Rhizome Development Research Articles

Analysis of Rhizome Development in Oryza longistaminata, a Wild Rice Species.

Vegetative reproduction is a form of asexual propagation in plants. A wide range of plants develop rhizomes, modified stems that grow underground horizontally, as a means of vegetative reproduction. In rhizomatous species, despite their distinct developmental patterns, both rhizomes and aerial shoots derive from axillary buds. Therefore, it is of interest to understand the basis of rhizome initiation and development. Oryza longistaminata, a wild rice species, develops rhizomes. We analyzed bud initiation and growth of O. longistaminata rhizomes using various methods of morphological observation. We show that, unlike aerial shoot buds that contain a few leaves only, rhizome buds initiate several leaves and bend to grow at right angles to the original rhizome. Rhizomes are maintained in the juvenile phase irrespective of the developmental phase of the aerial shoot. Stem elongation and reproductive transition are tightly linked in the aerial shoots, but are uncoupled in the rhizome. Our findings indicate that developmental programs operate independently in the rhizomes and aerial shoots. Temporal modification of the developmental pathways that are common to rhizomes and aerial shoots may be the source of developmental plasticity. Furthermore, the creation of new developmental systems appears to be necessary for rhizome development.

Hormone regulation of rhizome development in tall fescue (Festuca arundinacea) associated with proteomic changes controlling respiratory and amino acid metabolism.

Rhizomes are underground stems with meristematic tissues capable of generating shoots and roots. However, mechanisms controlling rhizome formation and growth are yet to be completely understood. The objectives of this study were to investigate whether rhizome development could be regulated by cytokinins (CKs) and gibberellic acids (GAs), and determine underlying mechanisms of regulation of rhizome formation and growth of tall fescue (Festuca arundinacea) by a CK or GA through proteomic and transcript analysis. A rhizomatous genotype of tall fescue ('BR') plants were treated with 6-benzylaminopurine (BAP, a synthetic cytokinin) or GA3 in hydroponic culture in growth chambers. Furthermore, comparative proteomic analysis of two-dimensional electrophoresis and mass spectrometry were performed to investigate proteins and associated metabolic pathways imparting increased rhizome number by BAP and rhizome elongation by GA3 KEY RESULTS: BAP stimulated rhizome formation while GA3 promoted rhizome elongation. Proteomic analysis identified 76 differentially expressed proteins (DEPs) due to BAP treatment and 37 DEPs due to GA3 treatment. Cytokinin-related genes and cell division-related genes were upregulated in the rhizome node by BAP and gibberellin-related and cell growth-related genes in the rhizome by GA3 CONCLUSIONS: Most of the BAP- or GA-responsive DEPs were involved in respiratory metabolism and amino acid metabolism. Transcription analysis demonstrated that genes involved in hormone metabolism, signalling pathways, cell division and cell-wall loosening were upregulated by BAP or GA3 The CK and GA promoted rhizome formation and growth, respectively, by activating metabolic pathways that supply energy and amino acids to support cell division and expansion during rhizome initiation and elongation in tall fescue.

Gibberellin-Stimulation of Rhizome Elongation and Differential GA-Responsive Proteomic Changes in Two Grass Species.

