Day 3 :
- Track 15: Transcriptomics and Proteomics of Plants, Track 16: Transcriptome technologies market, Track 17: New Horizons to the Transcriptome
Chair
Patrick Xuechun Zhao
Samuel Roberts Noble Foundation, USA
Co-Chair
Zsolt Ponya
Kaposvar University, Hungary
Session Introduction
Patrick Xuechun Zhao
Samuel Roberts Noble Foundation, USA
Title: The LegumeIP (2015 release) - a web-based comparative genomics and gene expression atlas platform to study gene function and genome evolution in legumes
Time : 09:30-09:50
Biography:
Dr. Patrick Xuechun Zhao is an Associate Professor of Bioinformatics and Computational Biology at the Samuel Roberts Noble Foundation. Dr. Zhao received his Ph.D. degree in Communication and Information Systems from Shanghai Jiao Tong University in 2000. After his graduation, he joined the Department of Biochemistry and Molecular Biology, School of Medicine, University of Louisville, as a research associate developing bioinformatics technologies to discover genes and biological networks that are essential to the determination of the normal aging process, in particular those related to successful aging in centenarians. In 2004, he joined the Samuel Roberts Noble Foundation as an Assistant Professor and Faculty Principle Investigator. Dr. Zhao’s current research centers on bioinformatics and computational biology, plant and soil microbe functional genomics, statistical machine learning for ‘omics’ data mining and biological knowledge discovery. Dr. Zhao has published over 60 papers in refereed scientific journals. He also published a series of software and bioinformatics resources including a dozen of databases and web servers for plant gene function and gene regulatory network analysis, which are publicly available and used by life scientists from around the world.
Abstract:
Legumes are one of the most evolutionarily well-adapted plants that play vital roles in ecology and agriculture. They have the unique ability to carry out symbiotic nitrogen fixation (SNF) through endosymbiotic interactions with bacteria. Aside from the root nodulation and nitrogen fixation symbiosis with rhizobia, legumes possess many unique features that are not found in the model plant Arabidopsis thaliana, such as mycorrhization, compound leaf development, protein-rich physiology, a profuse secondary metabolism, glandular trichome development and border cells in roots. We present LegumeIP1 (http://plantgrn.noble.org/LegumeIP/v2/) - a web-based comparative genomics and gene expression atlas platform that integrates large-scale genomics, transcriptomics data and bioinformatics tools to study gene function and genome evolution in legumes. The LegumeIP (2015 release) hosts 1) genomic data such as genomics sequences, Sanger sequencing- and RNA-seq-based expressed sequence tag (EST) sequences, gene models, and annotations that are cross-refereed to the UniProt TrEMBL, InterProScan, Gene Ontology (GO) and the Kyoto Encyclopedia of Genes (KEGG) reference database for six model and crop legumes: Medicago truncatula, Glycine max (soybean), Lotus japonicus, Phaseolus vulgaris (common bean), Cicer arietinumx (chickpea) and Cajanus cajan (pigeon pea), and two reference model plants: A. thaliana and Poplar trichocarpa; 2) gene expression atlases that include 276 array hybridizations from L. japonicas, 1,915 array hybridizations from M. truncatula, 1,379 gene expression profiles of G. max, and 4,164 array hybridizations of A. thaliana; and 3) gene families, orthologous groups, gene family phylogenetic trees and syntenic regions across hosted species. LegumeIP also integrates a suite of bioinformatics tools for exploring and analyzing 1) whole-genome synteny and detailed syntenic gene alignments; 2) gene annotations, gene families and orthologous groups; and 3) gene expression patterns, clusters and co-expression networks.
Vishwanath Sollapura
Agriculture and Agri-Food, Canada
Title: Comparative transcriptome analysis between mature pollen and stigma of Brassicaceae and Triticeae crop species.
Time : 09:50-10:10
Biography:
Dr. Vishwanath Sollapura completed his PhD in plant molecular biology in 2013 from Carleton University, Ottawa, Canada, where he identified and characterized three alcohol-forming fatty acyl-CoA reductases associated with suberin biopolymer. Prior to that, he worked in India for the plant biotech company Avesthagen Ltd on a project to generate Poly Unsaturated Fatty Acids (PUFAs) in Sunflower and Mustard oilseed plants using recombinant approaches. Currently, he is working as a NSERC visiting post-doctoral fellow at Agriculture and Agrifood Canada in Dr. Laurian Robert’s laboratory focusing on the molecular genetics of crop flower development.
