Next-generation sequencing-based mRNA and microRNA expression profiling analysis revealed pathways involved in the rapid growth of developing culms in Moso bamboo

Transcriptomic Complexity of Culm Growth and Development in Different Types of Moso Bamboo

Moso bamboo is capable of both sexual and asexual reproduction during natural growth, resulting in four distinct types of culms: the bamboo shoot-culm, the seedling stem, the leptomorph rhizome, and a long-ignored culm-the outward-rhizome. Sometimes, when the outward rhizomes break through the soil, they continue to grow longitudinally and develop into a new individual. However, the roles of alternative transcription start sites (aTSS) or termination sites (aTTS) as well as alternative splicing (AS) have not been comprehensively studied for their development. To re-annotate the moso bamboo genome and identify genome-wide aTSS, aTTS, and AS in growing culms, we utilized single-molecule long-read sequencing technology. In total, 169,433 non-redundant isoforms and 14,840 new gene loci were identified. Among 1311 lncRNAs, most of which showed a positive correlation with their target mRNAs, one-third of these IncRNAs were preferentially expressed in winter bamboo shoots. In addition, the predominant AS type observed in moso bamboo was intron retention, while aTSS and aTTS events occurred more frequently than AS. Notably, most genes with AS events were also accompanied by aTSS and aTTS events. Outward rhizome growth in moso bamboo was associated with a significant increase in intron retention, possibly due to changes in the growth environment. As different types of moso bamboo culms grow and develop, a significant number of isoforms undergo changes in their conserved domains due to the regulation of aTSS, aTTS, and AS. As a result, these isoforms may play different roles than their original functions. These isoforms then performed different functions from their original roles, contributing to the transcriptomic complexity of moso bamboo. Overall, this study provided a comprehensive overview of the transcriptomic changes underlying different types of moso bamboo culm growth and development.

Comprehensive profiling of epigenetic modifications in fast-growing Moso bamboo shoots

The fast growth of Moso bamboo (Phyllostachys edulis) shoots is caused by the rapid elongation of each internode. However, the key underlying cellular processes and epigenetic mechanisms remain largely unexplored. We used microscopy and multi-omics approaches to investigate two regions (bottom and middle) of the 18th internode from shoots of two different heights (2 and 4 m). We observed that internode cells become longer, and that lignin biosynthesis and glycosyltransferase family 43 (GT43) genes are substantially upregulated with shoot height. Nanopore direct RNA sequencing (DRS) revealed a higher N6-methyladenine (m6A) modification rate in 2-m shoots than in 4-m shoots. In addition, different specific m6A modification sites were enriched at different growth stages. Global DNA methylation profiling indicated that DNA methylation levels are higher in 4-m shoots than in 2-m shoots. We also detected shorter poly(A) tail lengths (PALs) in 4-m shoots compared with 2-m shoots. Genes showing differential PAL were mainly enriched in the functional terms of protein translation and vesicle fusion. An association analysis between PALs and DNA methylation strongly suggested that gene body CG methylation levels are positively associated with PAL. This study provides valuable information to better understand post-transcriptional regulations responsible for fast-growing shoots in Moso bamboo.

Compatible Biomass Model of Moso Bamboo with Measurement Error

Moso bamboo is characterized by its fast growth and high yield and is important as a carbon sink species. Therefore, understanding the biomass distribution of its components is crucial. Based on the measured individual biomass data of 66 Phyllostachys heterocycla cv. Pubescens plants in the Yixing state-owned forest in Jiangsu Province, nonlinear simultaneous equations with measurement errors were constructed using nonlinear error-in-variable models (NEIVM) (one step, two step) and nonlinear seemingly unrelated regression (NSUR). Variables affecting biomass were evaluated, including diameter at breast height (DBH), bamboo height (H), height to crown base (HCB), node length at DBH (NL), base diameter (BD), and bamboo age (A). DBH, H, and HCB had significant effects on the biomass of each component. They were used to construct a one-predictor system using DBH, a two-predictor system using DBH and H, and a three-predictor system using DBH, H, and HCB. Regardless of the number of variables used, the fitting accuracy of the NEIVM one-step method exceeded that of the two-step method, and that of NEIVM exceeded that of NSUR estimation. As a system using three predictive variables is better than other systems, we recommend using the one-step NEIVM method for Moso bamboo biomass estimation.

Genome-wide identification and expression characterization of the DoG gene family of moso bamboo (Phyllostachys edulis)

BACKGROUND

The DoG (Delay of Germination1) family plays a key regulatory role in seed dormancy and germination. However, to date, there is no complete genomic overview of the DoG gene family of any economically valuable crop, including moso bamboo (Phyllostachys edulis), and no studies have been conducted to characterize its expression profile. To identify the DoG gene members of moso bamboo (PeDoG) and to investigate their family structural features and tissue expression profile characteristics, a study was conducted. Based on the whole genome and differential transcriptome data, in this investigation, we have scrutinized the physicochemical properties, gene structure, cis-acting elements, phylogenetic relationships, conserved structural (CS) domains, CS motifs and expression patterns of the PeDoG1 family of moso bamboo.

RESULTS

The DoG family genes of moso bamboo were found distributed across 16 chromosomal scaffolds with 24 members. All members were found to carry DoG1 structural domains, while 23 members additionally possessed basic leucine zipper (bZIP) structural domains. We could divide the PeDoG genes into three subfamilies based on phylogenetic relationships. Covariance analysis revealed that tandem duplication was the main driver of amplification of the PeDoG genes. The upstream promoter of these genes containing several cis-acting elements indicates a plausible role in abiotic stress and hormone induction. Gene expression pattern according to transcriptome data revealed participation of the PeDoG genes in tissue and organ development. Analysis using Short Time-series Expression Miner (STEM) tool revealed that the PeDoG gene family is also associated with rapid early shoot growth. Gene ontology (GO) and KEGG analyses showed a dual role of the PeDoG genes. We found that PeDoGs has a possible role as bZIP transcription factors by regulating Polar like1 (PL1) gene expression, and thereby playing a disease response role in moso bamboo. Quantitative gene expression of the PeDoG genes revealed that they were abundantly expressed in roots and leaves, and could be induced in response to gibberellin (GA).

CONCLUSION

In this study, we found that the PeDoG genes are involved in a wide range of activities such as growth and development, stress response and transcription. This forms the first report of PeDoG genes and their potential roles in moso bamboo.

New Genes Interacted with Recent Whole Genome Duplicates in the Fast Stem Growth of Bamboos

As drivers of evolutionary innovations, new genes allow organisms to explore new niches. However, clear examples of this process remain scarce. Bamboos, the unique grass lineage diversifying into the forest, have evolved with a key innovation of fast growth of woody stem, reaching up to 1 m/day. Here, we identify 1,622 bamboo-specific orphan genes that appeared in recent 46 million years, and 19 of them evolved from noncoding ancestral sequences with entire de novo origination process reconstructed. The new genes evolved gradually in exon−intron structure, protein length, expression specificity, and evolutionary constraint. These new genes, whether or not from de novo origination, are dominantly expressed in the rapidly developing shoots, and make transcriptomes of shoots the youngest among various bamboo tissues, rather than reproductive tissue in other plants. Additionally, the particularity of bamboo shoots has also been shaped by recent whole-genome duplicates (WGDs), which evolved divergent expression patterns from ancestral states. New genes and WGDs have been evolutionarily recruited into coexpression networks to underline fast-growing trait of bamboo shoot. Our study highlights the importance of interactions between new genes and genome duplicates in generating morphological innovation.