Rapid and extensive rhizome development is a desirable trait for perennial grass growth and adaptation to environmental stresses. The objective of this study was to determine proteomic changes and associated metabolic pathways of gibberellin (GA) -regulation of rhizome elongation in two perennial grass species differing in rhizome development. Plants of a short-rhizome bunch-type tall fescue (TF; Festuca arundinacea; ‘BR’) and an extensive rhizomatous Kentucky bluegrass (KB; Poa pratensis; ‘Baron’) were treated with 10 μM GA3 in hydroponic culture in growth chambers. The average rhizome length in KB was significantly longer than that in TF regardless of GA3 treatment, and increased significantly with GA3 treatment, to a greater extent than that in TF. Comparative proteomic analysis using two-dimensional electrophoresis and mass spectrometry was performed to further investigate proteins and associated metabolic pathways imparting increased rhizome elongation by GA. A total of 37 and 38 differentially expressed proteins in response to GA3 treatment were identified in TF and KB plants, respectively, which were mainly involved in photosynthesis, energy and amino acid metabolism, protein synthesis, defense and cell development processes. Accelerated rhizome elongation in KB by GA could be mainly associated with the increased abundance of proteins involved in energy metabolism (glyceraldehyde-3-phosphate dehydrogenase, fructose-bisphosphate aldolase, and ATP synthase), amino acid metabolism (S-adenosylmethionine and adenosylhomocysteinase), protein synthesis (HSP90, elongation factor Tu and eukaryotic translation initiation factor 5A), cell-wall development (cell dividion cycle protein, alpha tubulin-2A and actin), and signal transduction (calreticulin). These proteins could be used as candidate proteins for further analysis of molecular mechanisms controlling rhizome growth.

Chitosan elicitation for increased curcumin production and stimulation of defence response in turmeric (Curcuma longa L.)

Curcumin, the major secondary metabolite of turmeric plants is used for centuries as a dye, medicine and flavoring agent. Its production in the plant varies between genotypes and environmental conditions, and for improved industrial commercialization, there is a need to increase and standardize its production in the plant. Biosynthesis of secondary metabolites are affected by biotic and abiotic elicitors. Chitosan is a nontoxic, natural and biodegradable polymer that is known to elicit defense responses in plants and to stimulate plant development, processes that involve changes to the metabolite profile of plants. Little is known about the potential of chitosan to alter the chemical profile of the plant and especially to stimulate secondary metabolite production. The present study identified its potential as an exogenous elicitor for stimulated bioaccumulation of curcumin, in turmeric. Tumeric plants, cultivated in a greenhouse, were sprayed every 30days with water (control) or 0.1% chitosan solution. The chitosan treatment increased the production of curcumin in the rhizomes, by 100%, by stimulation of curcumin bioaccumulation in the rhizome tissue, by 56%, as well as rhizome development, by 38%. This dual stimulation response was accompanied by increased activity of the defense enzymes peroxidase, polyphenol oxidase, and β-1,3glucanases. Furthermore, the chitosan-elicited increase in activity of protease inhibitor in the leaves and the rhizomes correlated developmentally with the appearance of new isoforms of the protein. These results demonstrate that this eco-friendly compound can be used to stimulate curcumin production in turmeric for industrial endeavours, and points at its potential as a defence elicitor.

Differential Gene Expression between Leaf and Rhizome in Atractylodes lancea: A Comparative Transcriptome Analysis.

The rhizome of Atractylodes lancea is extensively used in the practice of Traditional Chinese Medicine because of its broad pharmacological activities. This study was designed to characterize the transcriptome profiling of the rhizome and leaf of Atractylodes lancea in an attempt to uncover the molecular mechanisms regulating rhizome formation and growth. Over 270 million clean reads were assembled into 92,366 unigenes, 58% of which are homologous with sequences in public protein databases (NR, Swiss-Prot, GO, and KEGG). Analysis of expression levels showed that genes involved in photosynthesis, stress response, and translation were the most abundant transcripts in the leaf, while transcripts involved in stress response, transcription regulation, translation, and metabolism were dominant in the rhizome. Tissue-specific gene analysis identified distinct gene families active in the leaf and rhizome. Differential gene expression analysis revealed a clear difference in gene expression pattern, identifying 1518 up-regulated genes and 3464 down-regulated genes in the rhizome compared with the leaf, including a series of genes related to signal transduction, primary and secondary metabolism. Transcription factor (TF) analysis identified 42 TF families, with 67 and 60 TFs up-regulated in the rhizome and leaf, respectively. A total of 104 unigenes were identified as candidates for regulating rhizome formation and development. These data offer an overview of the gene expression pattern of the rhizome and leaf and provide essential information for future studies on the molecular mechanisms of controlling rhizome formation and growth. The extensive transcriptome data generated in this study will be a valuable resource for further functional genomics studies of A. lancea.