Abstract:
Pollination is an important step in Angiosperm sexual reproduction that involves pollen adhesion, recognition, rejection/acceptance, hydration, germination, and other cell-cell interactions with the stigma (the female receptive tissue). A detailed knowledge of the transcriptomes of the mature pollen grain and stigma will help in further understand these interactions and identify the various molecular participants. This fundamental knowledge will in turn provide tools to enable molecular interventions aimed at managing pollination and thereby leading to improved sustainable crop production. We are currently working towards assembling high quality pollen and stigma reference transcriptomes for both dicots (Brassicaceae) and monocots (Triticeae) crops using next-generation sequencing of transcriptomes (RNA-seq). We report the results of transcriptome analyses performed on the mature pollen and stigma of Brassica carinata and Triticale (x Triticosecale Wittmack), two crops with potential applications as bio-industrial platforms. Both Illumina and 454 sequencing were performed generating about 100 million (100 bp lengths) and 1 million (400 bp lengths) paired reads per sample respectively. The RNA-seq analysis was carried out using CLC genomics workbench 7.0 (Qiagen Inc.). Comparisons of transcript profiles between pollen and stigma of B carinata and Triticale and the contribution of polyploidy to reproductive gene expression will be presented. The reference transcriptome generated for B carinata and triticale will facilitate the study of other members of the Brassicaceae (e.g. B. napus, B. oleracea, B. rapa) and Triticeae (wheat, barley, rye) which together represent the most cultivated crops in Canada
Zsolt Ponya
Kaposvar University, Hungary
Title: How gamete micromanipulation and cell engineering can contribute to establishing a time scale for performing transcriptomics studies in wheat (Triticum aestivum, L.) during fertilisation and proembryo formation
Time : 10:10-10:30
Biography:
Zsolt Pónya has completed his PhD at the age of 32 years from the Eötvös Lóránd University of Arts and Sciences, Budapest, Hungary, and following obtaining his degree, he has launched his postdoctoral studies at the University of Siena, Italy, followed by a postdoc research fellowship at the Ben-Gurion University of the Negev, Israel. He is currently a senior scientist at the University of Kaposvár, Hungary. He has published a number of papers in reputed international journals and is a member of the editorial board of several prestigious scientific journals
Abstract:
Land plants are sessile organisms; consequently they had to evolve powerful genetic and epigenetic tools and strategies to ward off perils of their surroundings and to render them adaptive to environmental stress. Additionally, they have to be capable of fast tracking the adaptive optima imposed by transient selective forces while permanently tuning their body to cope with the challenges posed by the ever-changing environment. Thus, in terms of genetic plasticity, land plants are by far more flexible organisms as compared to animals as they have much more dynamic and plastic genome. Furthermore, unlike in mammals, in angiosperm plants germline cells are not set aside at an early stage during development so cells partaking of reproduction can be viewed as the depositories of “cell memories” which have accumulated due to survival/adaptation strategies having proven successful in the cells of the mother plant that, through numerous cell divisions in the sporophytic generation, ultimately serves as the source of progenitor cells for the gametes produced during the haploid developmental stage. This very fact is thought to be behind the evolutionary success of land plants and also makes them an attractive system to study genetic plasticity. In this sense angiosperm nucellar cells are particularly interesting as they reveal versatile developmental modalities; they can either use or avoid meiosis without compromising subsequent development. Normally, once the molecular “decision” is made, a highly conserved, modular developmental pathway unfolds producing the female gametophyte (FG) with a haploid egg. Occasionally, the egg cell can go through parthenogenesis which is an extraordinary phenomenon whereby the egg cell initiates cell division without paternal genetic contribution. Although the study of parthenogenesis/apomixis in angiosperms has recently leapt ahead, the cellular and molecular events of the activation of the egg foregoing sperm incorporation remains to be elucidated. To explore whether the cascade events of signal transduction triggered by sperm-egg fusion and leading to egg activation can be elicited in lieu of fertilisation, egg cells of wheat isolated at different stages of in situ development were microinjected with the DefH9-iaaM gene, which had been previously demonstrated to confer auxin synthesis specifically on ovules and derived tissues in other systems as well as induce parthenocarpy in several plant species (tobacco, egg plant, tomato). Furthermore, wheat zygotes were used to