MicroRNAs play important roles in regulating the rapid growth of the Phyllostachys edulis culm internode

Moso bamboo (Phyllostachys edulis) is a fast-growing species with uneven growth and lignification from lower to upper segments within one internode. MicroRNAs (miRNAs) play a vital role in post-transcriptional regulation in plants. However, how miRNAs regulate fast growth in bamboo internodes is poorly understood. In this study, one moso bamboo internode was divided during early rapid growth into four segments called F4 (bottom) to F1 (upper) and these were then analysed for transcriptomes, miRNAs and degradomes. The F4 segment had a higher number of actively dividing cells as well as a higher content of auxin (IAA), cytokinin (CK) and gibberellin (GA) compared with the F1 segment. RNA-seq analysis showed DNA replication and cell division-associated genes highly expressed in F4 rather than in F1. In total, 63 miRNAs (DEMs) were identified as differentially expressed between F4 and F1. The degradome and the transcriptome indicated that many downstream transcription factors and hormonal responses genes were modulated by DEMs. Several miR-target interactions were further validated by tobacco co-infiltration. Our findings give new insights into miRNA-mediated regulatory pathways in bamboo, and will contribute to a comprehensive understanding of the molecular mechanisms governing rapid growth.

Transcriptome-wide identification and characterization of microRNAs in diverse phases of wood formation in Populus trichocarpa

We applied miRNA expression profiling method to Populus trichocarpa stems of the three developmental stages, primary stem (PS), transitional stem (TS), and secondary stem (SS), to investigate miRNA species and their regulation on lignocellulosic synthesis and related processes. We obtained 892, 872, and 882 known miRNAs and 1727, 1723, and 1597 novel miRNAs, from PS, TS, and SS, respectively. Comparisons of these miRNA species among different developmental stages led to the identification of 114, 306, and 152 differentially expressed miRNAs (DE-miRNAs), which had 921, 2639, and 2042 candidate target genes (CTGs) in the three respective stages of the same order. Correlation analysis revealed 47, 439, and 71 DE-miRNA-CTG pairs of high negative correlation in PS, TS, and SS, respectively. Through biological process analysis, we finally identified 34, 6, and 76 miRNA-CTG pairs from PS, TS, and SS, respectively, and the miRNA target genes in these pairs regulate or participate lignocellulosic biosynthesis-related biological processes: cell division and differentiation, cell wall modification, secondary cell wall biosynthesis, lignification, and programmed cell death processes. This is the first report on an integrated analysis of genome-wide mRNA and miRNA profilings during multiple phases of poplar stem development. Our analysis results imply that individual miRNAs modulate secondary growth and lignocellulosic biosynthesis through regulating transcription factors and lignocellulosic biosynthetic pathway genes, resulting in more dynamic promotion, suppression, or regulatory circuits. This study advanced our understanding of many individual miRNAs and their essential, diversified roles in the dynamic regulation of secondary growth in woody tree species.

Study on the differences of gene expression between pear and apple wild cultivation materials based on RNA-seq technique

BACKGROUND

Pears and apples are both perennial deciduous trees of the Rosaceae family, and both are important economic fruit trees worldwide. The emergence of many varieties in the market has been mostly domesticated from wild to cultivated and regulated by the differential expression of genes. However, the molecular process and pathways underlying this phenomenon remain unclear. Four typical wild and cultivar pear and apple trees at three developmental stages were used in our study to investigate the molecular process at the transcriptome level.

RESULT

Physiological observations indicated the obvious differences of size, weight, sugar acid content and peel color in wild and cultivar fruit among each developmental stage. Using next-generation sequencing based RNA-seq expression profiling technology, we produced a transcriptome in procession of a large fraction of annotated pear and apple genes, and provided a molecular basis underlying the phenomenon of wild and cultivar fruit tree differences. 5921 and 5744 differential expression genes were identified in pear and apple at three developmental stages respectively. We performed temporal and spatial differential gene expression profiling in developing fruits. Several key pathways such as signal transduction, photosynthesis, translation and many metabolisms were identified as involved in the differentiation of wild and cultivar fruits.

CONCLUSION

In this study, we reported on the next-generation sequencing study of the temporal and spatial mRNA expression profiling of pear and apple fruit trees. Also, we demonstrated that the integrated analysis of pear and apple transcriptome, which strongly revealed the consistent process of domestication in Rosaceae fruit trees. The results will be great influence to the improvement of cultivar species and the utilization of wild resources.

Multi-analysis of sheath senescence provides new insights into bamboo shoot development at the fast growth stage

Sheath senescence is an important part of bamboo shoot development during the fast growth stage. However, no information has been reported about this distinctive process until now. Using multiple approaches, we found that sheath senescence is a complex process that occurs sequentially with chloroplast corruption, chlorophyll degradation and water loss. Reactive oxygen species (ROS), salicylic acid and abscisic acid also accumulate in the senescing sheath. Transcriptome analysis showed that NAC and WRKY transcription factors, such as NAC2 and WRKY75, as well as their possible downstream target genes, such as those involved in ROS production, proteolysis and nutrition recycling, constitute the gene network of the bamboo sheath senescence process. Furthermore, the initiation of sheath senescence might be triggered by hexokinase genes, such as HXK6, which is localized to the mitochondrion and could promote leaf senescence when overexpressed in Arabidopsis. Sheath senescence occurs after the growth decrease of the internodes, which provides assimilates. The slowing of internode growth possibly results in sugar accumulation, such as glucose, in the sheath, which finally upregulates hexokinase genes and initiates sheath senescence. These findings reveal that sheath senescence is a multilevel regulation process and has a close link to the corresponding internode growth, which provides new insights into the shoot development of bamboo during the fast growth stage.

Multi-omics analysis of cellular pathways involved in different rapid growth stages of moso bamboo

Moso bamboo (Phyllostachys edulis (Carriere) J. Houzeau) is a rapidly growing grass of industrial and ecological importance. However, the molecular mechanisms of its remarkable growth are not well understood. In this study, we investigated the early-stage growth of moso bamboo shoots and defined three different growth stages based on histological and biochemical analyses, namely, starting of cell division (SD), rapid division (RD) and rapid elongation (RE). Further analyses on potentially relevant cellular pathways in these growth stages using multi-omics approaches such as transcriptomics and proteomics revealed the involvement of multiple cellular pathways, including DNA replication, repair and ribosome biogenesis. A total of 8045 differentially expressed genes (DEGs) and 1053 differentially expressed proteins (DEPs) were identified in our analyses. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses of detected DEGs identified several key biological pathways such as phytohormone metabolism, signal transduction, cell wall development and carbohydrate metabolism. The comparative analysis of proteins displayed that a total of 213 DEPs corresponded with DEGs and 3 significant expression profiles that could be promoting the fast growth of bamboo internodes. Moreover, protein-protein interaction network prediction analysis is suggestive of the involvement of five major proteins of signal transduction, DNA synthesis and RNA transcription, and may act as key elements responsible for the rapid shoot growth. Our work exploits multi-omics and bioinformatic approaches to unfurl the complexity of molecular networks involved in the rapid growth of moso bamboo and opens up questions related to the interactions between the functions played by individual molecular pathway.

The acid invertase gene family is involved in internode elongation in Phyllostachys heterocycla cv. pubescens

Acid invertases (INVs) play a pivotal role in both vegetative and reproductive growth of plants. However, their possible functions in fast-growing plants such as bamboo are largely unknown. Here, we report the molecular characterization of acid INVs in Phyllostachys heterocycla cv. pubescens, a fast-growing bamboo species commercially grown worldwide. Nine acid INVs (PhINVs), including seven cell wall INVs (PhCWINV1, PhCWINV2, PhCWINV3, PhCWINV4, PhCWINV5, PhCWINV6 and PhCWINV7) and two vacuolar INVs (PhVINV11 and PhVINV12) were isolated. Bioinformatic analyses demonstrated that they all share high amino acid identity with other INVs from different plant species and contain the motifs typically conserved in acid INV. Enzyme activity assays revealed a significantly higher INV activity in the fast-growing tissues, such as the elongating internodes of stems. Detailed quantitative reverse-transcription PCR analyses showed various expression patterns of PhINVs at different developmental stages of the elongating stems. With the exception of PhCWINV6, all PhINVs were ubiquitously expressed in a developmental-specific manner. Further studies in Arabidopsis exhibited that constitutive expression of PhCWINV1, PhCWINV4 or PhCWINV7 increased the biomass production of transgenic plants, as indicated by augmented plant heights and shoot dry weights than the wild-type plants. All these results suggest that acid INVs play a crucial role in the internode elongation of P. heterocycla cv. pubescens and would provide valuable information for the dissection of their exact biological functions in the fast growth of bamboo.

