriously suppressed. Compared with Col-0, sense OX-PeSNAC1 plants grew rapidly and flowered earlier, whereas antisense plants grew slowly and exhibited delayed flowering. Sense OX-PeSNAC1 plants had the greatest number of lateral roots, while antisense OX-PeSNAC1 and OX-ped-miR164b plants had fewer lateral roots than Col-0. Under NaCl and PEG6000 stresses, survival rates were higher and F v/F m values declined more slowly in sense OX-PeSNAC1 plants than in Col-0, with lower survival rates and a more rapid decrease in F v/F m values conversely observed in antisense OX-PeSNAC1 and OX-ped-miR164b plants. These findings indicated that ped-miR164b-targeted PeSNAC1 may play key roles in plant development and tolerance to salinity and drought stresses.

Background Bamboo is one of the most important nontimber forestry products worldwide. However, a chromosome-level reference genome is lacking, and an evolutionary view of alternative splicing (AS) in bamboo remains unclear despite emerging omics data and improved technologies. Results Here, we provide a chromosome-level de novo genome assembly of moso bamboo (Phyllostachys edulis) using additional abundance sequencing data and a Hi-C scaffolding strategy. The significantly improved genome is a scaffold N50 of 79.90 Mb, approximately 243 times longer than the previous version. A total of 51,074 high-quality protein-coding loci with intact structures were identified using single-molecule real-time sequencing and manual verification. Moreover, we provide a comprehensive AS profile based on the identification of 266,711 unique AS events in 25,225 AS genes by large-scale transcriptomic sequencing of 26 representative bamboo tissues using both the Illumina and Pacific Biosciences sequencing platforms. Through comparisons with orthologous genes in related plant species, we observed that the AS genes are concentrated among more conserved genes that tend to accumulate higher transcript levels and share less tissue specificity. Furthermore, gene family expansion, abundant AS, and positive selection were identified in crucial genes involved in the lignin biosynthetic pathway of moso bamboo. Conclusions These fundamental studies provide useful information for future in-depth analyses of comparative genome and AS features. Additionally, our results highlight a global perspective of AS during evolution and diversification in bamboo.

The understanding of genome characteristics for a given new species, i.e., genome size and heterozygosity, facilitates customizing a specific sequencing and assembling strategy. Thus, the genome size was estimated using four independence methods, i.e., a script of KmerSpectrumPlot.pl in ALLPATHS-LG (version r52488), GCE (Genome Characteristics Estimation, released 20150107, ftp://ftp.genomics.org.cn/pub/gce), JELLYFISH (version 2.0) and flow cytometry.

We performed a considerate prediction of intact protein-coding gene models using three independent approaches, i.e.,de novoprediction, homology-based method, and RNA-Seq approach.

Background Calamus simplicifolius and Daemonorops jenkinsiana are two representative rattans, the most significant material sources for the rattan industry. However, the lack of reference genome sequences is a major obstacle for basic and applied biology on rattan. Findings We produced two chromosome-level genome assemblies of C. simplicifolius and D. jenkinsiana using Illumina, Pacific Biosciences, and Hi-C sequencing data. A total of ∼730 Gb and ∼682 Gb of raw data covered the predicted genome lengths (∼1.98 Gb of C. simplicifolius and ∼1.61 Gb of D. jenkinsiana) to ∼372 × and ∼426 × read depths, respectively. The two de novo genome assemblies, ∼1.94 Gb and ∼1.58 Gb, were generated with scaffold N50s of ∼160 Mb and ∼119 Mb in C. simplicifolius and D. jenkinsiana, respectively. The C. simplicifolius and D. jenkinsiana genomes were predicted to harbor 51,235 and 53,342 intact protein-coding gene models, respectively. Benchmarking Universal Single-Copy Orthologs evaluation demonstrated that genome completeness reached 96.4% and 91.3% in the C. simplicifolius and D. jenkinsiana genomes, respectively. Genome evolution showed that four Arecaceae plants clustered together, and the divergence time between the two rattans was ∼19.3 million years ago. Additionally, we identified 193 and 172 genes involved in the lignin biosynthesis pathway in the C. simplicifolius and D. jenkinsiana genomes, respectively. Conclusions We present the first de novo assemblies of two rattan genomes (C. simplicifolius and D. jenkinsiana). These data will not only provide a fundamental resource for functional genomics, particularly in promoting germplasm utilization for breeding, but also serve as reference genomes for comparative studies between and among different species.

Rattan is an important group of regenerating non-wood climbing palm in tropical forests. The cirrus is an essential climbing organ and provides morphological evidence for evolutionary and taxonomic studies. However, limited data are available on the molecular mechanisms underlying the development of the cirrus. Thus, we performed in-depth transcriptomic sequencing analyses to characterize the cirrus development at different developmental stages of Daemonorops jenkinsiana. The result showed 404,875 transcripts were assembled, including 61,569 high-quality unigenes were identified, of which approximately 76.16% were annotated and classified by seven authorized databases. Moreover, a comprehensive analysis of the gene expression profiles identified differentially expressed genes (DEGs) concentrated in developmental pathways, cell wall metabolism, and hook formation between the different stages of the cirri. Among them, 37 DEGs were validated by qRT-PCR. Furthermore, 14,693 transcriptome-based microsatellites were identified. Of the 168 designed SSR primer pairs, 153 were validated and 16 pairs were utilized for the polymorphic analysis of 25 rattan accessions. These findings can be used to interpret the molecular mechanisms of cirrus development, and the developed microsatellites markers provide valuable data for assisting rattan taxonomy and expanding the understanding of genomic study in rattan.

GRAS family is one of plant specific transcription factors and plays diverse roles in the regulation of plant growth and development as well as in the plant disease resistance and abiotic stress responses. However, the investigation of GRAS family and multi-tissue gene expression profiles still remains unavailable in bamboo (Phyllostachys edulis). Here, we applied RNA-Seq analysis to monitor global transcriptional changes and investigate expression patterns in the five tissues of Ph. edulis, and analyzed a large-scale transcriptional events and patterns. Moreover, the tissue-specific genes and DEGs in different tissues were detected. For example, DEGs in panicle and leaf tissues were abundant in photosynthesis, glutathione, porphyrin and chlorophyll metabolism, whereas those in shoot and rhizome were majority in glycerophospholipid metabolism. In the portion of Ph. edulis GRAS (PeGRAS) analyses, we performed the analysis of phylogenetic, gene structure, conserved motifs, and analyzed the expression profiles of PeGRASs in response to high light and made a co-expression analysis. Additionally, the expression profiles of PeGRASs were validated using quantitative real-time PCR. Thus, PeGRASs based on dynamics profiles of gene expression is helpful in uncovering the specific biological functions which might be of critical values for bioengineering to improve bamboo breeding in future.