Current Genomics - Volume 11, Issue 1, 2010

It is my great pleasure as a Guest Editor of the journal Current Genomics to present you with a ‘hot topic issue’ on plant genomics. The complete sequence of genome of model plant Arabidopsis thaliana was a boost for plant genomics research. Following the path of Arabidopsis sequencing, hundreds of plant genomes are being sequenced and we have ocean of sequence data. It is a challenge for us to interpret the functions of thousands of genes. Surely, computational biology will be a great help in predicting functions of plant genes. Publicly available web based sequence annotation softwares are another resource to annotate and characterize plant genes. It is a challenge and responsibility for plant biologists to provide food, fiber and fuel for this exponentially increasing population. Sequences of model plants and crop plants will help us to understand the genome architectures of the plants and will help us to identify economically important genes. It is a well-established fact that a great alternative for whole genome sequencing is development of an EST (Expressed Sequence Tags) database. The ESTs will give us a snapshot of whole genome with a small percentage of cost of whole genome sequencing. The next generation sequencing including 454 sequencing (Roche Applied Sciences), Solexa system (Illumina) and SOliD system (Applied Biosystems) are also great resources for plant genomicists. These technologies will generate enormous amount of sequencing data, which will be beneficial to understand the basic physiology of plants. This issue of Current Genomics is a compilation of review articles on various facets of plant genomics written by experts. Das and Pandey discussed roles of calcium sensing proteins such calmodulin in abiotic stress response in plants. They especially discussed the roles of calcium dependent kinase genes in rice. Lelandais-Briere et al. elaborated the roles of micro RNAs, a group of non coding RNAs, in root development. Micro RNAs and short interfering RNAs are very powerful tools to suppress gene expressions and surely will become more effective means to study plant genomes since we have more and more plant genome sequence information available. Volk described how some of the tools of genomics could be used to study plant cryobiology. Microarray technology could be used to study gene expression in cryostressed plants. This will help us to understand plant stress response in cryogenic conditions and will help us to design better plant germplasm conservation strategies. Panthee and Cheng discussed use of molecular markers, and tools of transcriptomics, proteomics and metabolomics to study fungal disease in tomatoes. They highlighted how tools of genomics and other transgenic approaches could be implemented to develop disease resistant tomato cultivars. Zhang et al. presented a systems biology approach to study protein-protein interactome in plants. They explained how in silico methods along with experimental approaches like yeast two hybrid systems, affinity purification and mass spectrometry, biomolecular fluorescence complementation etc. could be used to understand the proteome of plants. Horvath discussed on applications of tools of genomics to understand the weediness traits of weeds. In particular, the author focused on use of EST databases and microarrays to understand the biology of weeds. Understanding the genomic architecture of weeds will help us to develop better weed control strategies. I would like to sincerely thank all the reviewers from across the globe for their valuable suggestions to improve the quality of research articles. Special thanks to Editor-in-Chief Dr. Christian Neri for encouragement for this special issue. It was a great opportunity for me to interact with scientists from all over the world including USA, India and France. I am convinced this issue will be useful for the plant scientists, academicians, industry professionals, students and plant genomics enthusiasts. I will be looking forward to editing another issue on plant genomics in future.

Perception of stimuli and activation of a signaling cascade is an intrinsic characteristic feature of all living organisms. Till date, several signaling pathways have been elucidated that are involved in multiple facets of growth and development of an organism. Exposure to unfavorable stimuli or stress condition activates different signaling cascades in both plants and animal. Being sessile, plants cannot move away from an unfavorable condition, and hence activate the molecular machinery to cope up or adjust against that particular stress condition. In plants, role of calcium as second messenger has been studied in detail in both abiotic and biotic stress signaling. Several calcium sensor proteins such as calmodulin (CaM), calcium dependent protein kinases (CDPK) and calcinuerin B-like (CBL) were discovered to play a crucial role in abiotic stress signaling in plants. Unlike CDPK, CBL and CaM are calcium-binding proteins, which do not have any protein kinase enzyme activity and interact with a target protein kinase termed as CBL-interacting protein kinase (CIPK) and CaM kinases respectively. Genome sequence analysis of Arabidopsis and rice has led to the identification of multigene familes of these calcium signaling protein kinases. Individual and global gene expression analysis of these protein kinase family members has been analyzed under several developmental and different abiotic stress conditions. In this review, we are trying to overview and emphasize the expressional analysis of calcium signaling protein kinases under different abiotic stress and developmental stages, and linking the expression to possible function for these kinases.