Transcriptome analysis of lateral buds from Phyllostachys edulis rhizome during germination and early shoot stages

BACKGROUND

The vegetative growth is an important stage for plants when they conduct photosynthesis, accumulate and collect all resources needed and prepare for reproduction stage. Bamboo is one of the fastest growing plant species. The rapid growth of Phyllostachys edulis results from the expansion of intercalary meristem at the basal part of nodes, which are differentiated from the apical meristem of rhizome lateral buds. However, little is known about the major signaling pathways and players involved during this rapid development stage of bamboo. To study this question, we adopted the high-throughput sequencing technology and compared the transcriptomes of Moso bamboo rhizome buds in germination stage and late development stage.

RESULTS

We found that the development of Moso bamboo rhizome lateral buds was coordinated by multiple pathways, including meristem development, sugar metabolism and phytohormone signaling. Phytohormones have fundamental impacts on the plant development. We found the evidence of several major hormones participating in the development of Moso bamboo rhizome lateral bud. Furthermore, we showed direct evidence that Gibberellic Acids (GA) signaling participated in the Moso bamboo stem elongation.

CONCLUSION

Significant changes occur in various signaling pathways during the development of rhizome lateral buds. It is crucial to understand how these changes are translated to Phyllostachys edulis fast growth. These results expand our knowledge on the Moso bamboo internodes fast growth and provide research basis for further study.

Genome-Wide Characterization and Gene Expression Analyses of GATA Transcription Factors in Moso Bamboo (Phyllostachys edulis)

Moso bamboo is well-known for its rapid-growth shoots and widespread rhizomes. However, the regulatory genes of these two processes are largely unexplored. GATA transcription factors regulate many developmental processes, but their roles in moso bamboo height control and rhizome development remains unexplored. Here, thirty-one bamboo GATA factors (PeGATAs) were identified, which are evolutionarily closer to rice than Arabidopsis, and their gene expression patterns were analyzed in bamboo development and phytohormone response with bioinformatics and molecular methods. Interestingly, PeGATAs could only be classified into three groups. Phytohormone responsive cis-elements were found in PeGATA promoters and the expression profiles showed that PeGATA genes might respond to gibberellin acid and abscisic acid but not to auxin at the transcriptional level. Furthermore, PeGATA genes have a tissue-specific expression pattern in bamboo rhizomes. Interestingly, most PeGATA genes were down-regulated during the rapid-growth of bamboo shoots. In addition, over-expressing one of the PeGATA genes, PeGATA26, significantly repressed the primary root length and plant height of transgenic Arabidopsis plants, which may be achieved by promoting the gibberellin acid turnover. Overall, our results provide insight into the function of GATA transcription factors in bamboo, and into genetic resources for engineering plant height.

Characterization of the developmental dynamics of the elongation of a bamboo internode during the fast growth stage

Previous studies on the fast growth of bamboo shoots mainly focused on the entire culm. No work about the fast elongation of a single internode, which is the basic unit for the fast growth of bamboo shoots, has been reported so far according to our knowledge. In this study, we have systematically investigated the regulating mechanisms underlying the fast growth of a single bamboo internode of Bambusa multiplex (Lour.) Raeusch. ex Schult. We discovered that the growth of the internode displays a logistic pattern, and the two sections located in the bottom of the internode, one for cell division and, another for cell elongation, each with an ~1-cm length, comprise the effective zones for the internode growth. RNA-Seq analysis identified a number of genes potentially involved in regulating the fast growth of bamboo internode such as those that have positive roles in promoting cell growth or division, which were dramatically down-regulated in the internode at fast growth decreasing stage. Further analysis revealed that sugar plays an important role in promoting the fast growth of bamboo internodes through inhibition of BmSnf1. Mechanical stress is found to be involved in the triggering of the internode growth decrease through activation of the generation of reactive oxygen species by upregulating Calmodulins. These results provide systematic insight into the biological mechanisms underlying the fast growth of bamboo shoots based on the behavior of a single internode.

GSK3/shaggy-like kinase 1 ubiquitously regulates cell growth from Arabidopsis to Moso bamboo (Phyllostachys edulis)

Moso bamboo (Phyllostachys edulis) is one of the fastest growing species with a maximum growth rate of 1 m/day. However, the regulator genes for this explosive growth phenomenon have not been functionally studied. Here, we found that Moso bamboo GSK3/shaggy-like kinase 1 (PeGSK1) acts as a negative regulator of cell growth. Over-expression of PeGSK1 in Arabidopsis showed significant growth arrest phenotypes, including dwarfism, small leaves, reduced cell length, and disturbed cell elongation of petiole. Furthermore, Overexpression of PeGSK1 fully inhibited the longer hypocotyl phenotype of Arabidopsis atgsk1 mutants. In addition, PeGSK1-overexpressing lines were resistant to exogenous BR treatment and PeGSK1 interacted with the brassinosteroid signal transduction key regulator BZR1. The BZR1-dependent cell growth genes were down-regulated in PeGSK1-overexpressing lines. These results indicated that PeGSK1 is functionally similar to AtGSK1 and inhibited cell growth via the brassinosteroid signaling pathway. Importantly, PeGSK1 also interacted with PeBZR1, and the expression pattern of PeGSK1 was negatively correlated with the internode elongation of bamboo, indicating that PeGSK1 is involved in the cell growth of bamboo. In summary, our results provide insight into the role of brassinosteroids in the rapid-growth of bamboo culms and identifying target genes for the genetic manipulation of plant height.

Morphological dissection and cellular and transcriptome characterizations of bamboo pith cavity formation reveal a pivotal role of genes related to programmed cell death

Pith cavity formation is critical for bamboo to overcome the bending force during its fast growth; however, the underlying molecular mechanisms remain largely unknown. Multiple approaches, including anatomical dissection, mathematical modelling and transcriptome profiling, were employed in this study to investigate the biology of pith cavity formation in bamboo Pseudosasa japonica. We found that the corruption of pith tissue occurred sequentially and asymmetrically from the top-centre of the internode down to the bottom, which might be caused by the combined effects of asymmetrical radial and axial tensile forces during shoot-wall cell elongation and spiral growth of bamboo internodes. Programmed cell death (PCD) in pitch manifested by TUNEL positive nuclei, DNA cleavage and degraded organelles, and potentially regulated by ethylene and calcium signalling pathway, ROS burst, cell wall modification, proteolysis and nutrient recycle genes, might be responsible for pith tissue corruption of Ps. japonica. Although similar physiological changes and transcriptome profiles were found in different bamboo species, different formation rates of pith cavity were observed, which might be caused by different pith cells across the internode that were negatively correlated with the culm diameter. These findings provided a systematical view on the formation of bamboo pith cavity and revealed that PCD plays an important role in the bamboo pith cavity formation.

The roles of Aux/IAA gene family in development of Dendrocalamus sinicus (Poaceae: Bambusoideae) inferred by comprehensive analysis and expression profiling

Auxin is an important hormone in many plant developmental processes. In this study, the auxin/indole acetic acid (Aux/IAA) gene family was comprehensively identified using Dendrocalamus sinicus transcriptome data. A total of 26 Aux/IAA genes (DsIAA1-DsIAA26) were mined using four conserved Aux/IAA family motifs (PF02309). They encoded hydrophilic proteins, including one or two nuclear localisation signals. The D. sinicus Aux/IAA proteins were classified into two groups, including seven sister-gene pairs based on their phylogenetic relationships. A phylogenetic tree generated by aligning 108 predicted protein sequences of 26 DsIAAs, 43 PhIAAs (Phyllostachys heterocycla), 29 AtIAAs (Arabidopsis), 31 OsIAAs (Oryza sativa) and 22 PtIAAs (Populus) revealed nine major groups. Among them, four groups, including 96 IAA proteins of all five species, suggested that the genes originated before divergence of monocots and dicots. The expression profiling in different tissues showed that most of the DsIAAs preferentially expressed in leaves and shoots, suggesting their important roles in the development of leaves and shoots in D. sinicus. Continuously high expression of DsIAA3, DsIAA4, DsIAA15, and DsIAA20 may be important for regulating shoot development in D. sinicus. These results provide useful information for further research into the function of Aux/IAA genes in woody sympodial bamboos.