Holdfast fragmentation of Macrocystis pyrifera (integrifolia morph) and Lessonia berteroana in Atacama (Chile): a novel approach for kelp bed restoration

The kelps Macrocystis pyrifera (integrifolia morph) and Lessonia berteroana (northern lineage of Lessonia nigrescens) are intensely harvested in Atacama, northern Chile, for abalone forage and alginate production. Local situations call for simple restoration techniques for over-exploited kelp beds. We excised holdfast portions from parental specimens, including parts of stipes and phylloids. Untreated adult thalli and unmanipulated specimens served as controls. Fragments of both species were attached to boulders or rock platforms with elastic bands or cyanoacrylate glue. Transplanted fragments quickly formed new haptera, colonized new substrata, and reached reproductive maturity. Macrocystis regenerates increased in total length and holdfast diameter in one or both directions of the rhizome, forming a pair of stipes, followed by rhizome and haptera development. In Lessonia, tissue of non-injured zones took over new holdfast growth. Success of this propagation method varied with season and substrata. Both species proceeded to complete regeneration of holdfasts. However, holdfasts of older Macrocystis thalli partly decomposed, resulting in two apparently identical individuals. Advantages of these propagation methods are discussed in ecological and restoration contexts.

Identification and analysis of miRNAs and their targets in ginger using bioinformatics approach

MicroRNAs (miRNAs) are a large family of endogenous small RNAs derived from the non-protein coding genes. miRNA regulates the gene expression at the post-transcriptional level and plays an important role in plant development. Zingiber officinale is an important medicinal plant having numerous therapeutic properties. Its bioactive compound gingerol and essential oil posses important pharmacological and physiological activities. In this study, we used a homology search based computational approach for identifying miRNAs in Z. officinale. A total of 16 potential miRNA families (miR167, miR407, miR414, miR5015, miR5021, miR5644, miR5645, miR5656, miR5658, miR5664, miR827, miR838, miR847, miR854, miR862 and miR864) were predicted in ginger. Phylogenetic and conserved analyses were performed for predicted miRNAs. Thirteen miRNA families were found to regulate 300 target transcripts and play an important role in cell signaling, reproduction, metabolic process and stress. To understand the miRNA mediated gene regulatory control and to validate miRNA target predictions, a biological network was also constructed. Gene ontology and pathway analyses were also done. miR5015 was observed to regulate the biosynthesis of gingerol by inhibiting phenyl ammonia lyase (PAL), a precursor enzyme in the biosynthesis of gingerol. Our results revealed that most of the predicted miRNAs were involved in the regulation of rhizome development. miR5021, miR854 and miR838 were identified to regulate the rhizome development and the essential oil biosynthesis in ginger.

Effect of mineral contents on the growth of vietnamese ginseng (Panax vietnamensis Ha et Grushv.) cultured in vitro photoautotrophically

Panax vietnamensis Ha et Grushv. is one of valuable ginseng plants in Vietnam for illness treatment and health maintenance in traditional medicine. With the aim of finding proper culture medium to produce in vitro plants of a high quality, in vitro ginseng shoots, each with an unfolded leaf, were used as explants and cultured photoautotrophically by a natural ventilation method. The culture medium was not supplemented with sucrose, vitamins and plant growth substances. Explants were put into Magenta vessels (V = 370 ml with 2 Millipore filter membranes on each vessel lid) contained 70 ml of one among four different culture media, including full-strength MS, modified MS, Enshi-Shoho or Heller medium. On day 90, ginseng plants cultured on the modified MS medium with a half-strength of both KNO3 and NH4NO3 had better photosynthetic ability and growth when compared with those cultured on the full-strength MS, Enshi-Shoho or Heller medium. The plants also had the greatest increase in plant fresh weight (261,3 mg/plant), dry weight (61,0 mg/plant), the greatest dry weight of rhizomes and roots (51,2 mg/plant) and the largest number of roots (7,6 roots/plants). Ginseng plants, cultured in vitro under photoautotrophic condition, of all treatments showed rhizome formation and development during the culture period.