MicroRNAs are a class of non-coding RNAs involved in post-transcriptional control of gene expression, either via degradation or translational inhibition of target mRNAs. Both experimental and computational approaches have been used to identify miRNAs and their target genes. In plants, deep sequencing methods have recently allowed the analysis of small RNA diversity in different species and/or mutants. Most sequencing efforts have been concentrated on the identification of miRNAs and their mRNA targets have been predicted based on complementarity criteria. The recent demonstration that certain plant miRNAs could act partly via inhibition of protein translation certainly opens new fields of analysis for plant miRNA function on a broader group of targets. The roles of conserved miRNAs on target mRNA stability have been analysed in different species and defined common mechanisms in development and stress responses. In contrast, much less is known about expression patterns or functions of non-conserved miRNAs. In this review, we focus on the comparative analyses of plant small RNA diversity and the action of si/miRNAs in post-transcriptional regulation of some key genes involved in root development.

Plant cryobiology has primarily emerged from the classical fields of cryobiology and plant stress physiology. Cryopreservation tools are now available to geneticists for germplasm preservation and the field itself is advancing significantly through the use of molecular techniques. Long-term preservation of vegetatively propagated tissues can minimize the risks of long-term maintenance under tissue culture or field conditions. Cells can be successfully cryopreserved when the adverse affects of ice crystal formation are mitigated by the removal of water or procedures to limit ice formation and crystal growth. The addition of cryoprotectant solutions to hydrated cells may improve the survival of microdissected shoot tips or embryonic axes. Recent discoveries in the genetic pathways leading to cold acclimation and freezing tolerance suggest the involvement of key cold-regulated genes in the acquisition of cold tolerance in plant tissues. Model systems of banana and Arabidopsis have revealed the involvement of genes and proteins in the glycolytic and other metabolic pathways, particularly processes involved in dehydration tolerance, osmoprotection, and membrane transport. Furthermore, successful recovery appears to be dependent upon the presence of antioxidant protection from reactive oxygen species. Characterization of specific genes and proteins will lead to significant advances in plant cryobiology research.

Tomato (Solanum lycopersicum) is an important vegetable crop worldwide. Often times, its production is hindered by fungal diseases. Important fungal diseases limiting tomato production are late blight, caused by Phytophthora infestans, early blight, caused by Alternaria solanii, and septoria leaf spot, caused by Septoria lycopersici, fusarium wilt caused by Fusarium oxysporium fsp. oxysporium, and verticilium wilt caused by Verticilium dahlea. The Phytophthora infestans is the same fungus that caused the devastating loss of potato in Europe in 1845. A similar magnitude of crop loss in tomato has not occurred but Phytophthora infestans has caused the complete loss of tomato crops around the world on a small scale. Several attempts have been made through conventional breeding and the molecular biological approaches to understand the biology of host-pathogen interaction so that the disease can be managed and crop loss prevented. In this review, we present a comprehensive analysis of information produced by molecular genetic and genomic experiments on host-pathogen interactions of late blight, early blight, septoria leaf spot, verticilim wilt and fusarium wilt in tomato. Furthermore, approaches adopted to manage these diseases in tomato including genetic transformation are presented. Attempts made to link molecular markers with putative genes and their use in crop improvement are discussed.

Protein-protein interaction network represents an important aspect of systems biology. The understanding of the plant proteinprotein interaction network and interactome will provide crucial insights into the regulation of plant developmental, physiological, and pathological processes. In this review, we will first define the concept of plant interactome and the protein-protein interaction network. The significance of the plant interactome study will be discussed. We will then compare the pros and cons for different strategies for interactome mapping including yeast two-hybrid system (Y2H), affinity purification mass spectrometry (AP-MS), bimolecular fluorescence complementation (BiFC), and in silico prediction. The application of these platforms on specific plant biology questions will be further discussed. The recent advancements revealed the great potential for plant protein-protein interaction network and interactome to elucidate molecular mechanisms for signal transduction, stress responses, cell cycle control, pattern formation, and others. Mapping the plant interactome in model species will provide important guideline for the future study of plant biology.