Heterologous overexpression, purification and functional analysis of plant cellulose synthase from green bamboo

BACKGROUND

The cellulose synthase complex (CSC), composed of cellulose synthase (CesA) proteins, is a catalytic enzyme complex involved in cellulose synthesis in the plant cell. CesA proteins synthesize cellulose microfibrils corresponding to the microtubule direction and export linear products across the plasma membrane. However, the CSC arrangement and the mechanism of cellulose synthesis in plant cells remain unclear. Purified CesA proteins are required to determine biochemical and biophysical characteristics.

RESULTS

In this study, we constructed, expressed, and purified six heterologously expressed cellulose synthases from Bambusa oldhamii (BoCesA) and analyzed the associated enzyme activity. The conjugating sequences of the maltose-binding protein (MBP) gene and the BoCesA genes were constructed into the expression vector pYES2/CT and were further transformed into yeast cells (BCY123) for fermentation culturing. Purified BoCesA recombinant proteins were obtained by a two-step purification procedure, consisting of immobilized metal affinity chromatography to purify MBP-BoCesAs and size-exclusion chromatography (Superdex-200) to isolate BoCesAs in oligomeric form. The enzymatic activity of oligomeric BoCesAs with 80% purity was determined by partially methylated alditol acetate (PMAA)-coupled gas chromatography-mass spectrometry (GC-MS) analysis. Furthermore, the long fiber-like products synthesized by oligomeric BoCesAs were observed under a transmission electron microscope (TEM) and were further confirmed as cellulose microfibril products.

CONCLUSIONS

In this study, we successfully established a heterologous expression and purification system for BoCesAs. The purified recombinant BoCesA proteins display enzyme activity and can produce protein in milligram quantities for further studies on molecular composition and structure.

Molecular Mechanism of Xylogenesis in Moso Bamboo (Phyllostachys edulis) Shoots during Cold Storage

A bamboo shoot is the immature stem of the woody grass and a nutritious and popular vegetable in East Asia. However, it undergoes a rapid xylogenesis process right after harvest, even being stored in a cold chamber. To investigate the molecular regulation mechanisms of xylogenesis in Moso bamboo (Phyllostachys edulis) shoots (MBSes) during cold storage, the measurement of cell wall polymers (cellulose, hemicellulose, and lignin) and related enzyme activities (phenylalanine ammonia lyase (PAL), cinnamyl alcohol dehydrogenase (CAD), peroxidase (POD), and xylan xylosyltransferase (XylT)) and transcriptomic analysis were performed during cold storage. It was noticed that cellulose and lignin contents increased, while hemicellulose content exhibited a downward trend. PAL, CAD, and POD activity presented an upward trend generally in MBS when stored at 4 °C for 16 days. XylT activity showed a descending trend during the stages of storage, but slightly increased during the 8th to 12th days after harvest at 4 °C. Transcriptomic analysis identified 72, 28, 44, and 31 functional unigenes encoding lignin, cellulose, xylan biosynthesis enzymes, and transcription factors (TFs), respectively. Many of these secondary cell wall (SCW)-related genes showed higher expression levels in the later period of cold storage. Quantitative RT-PCR analysis of the selected genes conformed to the expression pattern. Our study provides a comprehensive analysis of MBS secondary wall biosynthesis at the molecular level during the cold storage process. The results give insight into the xylogenesis process of this economically important vegetable and shed light on solving this problem of the post-harvest industry.

Co-expression Gene Network Analysis and Functional Module Identification in Bamboo Growth and Development

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.

Transcriptome characterization of moso bamboo (Phyllostachys edulis) seedlings in response to exogenous gibberellin applications

BACKGROUND

Moso bamboo (Phyllostachys edulis) is a well-known bamboo species of high economic value in the textile industry due to its rapid growth. Phytohormones, which are master regulators of growth and development, serve as important endogenous signals. However, the mechanisms through which phytohormones regulate growth in moso bamboo remain unknown to date.

RESULTS

Here, we reported that exogenous gibberellins (GA) applications resulted in a significantly increased internode length and lignin condensation. Transcriptome sequencing revealed that photosynthesis-related genes were enriched in the GA-repressed gene class, which was consistent with the decrease in leaf chlorophyll concentrations and the lower rate of photosynthesis following GA treatment. Exogenous GA applications on seedlings are relatively easy to perform, thus we used 4-week-old whole seedlings of bamboo for GA- treatment followed by high throughput sequencing. In this study, we identified 932 cis-nature antisense transcripts (cis-NATs), and 22,196 alternative splicing (AS) events in total. Among them, 42 cis-nature antisense transcripts (cis-NATs) and 442 AS events were differentially expressed upon exposure to exogenous GA3, suggesting that post-transcriptional regulation might be also involved in the GA3 response. Targets of differential expression of cis-NATs included genes involved in hormone receptor, photosynthesis and cell wall biogenesis. For example, LAC4 and its corresponding cis-NATs were GA3-induced, and may be involved in the accumulation of lignin, thus affecting cell wall composition.

CONCLUSIONS

This study provides novel insights illustrating how GA alters post-transcriptional regulation and will shed light on the underlying mechanism of growth modulated by GA in moso bamboo.

Comparative Analyses of Anatomical Structure, Phytohormone Levels, and Gene Expression Profiles Reveal Potential Dwarfing Mechanisms in Shengyin Bamboo (Phyllostachys edulis f. tubaeformis)

Moso bamboo (Phyllostachys edulis) is one of the most important bamboo species in China and the third most important plant species for timber production. However, the dwarf variant of moso bamboo, P. edulis f. tubaeformis (shengyin bamboo), which has shortened internodes, is not well studied. We used anatomical, hormonal, and transcriptomic approaches to study internode shortening and shoot growth in dwarf shengyin and wild moso bamboo. Phenotypic and anatomical observations showed that dwarfing in shengyin bamboo is due to reduced internode length, and the culm fibers in shengyin bamboo are significantly shorter and thicker than in wild moso bamboo. We measured the levels of endogenous hormones in the internodes and found that shengyin bamboo had lower levels of four hormones while two others were higher in wild moso bamboo. Comparative transcriptome analyses revealed a potential regulating mechanism for internode length involving genes for cell wall loosening-related enzymes and the cellulose and lignin biosynthesis pathways. Genes involved in hormone biosynthesis and signal transduction, especially those that showed significant differential expression in the internodes between shengyin and wild moso bamboo, may be important in determining the shortened internode phenotype. A hypothesis involving possible cross-talk between phytohormone signaling cues and cell wall expansion leading to dwarfism in shengyin bamboo is proposed. The results presented here provide a comprehensive exploration of the biological mechanisms that determine internode shortening in moso bamboo.

Co-sequencing and novel delayed anti-correlation identify function for pancreatic enriched microRNA biomarkers in a rat model of acute pancreatic injury

Background

Co-sequencing of messenger ribonucleic acid (mRNA) and micro ribonucleic acid (miRNA) across a time series (1, 3, 6, 24, and 48 h post injury) was used to identify potential miRNA-gene interactions during pancreatic injury, associate serum and tissue levels of candidate miRNA biomarkers of pancreatic injury, and functionally link these candidate miRNA biomarkers to observed histopathology. RNAs were derived from pancreatic tissues obtained in experiments characterizing the serum levels of candidate miRNA biomarkers in response to acute pancreatic injury in rats.