Comparative transcriptome of rhizome and leaf in Ligusticum Chuanxiong

The rhizome was the pharmaceutical and breeding organ of Ligusticum chuanxiong, a well-known medicinal herb. In order to understand the molecular mechanism of rhizome formation and development, and the biosynthesis of active metabolites in rhizome of L. chuanxiong, it was necessary to obtain the functional genomic information. In this study, two cDNA libraries, which were constructed from the rhizome and leaf of L. chuanxiong, were sequenced using Illumina platform. More than 26,540,629 high-quality reads were obtained, generating 5.36 gigabase pairs of sequencing data. These reads were assembled into 109,486 unigenes and more than 44,345 unigenes (>40 %) were larger than 500 bp. Among them, 67,373 unique sequences were annotated and 14,494 of the unique sequences were assigned to specific metabolic pathways by the Kyoto Encyclopedia of Genes and Genomes. A total of 4102 unigenes were differentially expressed between rhizome and leaf, indicating their different roles in physiological processes. 2677 and 1425 unigenes were up-regulated in rhizome and leaf, respectively. In total, 82 and 124 transcriptional factor genes were up-regulated in rhizome and leaf, respectively. Meanwhile, 22 unigenes, which were involved with the organ formation and development, were discovered in the up-regulated unigenes in rhizome. Analysis of unigenes which were involved in the biosynthesis of ferulic acid indicated that Caffeic acid O-methyltransferase might be the candidate gene of the key enzyme. In conclusion, the extensive transcriptome provided a useful resource for the L. chuanxiong research. Using comparative transcriptome analysis, we detected differently expressing genes and identified a group of potential candidate unigenes by qRT-PCR. These candidate unigenes provide a foundation for future studies on molecular mechanisms underlying formation, development, and secondary metabolism of rhizome.

Comparative Proteomic Analysis of Developing Rhizomes of the Ancient Vascular Plant Equisetum hyemale and Different Monocot Species

The rhizome is responsible for the invasiveness and competitiveness of many plants with great economic and agricultural impact worldwide. Besides its value as an invasive organ, the rhizome plays a role in the establishment and massive growth of forage, providing biomass for biofuel production. Despite these features, little is known about the molecular mechanisms that contribute to rhizome growth, development, and function in plants. In this work, we characterized the proteome of rhizome apical tips and elongation zones from different species using a GeLC-MS/MS (one-dimensional electrophoresis in combination with liquid chromatography coupled online with tandem mass spectrometry) spectral-counting proteomics strategy. Five rhizomatous grasses and an ancient species were compared to study the protein regulation in rhizomes. An average of 2200 rhizome proteins per species were confidently identified and quantified. Rhizome-characteristic proteins showed similar functional distributions across all species analyzed. The over-representation of proteins associated with central roles in cellular, metabolic, and developmental processes indicated accelerated metabolism in growing rhizomes. Moreover, 61 rhizome-characteristic proteins appeared to be regulated similarly among analyzed plants. In addition, 36 showed conserved regulation between rhizome apical tips and elongation zones across species. These proteins were preferentially expressed in rhizome tissues regardless of the species analyzed, making them interesting candidates for more detailed investigative studies about their roles in rhizome development.

Growth-defence balance in grass biomass production: the role of jasmonates.