study the relationship between cell cycle and morphogenesis, as in the angiosperm zygote cellular differentiation and cell cycle control are closely linked because cytoplasmic reorganisation occurs concomitantly upon fertilisation leading to asymmetrical cell cleavage. By exploiting a protein delivery system facilitating functional studies in living cells, an antibody raised against the 17-amino acids at the C-terminus of a synthetic peptide based on the deduced protein encoded by the cdc2 gene, a key protein in cell cycle regulation isolated previously from wheat, was introduced into in vitro fertilized wheat egg cells at defined times permitting the chronological follow-up of the impact of blocking cdc2 activity on morphogenesis during wheat zygote/proembryo development. The findings of microinjecting DNA encoding Rho GTPases implicated in cellular response to extracellular signals by inducing coordinated changes in the organisation of the actin cytoskeleton and in transcription to drive a wide range of fundamental biological processes such as cell cycle and morphogenesis, will also be presented. In order to ensure the maintenance of in planta observed polarity of in vitro fertilised egg cells, which was found to be lost during in vitro culture, a micromanipulation-based technique enabling re-implantation of fusion products into maternal tissues (ovules) was elaborated. The relevance to stem cell research of our preliminary results of exploratory cell engineering experiments on the creation of half clones/cybrids via fusion of karyoplasts isolated from unfertilised wheat egg cells and cytoplasts stemming from in vitro fertilised female gametes, will be addressed. In practical terms research of this kind may ultimately have ramifications in achieving clonal propagation in agriculturally important plants through seeds hence contributing to efforts aimed at fixing desirable gene combinations/hybrid vigour in crops and to defining time windows for isolating egg cells/zygotes/proembryos for trancriptomics studies in wheat.
Jianbo Wang
Wuhan University, China
Title: Transcriptome and small RNA gene expression changes in synthetic allohexaploids of Brassica
Time : 10:45-11:05
Biography:
Jianbo Wang has completed his PhD from Wuhan University. He is interested in the research on plant molecular evolution and has published more than 30 papers in reputed journals.
Abstract:
Polyploidy played important roles in promoting plant genome evolution through genomic merging and doubling. We compared transcriptome and small RNA expression differences between a synthetic Brassica allohexaploid and its parents using RNA-seq approach. Total of 29260, 29060 and 29697 genes were expressed in B. rapa, B.carinata and the allohexaploid respectively. The majority of the 3184 DEGs between the allohexaploid and B. rapa were involved in photosynthesis, biosynthesis of secondary metabolites and circadian rhythm. For the 2233 DEGs between the hexaploid and B. carinata, many played roles in photosynthesis, plant hormone signal transduction, biosynthesis of secondary metabolites and limonene and pinene degradation. There were more differences between the allohexaploid and its paternal parent than that between it and its maternalparent in gene expression. Many methyltransferase genes and transcription factor genes showed differential expression between the hexaploid and its parents. On the other hand, we detected 613, 784 and 742 miRNAs expressed in B. rapa, B. carinata and the allohexaploid respectively and 618 miRNA genes were differentially expressed between Brassica hexaploid and its parents while 425 miRNA genes showed non-additive expression in the allohexaploid. Moreover, many non-additively expressed miRNAs were repressed in the allohexaploid and there was a bias towards repression of B. rapami RNA genes which is consistent with progenitor biased gene repression in these allopolyploids. Our study represented the comprehensive analysis of functional gene and small RNA gene expressions in allopolyploid which would lead to better understanding of plasticity of allopolyploid genomes.
Lerato BameTsalaemang Matsaunyane
Agricultural Research Council-Vegetable and Ornamental Plant Institute (ARC-VOPI), South Africa
Title: Molecular characterization of the unintended and unexpected effects of genetic engineering on the endogenous Solanum tuberosum genome
Time : 11:05-11:25
Biography:
Lerato Bame Tsalaemang Matsaunyane is an alumni of the University of Free State, and she has done her BSc in Biological Sciences and completed her Master’s degree from University of Pretoria. After completion of her postgraduate studies, she then joined the University of Johannesburg as a Doctorate student. She has presented her research findings from her postgraduate degrees in both national and international conferences and has used her skill to mentor and train students for internships as well as postgraduate qualifications. She is currently a Molecular Biologist at the Agricultural Research Council (ARC) at the Vegetable and Ornamental Plant Institute (South Africa) in the Crop Protection Division.