Results

No correlation was discovered between tissue and serum levels of the miRNAs. A combination of differential gene expression, novel delayed anti-correlation analysis and experimental database interrogation was used to identify messenger RNAs and miRNAs that experienced significant expression change across the time series, that were negatively correlated, that were complementary in sequence, and that had experimentally supported relationships. This approach yielded a complex signaling network for future investigation and a link for the specific candidate miRNA biomarkers, miR-216a-5p and miR-217-5p, to cellular processes that were in fact the prominent histopathology observations in the same experimental samples. RNA quality bias by treatment was observed in the study samples and a statistical correction was applied. The relevance and impact of that correction on significant results is discussed.

Conclusion

The described approach allowed extraction of miRNA function from genomic data and defined a mechanistic anchor for these miRNAs as biomarkers. Functional and mechanistic conclusions are supported by histopathology findings.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4657-2) contains supplementary material, which is available to authorized users.

Cellular and molecular characterizations of a slow-growth variant provide insights into the fast growth of bamboo

Few studies about bamboo naturally occurring mutants have been reported so far. Using an integrated anatomy, mathematics and genomics approach, we systematically characterized the cellular and molecular basis underlying the abnormal internode development of Pseudosasa japonica var. tsutsumiana, a stable variant with dwarf and swollen internodes that are caused by the compressed spiral growth and the swollen cells in the bottom part of the internode. P. japonica var. tsutsumiana is a slow-growth variant with disorderly cell division and cell growth during the fast growth stage. Comparative transcriptome analysis identified a number of genes related to cell growth that were significantly down-regulated in the variant, including those related to auxin, vesicle transport, cytoskeleton organization and cell wall modification, consistent with the thinner cell walls and lower contents of cellulose that were found in the variant, which together with the mechanic force composed by the extrusion pressure from the neighboring fast growth cells and the weight pressure above the growing cells might finally result in the radial and irregular growth of the variant cells. This study provides key candidate genes involved in the fast growth of bamboo from a 'mutant' perspective, and supports a plausible mechanism underlying the dwarf and swollen internodes of P. japonica var. tsutsumiana.

Transcriptome analysis provides insights into xylogenesis formation in Moso bamboo (Phyllostachys edulis) shoot

Maturation-related changes in cell wall composition and the molecular mechanisms underlying cell wall changes were investigated from the apical, middle and basal segments in moso bamboo shoot (MBS). With maturation extent from apical to basal regions in MBS, lignin and cellulose content increased, whereas heteroxylan exhibited a decreasing trend. Activities of phenylalanine amonnialyase (PAL), cinnamyl alcohol dehydrogenase (CAD) and cinnamate-4-hydroxylase (C4H), which are involved in lignin biosynthesis, increased rapidly from the apex to the base sections. The comparative transcriptomic analysis was carried out to identify some key genes involved in secondary cell walls (SCW) formation underlying the cell wall compositions changes including 63, 8, 18, and 31 functional unigenes encoding biosynthesis of lignin, cellulose, xylan and NAC-MYB-based transcription factors, respectively. Genes related to secondary cell wall formation and lignin biosynthesis had higher expression levels in the middle and basal segments compared to those in the apical segments. Furthermore, the expression profile of PePAL gene showed positive relationships with cellulose-related gene PeCESA4, xylan-related genes PeIRX9 and PeIRX10. Our results indicated that lignification occurred in the more mature middle and basal segments in MBS at harvest while lignification of MBS were correlated with higher expression levels of PeCESA4, PeIRX9 and PeIRX10 genes.

The association of hormone signalling genes, transcription and changes in shoot anatomy during moso bamboo growth

Moso bamboo is a large, woody bamboo with the highest ecological, economic and cultural value of all the bamboo types and accounts for up to 70% of the total area of bamboo grown. However, the spatiotemporal variation role of moso bamboo shoot during growth period is still unclear. We found that the bamboo shoot growth can be divided into three distinct periods, including winter growth, early growth and late growth based on gene expression and anatomy. In the early growth period, lateral buds germinated from the top of the bamboo joint in the shoot tip. Intercalary meristems grew vigorously during the winter growth period and early growth period, but in the late growth period, mitosis in the intercalary meristems decreased. The expression of cell cycle-associated genes and the quantity of differentially expressed genes were higher in early growth than those in late growth, appearing to be influenced by hormonal concentrations. Gene expression analysis indicates that hormone signalling genes play key roles in shoot growth, while auxin signalling genes play a central role. In situ hybridization analyses illustrate how auxin signalling genes regulate apical dominance, meristem maintenance and lateral bud development. Our study provides a vivid picture of the dynamic changes in anatomy and gene expression during shoot growth in moso bamboo, and how hormone signalling-associated genes participate in moso bamboo shoot growth.

Comparative Transcriptome Analysis Reveals Hormone Signaling Genes Involved in the Launch of Culm-Shape Differentiation in Dendrocalamus sinicus

Dendrocalamus sinicus is a sympodial bamboo species endemic to Yunnan Province, China, and is the strongest bamboo species in the world. However, there is substantial variation in the basal culm shape, i.e., straight culm (SC) and bent culm (BC), among different D. sinicus as a result of genetic and growth factors. This study performed a comparative transcriptomic analysis of bamboo shoots of two variants at the early, mid-, and late shoot-development stages to examine the molecular basis of this variation. In total, 98,479 unigenes were annotated, of which 13,495 were differentially expressed in pairwise comparisons of the six libraries. More differentially expressed genes (DEGs) were involved in SC than in BC culm development. The DEGs between BC and SC were assigned to 108 metabolic pathways. The 1064 DEGs in early development might mainly control the launch of culm-shape differentiation. Sixty genes encoding components of hormone signaling pathways were differentially expressed between BC5 and SC5, indicating complex hormonal regulation of culm differentiation. The AUX/IAA, ARF, PP2C, SnRK2, and ABF genes involved in auxin and abscisic acid signaling played key roles. These results help us to understand the molecular mechanism of culm variation and other aspects of culm development in D. sinicus.

Detecting latitudinal and altitudinal expansion of invasive bamboo Phyllostachys edulis and Phyllostachys bambusoides (Poaceae) in Japan to project potential habitats under 1.5°C-4.0°C global warming

Rapid expansion of exotic bamboos has lowered species diversity in Japan's ecosystems by hampering native plant growth. The invasive potential of bamboo, facilitated by global warming, may also affect other countries with developing bamboo industries. We examined past (1975-1980) and recent (2012) distributions of major exotic bamboos (Phyllostachys edulis and P. bambusoides) in areas adjacent to 145 weather stations in central and northern Japan. Bamboo stands have been established at 17 sites along the latitudinal and altitudinal distributional limit during the last three decades. Ecological niche modeling indicated that temperature had a strong influence on bamboo distribution. Using mean annual temperature and sun radiation data, we reproduced bamboo distribution (accuracy = 0.93 and AUC (area under the receiver operating characteristic curve) = 0.92). These results infer that exotic bamboo distribution has shifted northward and upslope, in association with recent climate warming. Then, we simulated future climate data and projected the climate change impact on the potential habitat distribution of invasive bamboos under different temperature increases (i.e., 1.5°C, 2.0°C, 3.0°C, and 4.0°C) relative to the preindustrial period. Potential habitats in central and northern Japan were estimated to increase from 35% under the current climate (1980-2000) to 46%-48%, 51%-54%, 61%-67%, and 77%-83% under 1.5°C, 2.0°C, 3.0°C, and 4.0°C warming levels, respectively. These infer that the risk areas can increase by 1.3 times even under a 1.5°C scenario and expand by 2.3 times under a 4.0°C scenario. For sustainable ecosystem management, both mitigation and adaptation are necessary: bamboo planting must be carefully monitored in predicted potential habitats, which covers most of Japan.