Growth-defence balance is the selective partitioning of resources between biomass accumulation and defence responses. Although it is generally postulated that reallocation of limited carbon pools drives the antagonism between growth and defence, little is known about the mechanisms underlying this regulation. Jasmonates (JAs) are a group of oxylipins that are required for a broad range of responses from defence against insects to reproductive growth. Application of JAs to seedlings also leads to inhibited growth and repression of photosynthesis, suggesting a role for JAs in regulating growth-defence balance. The majority of JA research uses dicot models such as Arabidopsis and tomato, while understanding of JA biology in monocot grasses, which comprise most bioenergy feedstocks, food for human consumption, and animal feed, is limited. Interestingly, JA mutants of grasses exhibit unique phenotypes compared with well-studied dicot models. Gene expression analyses in bioenergy grasses also suggest roles for JA in rhizome development, which has not been demonstrated in Arabidopsis. In this review we summarize current knowledge of JA biology in panicoid grasses-the group that consists of the world's emerging bioenergy grasses such as switchgrass, sugarcane, Miscanthus, and sorghum. We discuss outstanding questions regarding the role of JAs in panicoid grasses, and highlight the importance of utilizing emerging grass models for molecular studies to provide a basis for engineering bioenergy grasses that can maximize biomass accumulation while efficiently defending against stress.

Photoperiod and Temperature Effects on Rhizome Production and Tillering Rate in Tall Fescue [Lolium arundinaceum (Schreb.) Darby.

ABSTRACTTemperature and photoperiod are key factors regulating plant growth and development. The objective of this study was to investigate the effects of temperature and photoperiod on tillering and rhizome formation in tall fescue [Lolium arundinaceum (Schreb.) Darby.]. Different genotypes were selected based on tillering ability and/or rhizome production. Plants were grown in growth chambers with a combination of different photoperiods and day/night temperatures: short photoperiod (9 h) and low temperature (day/night at 15/10°C) (SL), long photoperiod (18 h) and low temperature (LL), short photoperiod and high temperature (day/night at 25/15°C) (SH), and long photoperiod and high temperature (LH). The SL treatment resulted in significant increases in the number of tillers in the experiment and Genotype 1109 produced the maximum number of tillers. The number of rhizomes was increased under LL and LH conditions in three clonal lines. Our results suggested that the responses of tiller and rhizome development to temperature and photoperiod varied with genotypes; in addition, longer photoperiod appeared to promote rhizome formation, regardless of temperature, whereas lower temperature stimulated rapid tiller production in some genotypes of tall fescue. This study will help to determine the performance of tall fescue under the longer/shorter photoperiod and variable temperature conditions in different parts of United States.

Differential microRNA expression between shoots and rhizomes in Oryza longistaminata using high-throughput RNA sequencing

Plant microRNAs (miRNAs) play important roles in biological processes such as development and stress responses. Although the diverse functions of miRNAs in model organisms have been well studied, their function in wild rice is poorly understood. In this study, high-throughput small RNA sequencing was performed to characterize tissue-specific transcriptomes in Oryza longistaminata. A total of 603 miRNAs, 380 known rice miRNAs, 72 conserved plant miRNAs, and 151 predicted novel miRNAs were identified as being expressed in aerial shoots and rhizomes. Additionally, 99 and 79 miRNAs were expressed exclusively or differentially, respectively, in the two tissues, and 144 potential targets were predicted for the differentially expressed miRNAs in the rhizomes. Functional annotation of these targets suggested that transcription factors, including squamosa promoter binding proteins and auxin response factors, function in rhizome growth and development. The expression levels of several miRNAs and target genes in the rhizomes were quantified by RT-PCR, and the results indicated the existence of complex regulatory mechanisms between the miRNAs and their targets. Eight target cleavage sites were verified by RNA ligase-mediated rapid 5′ end amplification. These results provide valuable information on the composition, expression and function of miRNAs in O. longistaminata, and will aid in understanding the molecular mechanisms of rhizome development.

A systems-wide comparison of red rice (Oryza longistaminata) tissues identifies rhizome specific genes and proteins that are targets for cultivated rice improvement.