Abstract:
Genetically modified (GM) crops with diverse traits are currently developed and produced to generate social, economic and environmental benefits focused on amongst others, resource-poor farmers. However, current safety assessments of these GM crops are thought to be biased as they focus on potential hazards posed by the inserted transgene and its products. As a result, a project was initiated to study the unintended effects of the integration of the transgene within the host genome. The model plant for the study was a Malus domestica polygalacturonase inhibiting protein 1 (Mdpgip1) transgenic potato produced for enhanced resistance against Verticillium wilt. Genome walking revealed that the T-DNA containing the transgene was successfully inserted into the potato genome with no non-T-DNA sequences from the binary vector having been inserted into the potato genome. Furthermore, studies indicated the insertion site of the Mdpgip1 transgene as being adjacent to the photosystem QB gene on chromosome 1 of the potato genome. DNA fingerprinting analysis revealed unintended effects that resulted in alterations in the expression genes encoding the PsaC, AFG3, 25S rRNA, tryptophan/tyrosine permease, Ef-Tu domain, SKP1-like 1A, StPGIP1 and XTH proteins in the transgenic. It can thus be concluded that the insertion and expression of the Mdpgip1 transgene in the transgenic potato does not appear to have a major effect on the gene expression levels of the endogenous potato genes and that the transgenic potato is significantly equivalent to its traditional counterpart with a few quantifiable differences as determined by tools used for gene expression analysis.
Ozge Celik
Ä°stanbul Kultur University, Turkey
Title: Differential regulation of antioxidative gene expressions in response to salt stress in rice
Time : 11:25-11:45
Biography:
Özge Çelik has received her PhD degree from Istanbul University (Istanbul, Turkey) in 2010. She is working on mutation breeding, abiotic stress tolerance, molecular marker analysis and plant molecular biology. She is currently an Associate Professor of Molecular Biology and Genetics Department at the Istanbul Kultur University. She has authored more than 35 publications in the fields of plant stress tolerance and molecular biology and has been serving as an editorial board member of repute. She has published one scientific book and a chapter in a reputed book in the field of Plant Science.
Abstract:
Rice (Oryza sativa L.) is one of the most important crops because it is a nutritional source of more than one-third of the world population. Soil salinity is one of the most important abiotic stress factors that affects plant growth and productivity adversely. Rice growth and yield is also affected by salinity and at the seedling stage although it is known to be susceptible to salinity. Reactive oxygen species are induced by salt stress and some responsive mechanisms are evolved against to the detrimental effects caused by salt stress. Salinity response is especially controlled by obtaining homeostasis between antioxidative mechanisms and accumulation of reactive oxygen species (ROS) produced as a result of oxidative stress caused by salinity. It is known that combined expression profiles of antioxidative system enzymes may provide increased tolerance capacity. Therefore, the expression profiles of antioxidative enzymes in two different rice cultivars which have different salt sensitivities at four different salt stress conditions, were determined. Salinity responses of two different rice varieties were investigated at seedling stage. Four different salinity treatments were then applied using Yoshida solution containing 0, 30, 90, 150 and 210 mM NaCl to the nutrient solution for seven days. At the end of the seven days, the leaves were harvested and stored at −20oC for further experiments. The salt stress responsive gene specific primers were amplified by designed primers due to the 3’-UTR regions of each of the following genes by aligning all available related genes in the databases of NCBI and KOME: Mn-SOD, Cu/Zn-SOD, Fe-SOD, Cytosolic APX, Thylakoid-bound APX, stromal APX, Cytosolic GR and CatA. Mn-SOD was consisted with the trend of variation in SOD activities of rice varieties. The expression pattern of CAT A gene was markedly decreased compared to control in both rice varieties. Str-APX gene expression was up-regulated during salt stress treatments in both rice varieties. Transcript levels of Cyt-APX and Thy-APX were up-regulated in accordance with increasing salt stress in Osmancık-97 variety. The expression pattern of gene encoding enzyme Cyt-GR1 showed a gradual up-regulation as a response to subjected increasing NaCl stress in Mevlutbey variety while only after 90 mM treatment, an upregulation was observed for Osmancık variety. These data indicated that the antioxidative responses of salt tolerant and salt sensitive rice varieties are differentially regulated.