Comprehensive profiling of rhizome-associated alternative splicing and alternative polyadenylation in moso bamboo (Phyllostachys edulis)

Moso bamboo (Phyllostachys edulis) represents one of the fastest-spreading plants in the world, due in part to its well-developed rhizome system. However, the post-transcriptional mechanism for the development of the rhizome system in bamboo has not been comprehensively studied. We therefore used a combination of single-molecule long-read sequencing technology and polyadenylation site sequencing (PAS-seq) to re-annotate the bamboo genome, and identify genome-wide alternative splicing (AS) and alternative polyadenylation (APA) in the rhizome system. In total, 145 522 mapped full-length non-chimeric (FLNC) reads were analyzed, resulting in the correction of 2241 mis-annotated genes and the identification of 8091 previously unannotated loci. Notably, more than 42 280 distinct splicing isoforms were derived from 128 667 intron-containing full-length FLNC reads, including a large number of AS events associated with rhizome systems. In addition, we characterized 25 069 polyadenylation sites from 11 450 genes, 6311 of which have APA sites. Further analysis of intronic polyadenylation revealed that LTR/Gypsy and LTR/Copia were two major transposable elements within the intronic polyadenylation region. Furthermore, this study provided a quantitative atlas of poly(A) usage. Several hundred differential poly(A) sites in the rhizome-root system were identified. Taken together, these results suggest that post-transcriptional regulation may potentially have a vital role in the underground rhizome-root system.

A new outlook on sporadic flowering of bamboo

Moso bamboo (Phyllostachys edulis) is a temperate grass species with a tree-like habitus and an unusual reproduction strategy. While flowering is irregular and infrequent, new clonal bamboo shoots are established from an underground rhizome network during the spring season. In our previous study, we performed transcriptome analyses using bamboo shoot buds to understand the initiation of bamboo stem elongation. Interestingly, the expression profile in the shoot apical meristem (SAM) region of young bamboo shoots is similar to that of other plants. Specifically, some of the genes that control the timing of flowering and floral development are active in the SAM region. This data raises the question of how bamboo shoots start to elongate, and why they do not proceed to a seasonal cycle of flowering. Our analyses of the activation of shoot buds and subsequent rapid stem elongation provide new hints to unravel the unpredictable flowering pattern of bamboo. In this short communication, we discuss how bamboo might coordinate and integrate the vegetative and reproductive phases in relation to shoot emergence and stem elongation.

Phenotypic and genome-wide association analysis of spike ethylene in diverse wheat genotypes under heat stress

The gaseous phytohormone ethylene plays an important role in spike development in wheat (Triticum aestivum). However, the genotypic variation and the genomic regions governing spike ethylene (SET) production in wheat under long-term heat stress remain unexplored. We investigated genotypic variation in the production of SET and its relationship with spike dry weight (SDW) in 130 diverse wheat elite lines and landraces under heat-stressed field conditions. We employed an Illumina iSelect 90K single nucleotide polymorphism (SNP) genotyping array to identify the genetic loci for SET and SDW through a genome-wide association study (GWAS) in a subset of the Wheat Association Mapping Initiative (WAMI) panel. The SET and SDW exhibited appreciable genotypic variation among wheat genotypes at the anthesis stage. There was a strong negative correlation between SET and SDW. The GWAS uncovered five and 32 significant SNPs for SET, and 22 and 142 significant SNPs for SDW, in glasshouse and field conditions, respectively. Some of these SNPs closely localized to the SNPs for plant height, suggesting close associations between plant height and spike-related traits. The phenotypic and genetic elucidation of SET and its relationship with SDW supports future efforts toward gene discovery and breeding wheat cultivars with reduced ethylene effects on yield under heat stress.

Hormone Distribution and Transcriptome Profiles in Bamboo Shoots Provide Insights on Bamboo Stem Emergence and Growth

Growth and development are tightly co-ordinated events in the lifetime of living organisms. In temperate bamboo plants, spring is the season when environmental conditions are suitable for the emergence of new shoots. Previous studies demonstrated that bamboo plants undergo an energy-consuming 'fast stem growth' phase. However, the events during the initiation of stem elongation in bamboo are poorly understood. To understand the onset of bamboo stem growth, we performed hormone and transcriptome profiling of tissue regions in newly elongating shoots of the Moso bamboo Phyllostachys edulis. The growth hormones auxins, cytokinins and gibberellins accumulated in the shoot apex, while the stress hormones ABA, salicylic acid (SA) and jasmonic acid (JA) are predominantly found in the lower part of the stem. The mature basal part of the stem showed enrichment of transcripts associated with cell wall metabolism and biosynthesis of phenylpropanoid metabolites, such as lignin. In the young upper stem region, expression of cell formation- and DNA synthesis-related genes was enriched. Moreover, the apical region showed enhanced expression of genes involved in meristem maintenance, leaf differentiation and development, abaxial/adaxial polarity and flowering. Our findings integrate the spatial regulation of hormones and transcriptome programs during the initiation of bamboo stem growth.

Exploring key cellular processes and candidate genes regulating the primary thickening growth of Moso underground shoots

The primary thickening growth of Moso (Phyllostachys edulis) underground shoots largely determines the culm circumference. However, its developmental mechanisms remain largely unknown. Using an integrated anatomy, mathematics and genomics approach, we systematically studied cellular and molecular mechanisms underlying the growth of Moso underground shoots. We discovered that the growth displayed a spiral pattern and pith played an important role in promoting the primary thickening process of Moso underground shoots and driving the evolution of culms with different sizes among different bamboo species. Different with model plants, the shoot apical meristem (SAM) of Moso is composed of six layers of cells. Comparative transcriptome analysis identified a large number of genes related to the vascular tissue formation that were significantly upregulated in a thick wall variant with narrow pith cavity, mildly spiral growth, and flat and enlarged SAM, including those related to plant hormones and those involved in cell wall development. These results provide a systematic perspective on the primary thickening growth of Moso underground shoots, and support a plausible mechanism resulting in the narrow pith cavity, weak spiral growth but increased vascular bundle of the thick wall Moso.

Genome-Wide Transcriptional Profiling to Elucidate Key Candidates Involved in Bud Burst and Rattling Growth in a Subtropical Bamboo (Dendrocalamus hamiltonii)

Bamboo, one of the fastest growing plants, can be a promising model system to understand growth. The study provides an insight into the complex interplay between environmental signaling and cellular machineries governing initiation and persistence of growth in a subtropical bamboo (Dendrocalamus hamiltonii). Phenological and spatio-temporal transcriptome analysis of rhizome and shoot during the major vegetative developmental transitions of D. hamiltonii was performed to dissect factors governing growth. Our work signifies the role of environmental cues, predominantly rainfall, decreasing day length, and high humidity for activating dormant bud to produce new shoot, possibly through complex molecular interactions among phosphatidylinositol, calcium signaling pathways, phytohormones, circadian rhythm, and humidity responses. We found the coordinated regulation of auxin, cytokinin, brassinosteroid signaling and cell cycle modulators; facilitating cell proliferation, cell expansion, and cell wall biogenesis supporting persistent growth of emerging shoot. Putative master regulators among these candidates were identified using predetermined Arabidopsis thaliana protein-protein interaction network. We got clues that the growth signaling begins far back in rhizome even before it emerges out as new shoot. Putative growth candidates identified in our study can serve in devising strategies to engineer bamboos and timber trees with enhanced growth and biomass potentials.