BackgroundThe rhizome, the original stem of land plants, enables species to invade new territory and is a critical component of perenniality, especially in grasses. Red rice (Oryza longistaminata) is a perennial wild rice species with many valuable traits that could be used to improve cultivated rice cultivars, including rhizomatousness, disease resistance and drought tolerance. Despite these features, little is known about the molecular mechanisms that contribute to rhizome growth, development and function in this plant.ResultsWe used an integrated approach to compare the transcriptome, proteome and metabolome of the rhizome to other tissues of red rice. 116 Gb of transcriptome sequence was obtained from various tissues and used to identify rhizome-specific and preferentially expressed genes, including transcription factors and hormone metabolism and stress response-related genes. Proteomics and metabolomics approaches identified 41 proteins and more than 100 primary metabolites and plant hormones with rhizome preferential accumulation. Of particular interest was the identification of a large number of gene transcripts from Magnaportha oryzae, the fungus that causes rice blast disease in cultivated rice, even though the red rice plants showed no sign of disease.ConclusionsA significant set of genes, proteins and metabolites appear to be specifically or preferentially expressed in the rhizome of O. longistaminata. The presence of M. oryzae gene transcripts at a high level in apparently healthy plants suggests that red rice is resistant to this pathogen, and may be able to provide genes to cultivated rice that will enable resistance to rice blast disease.

Genetic control of rhizomes and genomic localization of a major-effect growth habit QTL in perennial wildrye

Rhizomes are prostrate subterranean stems that provide primitive mechanisms of vegetative dispersal, survival, and regrowth of perennial grasses and other monocots. The extent of rhizome proliferation varies greatly among grasses, being absent in cereals and other annuals, strictly confined in caespitose perennials, or highly invasive in some perennial weeds. However, genetic studies of rhizome proliferation are limited and genes controlling rhizomatous growth habit have not been elucidated. Quantitative trait loci (QTLs) controlling rhizome spreading were compared in reciprocal backcross populations derived from hybrids of rhizomatous creeping wildrye (Leymus triticoides) and caespitose basin wildrye (L. cinereus), which are perennial relatives of wheat. Two recessive QTLs were unique to the creeping wildrye backcross, one dominant QTL was unique to the basin wildrye backcross, and one additive QTL was detectable in reciprocal backcrosses with high log odds (LOD = 31.6) in the basin wildrye background. The dominant QTL located on linkage group (LG)-2a was aligned to a dominant rhizome orthogene (Rhz3) of perennial rice (Oryza longistamina) and perennial sorghum (Sorghum propinquum). Nonparametric 99 % confidence bounds of the 31.6-LOD QTL were localized to a distal 3.8-centiMorgan region of LG-6a, which corresponds to a 0.7-Mb region of Brachypodium Chromosome 3 containing 106 genes. An Aux/IAA auxin signal factor gene was located at the 31.6-LOD peak, which could explain the gravitropic and aphototropic behavior of rhizomes. Findings elucidate genetic mechanisms controlling rhizome development and architectural growth habit differences among plant species. Results have possible applications to improve perennial forage and turf grasses, extend the vegetative life cycle of annual cereals, such as wheat, or control the invasiveness of highly rhizomatous weeds such as quackgrass (Elymus repens).

Heavy metal tolerance in Agropyron repens (L.) P. Bauv. populations from the Legnica copper smelter area, Lower Silesia