Numerous genomic-based studies have provided insight to the physiological and evolutionary processes involved in developmental and environmental processes of model plants such as arabidopsis and rice. However, far fewer efforts have been attempted to use genomic resources to study physiological and evolutionary processes of weedy plants. Genomics-based tools such as extensive EST databases and microarrays have been developed for a limited number of weedy species, although application of information and resources developed for model plants and crops are possible and have been exploited. These tools have just begun to provide insights into the response of these weeds to herbivore and pathogen attack, survival of extreme environmental conditions, and interaction with crops. The potential of these tools to illuminate mechanisms controlling the traits that allow weeds to invade novel habitats, survive extreme environments, and that make weeds difficult to eradicate have potential for both improving crops and developing novel methods to control weeds.

Ascorbic acid (vitamin C, AA) has long been considered a food supplement necessary for life and for preventing scurvy. However, it has been reported that other small molecules such as retinoic acid (vitamin A) and different forms of calciferol (vitamin D) are directly involved in regulating the expression of numerous genes. These molecules bind to receptors that are differentially expressed in the embryo and are therefore crucial signalling molecules in vertebrate development. The question is: is ascorbic acid also a signalling molecule that regulates gene expression? We therefore present and discuss recent publications that demonstrate that AA regulates the expression of a battery of genes. We offer a clue to understanding the biochemical mechanism by which AA regulates gene expression. Finally we will discuss the question of a receptor for AA and its potential involvement in embryonic development and cell differentiation.

The importance of simulation software in current and future evolutionary and genomic studies is just confirmed by the recent publication of several new simulation tools. The forward-in-time simulation strategy has, therefore, re-emerged as a complement of coalescent simulation. Additionally, more efficient coalescent algorithms, the same as new ideas about the combined use of backward and forward strategies have recently appeared. In the present work, a previous review is updated to include some new forward simulation tools. When simulating at the genome-scale the conflict between efficiency (i.e. execution speed and memory usage) and flexibility (i.e. complex modeling capabilities) emerges. This is the pivot around which simulation of evolutionary processes should improve. In addition, some effort should be made to consider the process of developing simulation tools from the point of view of the software engineering theory. Finally, some new ideas and technologies as general purpose graphic processing units are commented.

High-throughput sequencing of eukaryotic genomes has revived interest in the structure and function of repetitive genomic sequences, previously referred to as junk DNA. Repetitive sequences, including transposable elements, are now believed to play a significant role in genomic differentiation and evolution. Some are also expressed as regulatory noncoding RNAs. Vast DNA databases exist for higher eukaryotes; however, with the exception of homologues of known repetitive-sequence-families and transposable elements, most repetitive elements still need to be annotated. Revolver and Superior, both discovered in the Triticeae, are novel classes of transposon- like genes and major components of large cereal genomes. Revolver was isolated from rye via genome subtraction of sequences common to rye and wheat. Superior was isolated from rye by cleavage with EcoO109I, the recognition sites of which consist of a 5'- PuGGNCCPy-3' multi-sequence. Revolver is 2929-3041 bp long with an inverted repeat sequence on each end. The Superior family elements are 1292-1432 bp in length, with divergent 5' regions, indicating the presence of considerable structural diversity. Revolver and Superior are transcriptionally active elements; Revolver harbors a single gene consisting of three exons and two introns, encoding a protein of 139 amino acid residues. Revolver variants range in size from 2665 bp to 4269 bp, with some variants lacking the 5' region, indicating structural diversity around the first exon. Revolver and Superior are dispersed across all seven chromosomes of rye. Revolver has existed since the diploid progenitor of wheat, and has been amplified or lost in several species during the evolution of the Triticeae. This article reviews the recently discovered Revolver and Superior families of plant transposons, which do not share identity with any known autonomous transposable elements or repetitive elements from any living species.

Recent advances into the understanding of molecular mechanism of chronic pain have been largely developed through the use of genetic manipulations. This is in part due to the scarcity of selective pharmacological tools, which can be readily solved by creating knockout or transgenic mice. By identifying new genes that are of import, our efforts can then be aimed at studying relevant signaling pathways, and combination of pharmacological manipulations with genetic models can be used to further examine the specific mechanisms involved in chronic pain. In this review, we will examine the genetic models that are currently in use to study chronic pain in the anterior cingulate cortex: knockout mice; transgenic mice; and the strength of combining pharmacology with these genetic models.