Genome-wide characterization and evolution analysis of miniature inverted-repeat transposable elements (MITEs) in moso bamboo (Phyllostachys heterocycla)

Moso bamboo MITEs were genome-wide identified first time, and data shows that MITEs contribute to the genomic diversity and differentiation of bamboo. Miniature inverted-repeat transposable elements (MITEs) are widespread in animals and plants. There are a large number of transposable elements in moso bamboo (Phyllostachys heterocycla var. pubescens) genome, but the genome-wide information of moso bamboo MITEs is not known yet. Here we identified 362 MITE families with a total of 489,592 MITE-related sequences, accounting for 4.74 % of the moso bamboo genome. The 362 MITE families are clustered into six known and one unknown super-families. Our analysis indicated that moso bamboo MITEs preferred to reside in or near the genes that might be involved in regulation of host gene expression. Of the seven super-families, three might undergo major expansion event twice, respectively, during 8-11 million years ago (mya) ago and 22-28 mya ago; two might experience a long expansion period from 6 to 13 mya. Almost 1/3 small RNAs might be derived from the MITE sequences. Some MITE families generate small RNAs mainly from the terminals, while others predominantly from the central region. Given the high copy number of MITEs, many siRNAs and miRNAs derived from MITE sequences and the preferential insertion of MITE into gene regions, MITEs may contribute to the genomic diversity and differentiation of bamboo.

Comprehensive analysis of multi-tissue transcriptome data and the genome-wide investigation of GRAS family in Phyllostachys edulis

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.

Transcriptome Sequencing and Analysis for Culm Elongation of the World's Largest Bamboo (Dendrocalamus sinicus)

Dendrocalamus sinicus is the world’s largest bamboo species with strong woody culms, and known for its fast-growing culms. As an economic bamboo species, it was popularized for multi-functional applications including furniture, construction, and industrial paper pulp. To comprehensively elucidate the molecular processes involved in its culm elongation, Illumina paired-end sequencing was conducted. About 65.08 million high-quality reads were produced, and assembled into 81,744 unigenes with an average length of 723 bp. A total of 64,338 (79%) unigenes were annotated for their functions, of which, 56,587 were annotated in the NCBI non-redundant protein database and 35,262 were annotated in the Swiss-Prot database. Also, 42,508 and 21,009 annotated unigenes were allocated to gene ontology (GO) categories and clusters of orthologous groups (COG), respectively. By searching against the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG), 33,920 unigenes were assigned to 128 KEGG pathways. Meanwhile, 8,553 simple sequence repeats (SSRs) and 81,534 single-nucleotide polymorphism (SNPs) were identified, respectively. Additionally, 388 transcripts encoding lignin biosynthesis were detected, among which, 27 transcripts encoding Shikimate O-hydroxycinnamoyltransferase (HCT) specifically expressed in D. sinicus when compared to other bamboo species and rice. The phylogenetic relationship between D. sinicus and other plants was analyzed, suggesting functional diversity of HCT unigenes in D. sinicus. We conjectured that HCT might lead to the high lignin content and giant culm. Given that the leaves are not yet formed and culm is covered with sheaths during culm elongation, the existence of photosynthesis of bamboo culm is usually neglected. Surprisedly, 109 transcripts encoding photosynthesis were identified, including photosystem I and II, cytochrome b6/f complex, photosynthetic electron transport and F-type ATPase, and 24 transcripts were characterized as antenna proteins that regarded as the main tool for capturing light of plants, implying stem photosynthesis plays a key role during culm elongation due to the unavailability of its leaf. By real-time quantitative PCR, the expression level of 6 unigenes was detected. The results showed the expression level of all genes accorded with the transcriptome data, which confirm the reliability of the transcriptome data. As we know, this is the first study underline the D. sinicus transcriptome, which will deepen the understanding of the molecular mechanisms of culm development. The results may help variety improvement and resource utilization of bamboos.

Characterization and primary functional analysis of a bamboo NAC gene targeted by miR164b

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.

microRNAs Databases: Developmental Methodologies, Structural and Functional Annotations

microRNA (miRNA) is an endogenous and evolutionary conserved non-coding RNA, involved in post-transcriptional process as gene repressor and mRNA cleavage through RNA-induced silencing complex (RISC) formation. In RISC, miRNA binds in complementary base pair with targeted mRNA along with Argonaut proteins complex, causes gene repression or endonucleolytic cleavage of mRNAs and results in many diseases and syndromes. After the discovery of miRNA lin-4 and let-7, subsequently large numbers of miRNAs were discovered by low-throughput and high-throughput experimental techniques along with computational process in various biological and metabolic processes. The miRNAs are important non-coding RNA for understanding the complex biological phenomena of organism because it controls the gene regulation. This paper reviews miRNA databases with structural and functional annotations developed by various researchers. These databases contain structural and functional information of animal, plant and virus miRNAs including miRNAs-associated diseases, stress resistance in plant, miRNAs take part in various biological processes, effect of miRNAs interaction on drugs and environment, effect of variance on miRNAs, miRNAs gene expression analysis, sequence of miRNAs, structure of miRNAs. This review focuses on the developmental methodology of miRNA databases such as computational tools and methods used for extraction of miRNAs annotation from different resources or through experiment. This study also discusses the efficiency of user interface design of every database along with current entry and annotations of miRNA (pathways, gene ontology, disease ontology, etc.). Here, an integrated schematic diagram of construction process for databases is also drawn along with tabular and graphical comparison of various types of entries in different databases. Aim of this paper is to present the importance of miRNAs-related resources at a single place.

A small RNA targets pokeweed antiviral protein transcript

Ribosome-inactivating proteins (RIPs) are a class of plant defense proteins with N-glycosidase activity (EC 3.2.2.22). Pokeweed antiviral protein (PAP) is a Type I RIP isolated from the pokeweed plant, Phytolacca americana, thought to confer broad-spectrum virus resistance in this plant. Through a combination of standard molecular techniques and RNA sequencing analysis, we report here that a small RNA binds and cleaves the open reading frame of PAP mRNA. Additionally, sRNA targeting of PAP is dependent on jasmonic acid (JA), a plant hormone important for defense against pathogen infection and herbivory. Levels of small RNA increased with JA treatment, as did levels of PAP mRNA and protein, suggesting that the small RNA functions to moderate the expression of PAP in response to this hormone. The association between JA and PAP expression, mediated by sRNA299, situates PAP within a signaling pathway initiated by biotic stress. The consensus sequence of sRNA299 was obtained through bioinformatic analysis of pokeweed small RNA sequencing. To our knowledge, this is the first account of a sRNA targeting a RIP gene.

A developing Setaria viridis internode: an experimental system for the study of biomass generation in a C4 model species

BACKGROUND

Recently, there has been interest in establishing a monocot C4 model species with a small genome, short lifecycle, and capacity for genetic transformation. Setaria viridis has been adopted to fill this role, since reports of Agrobacterium-mediated transformation in 2010, and sequencing of its genome in 2012. To date, S. viridis has primarily been used to further our understanding of C4 photosynthesis, but is also an ideal system for the study of biomass crops, which are almost exclusively C4 panicoid grasses. Biogenesis of stem tissue, its cell wall composition, and soluble sugar content are important determinants of bioenergy crop yields. Here we show that a developing S. viridis internode is a valuable experimental system for gene discovery in relation to these important bioenergy feedstock traits.

RESULTS

The rate of maximal stem biomass accumulation in S. viridis A10 under long day growth was at the half-head emergence developmental stage. At this stage of development, internode 5 (of 7) was found to be rapidly expanding with an active meristem, a zone of cell expansion (primary cell walls), a transitional zone where cell expansion ceased and secondary cell wall deposition was initiated, and a mature zone that was actively accumulating soluble sugars. A simple method for identifying these zones was established allowing rapid dissection and snap-freezing for RNAseq analysis. A transcriptome profile was generated for each zone showing a transition from cell division and nucleic acid synthesis/processing in the meristem, to metabolism, energy synthesis, and primary cell wall synthesis in the cell expansion zone, to secondary cell wall synthesis in the transitional zone, to sugar transport, and photosynthesis in the mature zone.

CONCLUSION

The identification of these zones has provided a valuable experimental system for investigating key bioenergy traits, including meristematic activity, cell wall biosynthesis, and soluble sugar accumulation, in a C4 panicoid grass that has genetic resources, a short life cycle, and small stature allowing controlled experimental conditions in growth cabinets. Here we have presented a comprehensive map of gene expression and metabolites in this experimental system to facilitate gene discovery and controlled hypothesis testing for bioenergy research in S. viridis.