The copper smelter "Legnica" is one of the oldest plants in Lower Silesia. Among the few weed species spontaneously migrating to the area around the emitter there is couch grass (<em>Agropyron repens</em> (L.) P. Bauv.). The purpose of this study was to analyse whether the local couch grass populations, growing at various distances from the smelter, differ in tolerance to heavy metals occurring in this area. The populations were tested for tolerance to five metals (Cu, Zn, Pb, Cd, Ni) using the root elongation method. The highest tolerance to Pb developed in two populations localized nearest the smelter. Similarly, all populations of couch grass from the vicinity of the smelter show a high tolerance to copper, particularly the plants from the most contaminated site. The IT for the latter population is almost 1509r, even at the highest dose of Cu. For Zn a nearing IT as for Cu was obtained. Comparing the shape of IT curves for Cd, special emphasis is put on the fact that a fixed tolerance to cadmium occurs only in the population localized closest to the emitter. The analysis of Ni-tolerance curves, of which the content in local soil is minimal, does not confirm the thesis on possibility of development of co-tolerance in the surveyed populations. It appeared that stress conditions existing near the smelter do not inhibit seed production in couch grass, but prevent a successful course of their germination on polluted soil. The improvement of soil even by 50% (addition of unpolluted soil) does not improve the poor process of germination in couch grass growing nearest to the smelter. Of importance is the fact that the highest number of seeds germinated on their own, polluted soil. The need of metals' content for plant germination in populations most distant from the smelter is evidenced by an almost 30% reduction of germination ability of local seeds after addition of unpolluted soil. Another significant observation was the fact that, in spite of a poor germination of seeds on unpolluted soil, the further development of seedlings in populations more distant from the smelter was more intense and faster than on their native polluted soil. Thus, a certain amount of metals may stimulate the germination processes of seeds in tolerant populations, but on the other hand, it may be a hindrance to subsequent juvenile phases. During observations of development of rhizomes, taken from three polluted couch grass populations cultivated on unpolluted soil, in all of them a very slow development of rhizome buds was recorded. However, the slowest rate of appearance of buds was found in the population taken nearest the emitter which, in greenhouse conditions and at lack of metals in soil, showed a markedly poor tendency toward vegetative reproduction. All the contaminated populations display a high activity of peroxidase in leaves and roots, frequently more than twice as high than in control populations. The activity of catalase is also markedly higher, but only in two of the most contaminated populations. The recorded for the first time populations of couch grass tolerant to metals make them useful for recultivation purposes.

Next-Generation Sequencing-Based Transcriptional Profiling of Sacred Lotus “China Antique”

Rhizomes are underground stems that serve various purposes including vegetative propagation, invasion of new territory, and bioactive compound synthesis and storage. An important rhizomatous plant is sacred lotus (Nelumbo nucifera), which is prized in Asia as a medicine and a food. RNA-seq and total transcriptome analysis of rhizomes and other lotus tissues was applied to identify genes involved in rhizome growth, development and metabolism. Root, petiole, rhizome internode, and leaf tissues were used for single-read RNA-seq analysis. Two whole transcriptome paired-end read libraries from rhizome apical tip and elongation zone tissues were also generated in order to survey gene expression profiles. In this analysis, 22,803 genes were expressed: 20,476 in rhizome apical meristem and elongation zone, 17,171 in rhizome internode, 16,656 in leaf, 19,457 in root, and 16,845 in petiole. Gene ontology (GO) analysis indicated that “other membrane”, “nucleotide binding”, and “other cellular processes” were highly represented in the expressed genes. A total of 231 genes displayed rhizome-specific expression including several transcription factors, protein kinases, cytochromes P450 and a sulfate transporter. GOseq analysis showed that genes in the “molecular function” GO category and several genes related to cell proliferation based on KEGG IDs were preferentially up-regulated in rhizome tissue. In addition, 1,251 possible exon-skipping events were observed in 1,149 gene models. These results provide valuable insight into gene expression profiles and regulation in sacred lotus, and the identified rhizome-specific genes provide insight into important processes involved in the biology and development of sacred lotus rhizomes.

Genome-Wide Analysis of Differentially Expressed Genes Relevant to Rhizome Formation in Lotus Root (Nelumbo nucifera Gaertn).