Monika Bansal
Lovely Professsional University, India
Title: Isolation and functional characterization of cold stress inducible promoter CAT01 from tomato
Time : 11:45-12:05
Biography:
Monika Bansal completed her PhD on the topic “Genetic transformation of Tomato for introduction of salinity tolerance. She worked as Senior Research Fellow at Haryana Agriculture University (June 2003-Dec 2003). Later she completed her Post-Doctoral fellow in the UGC funded project “Isolation and characterization of stress Inducible Promoter from Tomato" at Delhi University South Campus with Dr. Arun Sharma (Aug 2008 –Aug2011). She joined as Assistant Professor at Asian Institution Affiliated to Punjab University, Patiala during August 2011-July 2013). From August 2014 till date she is working as Assistant Professor at School of Agriculture, Lovely Professional University.
Abstract:
Environmental stress such as drought, salinity and extreme temperatures are the major factors limiting plant growth and productivity. Cold stress leads to diverse change in transcription and translation of genes involved in developmental and physiological metabolism of plants. Constitutive over expression of transgenes imparting stress tolerance may hamper plant growth and productivity. It is desirable to produce transgenic plants that accumulate transgenic products only under stress conditions. To identify stress related transcripts we had utilized cold subtracted cDNA library to monitor gene expression changes after 24 hours of cold stress in tomato seedlings. Relative mRNA levels of cold stress associated gene CAT01 (NAC type transcription factor) from cold treated sample was compared with wild types. Sequence upstream of start codon from this transcript was selected to design the primers, promoter sequence was fused with GUS reporter gene and the recombinant transgenes was introduced into tomato cv. Pusa Ruby with Agrobacterium tumefaciens mediated genetic transformation. Histo-chemical and florometric analyses revealed promoter is inducible under all abioticstress conditions. This promoter is effective and desirable for deriving a low constitutive transgene expression under normal condition and high induction in response to cold, salt and drought stress. This method shall be advantageous as it will not have a major impact on plant biomass and yield.
Closing Ceremony
Hetalkumar J Panchal
Navsari Agricultural University, India
Title: De novo RNA seq assembly and annotation of important legume-Vicia sativa L. (SRR403901)
Biography:
Hetalkumar J Panchal is currently working as an Associate Professor at Gujarat Agricultural Biotechnology Institute, Navsari Agricultural University (NAU), Surat, Gujarat (India). He has published more than 35 papers in national/international Journals and more than 30 papers in national and international conferences & seminars. He worked as Faculty of Bioinformatics (10 years) at MSc (Bioinformatics) course at Department of Computer Science, Sardar Patel University, Vallabh Vidyanagar, Gujarat (India). He is guiding 3 PhD students and has been amentor of the more than 25 dissertation thesis. He has delivered so many keynote lectures /expert lectures/invited talks. He serves as a visiting faculty/external examiner at various universities. He is associated with so many national and international journals as member of editorial board and as reviewer. He has received Best Paper Award in faculty category at National Conference on “Advanced Data Computing Communications & Security”. He is a member of Indian Science Congress Association (ISCA) and a Life Member of Computer Society of India.
Abstract:
Vicia sativa L. which is also known as common vetch; is a nitrogen fixing leguminous plant in the family Fabaceae. This study is focus on RNA-seq of Vicia sativa L. of SRR403901 from NCBI database for de novo Transcriptome analysis. A total of 12.4 million single reads were generated with N50 of 588 bp. Sequence assembly contained total 22748 contigs which is further search with known proteins, a total of 7652 genes were identified. Among these, only 500 unigenes were annotated with 18761 gene ontology (GO) functional categories and sequences mapped to 122 pathways by searching against the Kyoto Encyclopedia of Genes and Genomes pathway database (KEGG). These data will be useful for gene discovery and functional studies and the large number of transcripts reported in the current study will serve as a valuable genetic resource of the Vicia sativa L.