Transcriptional identification and characterization of differentially expressed genes associated with embryogenesis in radish (Raphanus sativus L.)

Embryogenesis is an important component in the life cycle of most plant species. Due to the difficulty in embryo isolation, the global gene expression involved in plant embryogenesis, especially the early events following fertilization are largely unknown in radish. In this study, three cDNA libraries from ovules of radish before and after fertilization were sequenced using the Digital Gene Expression (DGE) tag profiling strategy. A total of 5,777 differentially expressed transcripts were detected based on pairwise comparison in the three libraries (0_DAP, 7_DAP and 15_DAP). Results from Gene Ontology (GO) and pathway enrichment analysis revealed that these differentially expressed genes (DEGs) were implicated in numerous life processes including embryo development and phytohormones biosynthesis. Notably, some genes encoding auxin response factor (ARF ), Leafy cotyledon1 (LEC1) and somatic embryogenesis receptor-like kinase (SERK ) known to be involved in radish embryogenesis were differentially expressed. The expression patterns of 30 genes including LEC1-2, AGL9, LRR, PKL and ARF8-1 were validated by qRT-PCR. Furthermore, the cooperation between miRNA and mRNA may play a pivotal role in the radish embryogenesis process. This is the first report on identification of DEGs profiles related to radish embryogenesis and seed development. These results could facilitate further dissection of the molecular mechanisms underlying embryogenesis and seed development in radish.

Transcriptome and comparative gene expression analysis of Phyllostachys edulis in response to high light

BACKGROUND

Photosynthesis plays a vital role as an energy source for plant metabolism, and its efficiency may be drastically reduced owing to abiotic stresses. Moso bamboo (Phyllostachys edulis), is a renewable and versatile resource with significant ecological and economic value, which encounters high light stress with large amplitude in natural environment. However, the gene expression profiles in response to high light were elusive in bamboo.

RESULTS

We firstly performed physiological experiments on moso bamboo leaves treated with high light (1200 μmol · m(-2) · s(-1)). Based on the physiological results, three samples of leaves treated with high light for 0 h (CK), 0.5 h (0.5H), and 8 h (8H) were selected to perform further high-throughput RNA sequencing (RNA-Seq), respectively. Then, the transcriptomic result demonstrated that the most genes were expressed at a statistically significant value (FPKM ≥ 1) and the RNA-Seq data were validated via quantitative real time PCR. Moreover, some significant gene expression changes were detected. For instance, 154 differentially expressed genes were detected in 0.5H vs. CK, those in 8H vs. CK were 710, and 429 differentially expressed genes were also identified in 0.5H vs.8 H. Besides, 47 gene annotations closely related to photosynthesis were refined, including 35 genes annotated as light-harvesting chlorophyll a/b-binding (LHC) proteins, 9 LHC-like proteins and 3 PsbSs. Furthermore, the pathway of reactive oxygen species (ROS) in photosynthesis was further analyzed. A total of 171 genes associated with ROS-scavenging were identified. Some up-regulated transcript factors, such as NAC, WRKY, AR2/ERF, and bHLH, mainly concentrated in short-term response, while C2H2, HSF, bZIP, and MYB were largely involved in short and middle terms response to high light.

CONCLUSION

Based on the gene expression analysis of moso bamboo in response to high light, we thus identified the global gene expression patterns, refined the annotations of LHC protein, LHC-like protein and PsbS, detected the pathway of ROS as well as identified ROS-scavenging genes and transcription factors in the regulation of photosynthetic and related metabolisms. These findings maybe provide a starting point to interpret the molecular mechanism of photosynthesis in moso bamboo under high light stress.

Identification of genes involved in color variation of bamboo culms by suppression subtractive hybridization

Phyllostachys vivax cv. aureocaulis is a widely planted ornamental bamboo with evergreen leaves. This plant's culm exhibits a golden-yellow background color marked randomly with narrow and broad green stripes but is occasionally light green with yellow stripes. In this study, we attempt to identify the molecular mechanism underlying the color variation in striped culms. We found that neither stroma nor grana lamellas were observed in plastids in yellow tissue cells, while complete chloroplasts were observed in green tissue. In addition, chlorophyll a and b were mainly distributed in ground tissue under the epiderm and in the cells surrounding the bundle sheath in the green portion of internodes. The amount of chlorophyll contained in cross-sections of the green portion of culms is significantly higher than in the yellow portion. However, carotenoid was nearly undetectable in both samples. In addition, we found that the expression levels of 7 ESTs, including PvESTs-F641 (JZ893845), PvESTs-F681 (JZ893885) and PvESTs-F798 (JZ894002), were significantly higher in green samples than that in yellow samples, while PvESTs-R200 (JZ894906), PvESTs-R541 (JZ895247), PvESTs-R333 (JZ895039) and PvESTs-R266 (JZ894972) were found at a higher level in yellow samples. These ESTs are thought to play a role in this color variation in plants. Our current results indicate that insufficient photosynthetic membrane proteins and lipids in yellow tissue could lead to chloroplast dysfunction and could result in the yellow appearance on certain P. vivax cv. aureocaulis culms.

An improved protocol for small RNA library construction using High Definition adapters

Next generation sequencing of small RNA (sRNA) libraries is widely used for studying sRNAs in various biological systems. However, cDNA libraries of sRNAs are biased for molecules that are ligated to adapters more or less efficiently than other molecules. One approach to reduce this ligation bias is to use a pool of adapters instead of a single adapter sequence, which allows many sRNAs to be ligated efficiently. We previously developed High Definition (HD) adapters for the Illumina sequencing platform, which contain degenerate nucleotides at the ligating ends of the adapters. However, the current commercial kits produced a large amount of 5’ adapter – 3’ adapter ligation product without the cDNA insert when HD adapters were used to replace the kit adapters. Here, we report a protocol to generate sRNA libraries using HD adapters with greatly reduced proportion of adapter-adapter products due to the degradation of nonligated 3’ adapters. The libraries can be completed within two days and can be used for various biological and clinical samples. As examples for using this protocol, we constructed sRNA libraries using total RNA extracted from cultured mammalian cells and plant leaf tissue.

High-throughput sequencing reveals miRNA effects on the primary and secondary production properties in long-term subcultured Taxus cells

Plant-cell culture technology is a promising alternative for production of high-value secondary metabolites but is limited by the decreased metabolite production after long-term subculture. The goal of this study was to determine the effects of miRNAs on altered gene expression profiles during long-term subculture. Two Taxus cell lines, CA (subcultured for 10 years) and NA (subcultured for 6 months), were high-throughput sequenced at the mRNA and miRNA levels. A total of 265 known (78.87% of 336) and 221 novel (79.78% of 277) miRNAs were differentially expressed. Furthermore, 67.17% of the known differentially expressed (DE) miRNAs (178) and 60.63% of the novel DE-miRNAs (134) were upregulated in NA. A total of 275 inverse-related miRNA/mRNA modules were identified by target prediction analysis. Functional annotation of the targets revealed that the high-ranking miRNA targets were those implicated in primary metabolism and abiotic or biotic signal transduction. For example, various genes for starch metabolism and oxidative phosphorylation were inversely related to the miRNA levels, thereby indicating that miRNAs have important roles in these pathways. Interestingly, only a few genes for secondary metabolism were inversely related to miRNA, thereby indicating that factors other than miRNA are present in the regulatory system. Moreover, miR8154 and miR5298b were upregulated miRNAs that targeted a mass of DE genes. The overexpression of these miRNAs in CA increased the genes of taxol, phenylpropanoid, and flavonoid biosynthesis, thereby suggesting their function as crucial factors that regulate the entire metabolic network during long-term subculture. Our current studies indicated that a positive conversion of production properties from secondary metabolism to primary metabolism occurred in long-term subcultured cells. miRNAs are important regulators in the upregulation of primary metabolism.