Lotus root is a popular wetland vegetable which produces edible rhizome. At the molecular level, the regulation of rhizome formation is very complex, which has not been sufficiently addressed in research. In this study, to identify differentially expressed genes (DEGs) in lotus root, four libraries (L1 library: stolon stage, L2 library: initial swelling stage, L3 library: middle swelling stage, L4: later swelling stage) were constructed from the rhizome development stages. High-throughput tag-sequencing technique was used which is based on Solexa Genome Analyzer Platform. Approximately 5.0 million tags were sequenced, and 4542104, 4474755, 4777919, and 4750348 clean tags including 151282, 137476, 215872, and 166005 distinct tags were obtained after removal of low quality tags from each library respectively. More than 43% distinct tags were unambiguous tags mapping to the reference genes, and 40% were unambiguous tag-mapped genes. From L1, L2, L3, and L4, total 20471, 18785, 23448, and 21778 genes were annotated, after mapping their functions in existing databases. Profiling of gene expression in L1/L2, L2/L3, and L3/L4 libraries were different among most of the selected 20 DEGs. Most of the DEGs in L1/L2 libraries were relevant to fiber development and stress response, while in L2/L3 and L3/L4 libraries, major of the DEGs were involved in metabolism of energy and storage. All up-regulated transcriptional factors in four libraries and 14 important rhizome formation-related genes in four libraries were also identified. In addition, the expression of 9 genes from identified DEGs was performed by qRT-PCR method. In a summary, this study provides a comprehensive understanding of gene expression during the rhizome formation in lotus root.

Secretome Prediction and Analysis in Sacred Lotus (Nelumbo nucifera Gaertn.)

Sacred lotus, Nelumbo nucifera (Gaertn.), is a basal eudicot with agricultural and medicinal importance. The secretome and proteins in some other subcellular locations including endoplasmic reticulum (ER), mitochondrion, chloroplast, and membrane of sacred lotus were predicted using a set of computational tools. The distribution of proteins in each subcellular location in sacred lotus was compared with proteins in five other plant species. Plant proteomes contained approximately 6–9 % of secreted proteins, 13–15 % membrane proteins, 12–20 % mitochondrial or chloroplast proteins, respectively. Plant secreted proteins consist of a large number of hydrolases and peroxidases which may contribute to cell wall formation, rhizome development and seed germination regulation. The information of secretome and other protein subcellular locations in sacred lotus and other species can be accessed at the PlantSecKB website ( http://proteomics.ysu.edu/secretomes/plant.php ).

Tissue-Specific Transcriptomic Profiling of Sorghum propinquum using a Rice Genome Array

Sorghum (Sorghum bicolor) is one of the world's most important cereal crops. S. propinquum is a perennial wild relative of S. bicolor with well-developed rhizomes. Functional genomics analysis of S. propinquum, especially with respect to molecular mechanisms related to rhizome growth and development, can contribute to the development of more sustainable grain, forage, and bioenergy cropping systems. In this study, we used a whole rice genome oligonucleotide microarray to obtain tissue-specific gene expression profiles of S. propinquum with special emphasis on rhizome development. A total of 548 tissue-enriched genes were detected, including 31 and 114 unique genes that were expressed predominantly in the rhizome tips (RT) and internodes (RI), respectively. Further GO analysis indicated that the functions of these tissue-enriched genes corresponded to their characteristic biological processes. A few distinct cis-elements, including ABA-responsive RY repeat CATGCA, sugar-repressive TTATCC, and GA-responsive TAACAA, were found to be prevalent in RT-enriched genes, implying an important role in rhizome growth and development. Comprehensive comparative analysis of these rhizome-enriched genes and rhizome-specific genes previously identified in Oryza longistaminata and S. propinquum indicated that phytohormones, including ABA, GA, and SA, are key regulators of gene expression during rhizome development. Co-localization of rhizome-enriched genes with rhizome-related QTLs in rice and sorghum generated functional candidates for future cloning of genes associated with rhizome growth and development.