Single-cell transcriptomics : a high-resolution avenue for plant functional genomics

Plant function is the result of the concerted action of single cells in different tissues. Advances in RNA-seq technologies and tissue processing allow us now to capture transcriptional changes at single-cell resolution. The incredible potential of single-cell RNA-seq lies in the novel ability to study and exploit regulatory processes in complex tissues based on the behaviour of single cells. Importantly, the independence from reporter lines allows the analysis of any given tissue in any plant. While there are challenges associated with the handling and analysis of complex datasets, the opportunities are unique to generate knowledge of tissue functions in unprecedented detail and to facilitate the application of such information by mapping cellular functions and interactions in a plant cell atlas. [Abstract copyright: Copyright © 2019 The Authors. Published by Elsevier Ltd.. All rights reserved.

Plant genomics – a way forward?

This report was presented at the UK Organic Research 2002 Conference. Diseases of plants cause significant losses in crop yield and quality. Plants contain a battery of genes whose role is to prevent pathogens invading. Their effective use in crop plants is very important in crop production and especially in chemical free cropping systems. Such genes are introduced into crop varieties by plant breeding. The new science of genomics may enable scientists to recognise all the resistance genes present in a plant. This will eventually allow plant breeders to more precisely and rapidly select useful resistant plants in their breeding programmes. Furthermore, genomics could enable effective deployment of these genes in cropping systems, so providing more durable resistance

Genomics Era for Plants and Crop Species – Advances Made and Needed Tasks Ahead

Historically, unintentional plant selection and subsequent crop domestication, coupled with the need and desire to get more food and feed products, have resulted in the continuous development of plant breeding and genetics efforts. The progress made toward this goal elucidated plant genome compositions and led to decoding the full DNA sequences of plant genomes controlling the entire plant life. Plant genomics aims to develop high-throughput genome-wide-scale technologies, tools, and methodologies to elucidate the basics of genetic traits/characteristics, genetic diversities, and by-product production; to understand the phenotypic development throughout plant ontogenesis with genetic by environmental interactions; to map important loci in the genome; and to accelerate crop improvement. Plant genomics research efforts have continuously increased in the past 30 years due to the availability of cost-effective, high-throughput DNA sequencing platforms that resulted in fully sequenced 100 plant genomes with broad implications for every aspect of plant biology research and application. These technological advances, however, also have generated many unexpected challenges and grand tasks ahead. In this introductory chapter, I aimed briefly to summarize some advances made in plant genomics studies in the past three decades, plant genome sequencing efforts, current state-of-the-art technological developments of genomics era, and some of current grand challenges and needed tasks ahead in the genomics and post-genomics era. I also highlighted the related book chapters contributed by different authors in this book

Multi-criteria assessment of ethical aspects in fresh tomato systems: Plant genomics technology innovation and food policy uses

Product assessment for imperceptible characteristics like environmental impact, healthfulness, naturalness, and fairness is a helpful tool in product innovation and for enhancing socially responsible conduct. In this study we apply multiple criteria analysis for the assessment of fresh tomatoes in terms of consumer perceptions regarding the above characteristics. The generated indices provide an explicit and comprehensive representation of consumer perceptions. Existing tomato products from the Dutch market are ranked alongside (reasonable conjectures of) potential products to be developed with the use of plant genomics technology. The results are interpreted to provide insights into the socially optimal use of (plant genomics) technology for fresh tomato production. Policy uses are highlighted.Ethical assessment, corporate societal responsibility, multiple criteria., Demand and Price Analysis, Research and Development/Tech Change/Emerging Technologies,

Sphagnum physiology in the context of changing climate: emergent influences of genomics, modelling and host-microbiome interactions on understanding ecosystem function.

Peatlands harbour more than one-third of terrestrial carbon leading to the argument that the bryophytes, as major components of peatland ecosystems, store more organic carbon in soils than any other collective plant taxa. Plants of the genus Sphagnum are important components of peatland ecosystems and are potentially vulnerable to changing climatic conditions. However, the response of Sphagnum to rising temperatures, elevated CO2 and shifts in local hydrology have yet to be fully characterized. In this review, we examine Sphagnum biology and ecology and explore the role of this group of keystone species and its associated microbiome in carbon and nitrogen cycling using literature review and model simulations. Several issues are highlighted including the consequences of a variable environment on plant-microbiome interactions, uncertainty associated with CO2 diffusion resistances and the relationship between fixed N and that partitioned to the photosynthetic apparatus. We note that the Sphagnum fallax genome is currently being sequenced and outline potential applications of population-level genomics and corresponding plant photosynthesis and microbial metabolic modelling techniques. We highlight Sphagnum as a model organism to explore ecosystem response to a changing climate and to define the role that Sphagnum can play at the intersection of physiology, genetics and functional genomics

GreenPhylDB: A Gene Family Database for plant functional Genomics

With the increasing number of genomes being sequenced, a major objective is to transfer accurate annotation from characterised proteins to uncharacterised sequences. Consequently, comparative genomics has become a usual and efficient strategy in functional genomics. The release of various annotated genomes of plants, such as _O. sativa_ and _A. thaliana_, has allowed setting up comprehensive lists of gene families defined by automated methods. However, like for gene sequence, manual curation of gene families is an important requirement that has to be undertaken. GreenPhylDB comprises protein sequences of 12 plant species fully sequenced that were grouped into homeomorphic families using similarity-based methods. Clusters are finally processed by phylogenetic analysis to infer orthologs and paralogs that will be particularly helpful to study genome evolution. Previously, each cluster has to be curated (i.e. properly named and classified) using different sources of information. A web interface for plant gene families’ curation was developed for that purpose. This interface, accessible on GreenPhylDB ("http://greenphyl.cirad.fr":http://greenphyl.cirad.fr), centralizes external references (e.g. InterPro, KEGG, Swiss-Prot, PIRSF, Pubmed) related to all gene members of the clusters and shows statistics and automatic analysis. We believe that this synthetic view of data available for a gene cluster, combined with basic guidelines, is an efficient way to provide reliable method for gene family annotations

GreenPhylDB v2.0: An improved database for plant functional genomics

Poster presented at 2009 Annual Research Meeting of the Generation Challenge Programme. Bamako (Mali), 20-23 September 200