The Duckweed Genomes


Book Description

This book tells the story behind the first Spirodela genome sequencing project. Further, it describes the current genomics applications of these findings, and efforts to sequence new genomes within the family. The closing chapters address the sequencing of the over 1 Gigabase Wolffia genomes, which could have major impacts on genome evolution and agricultural research. The duckweed or Lemnaceae family is a collection of 5 genera and 37 species of the smallest, fastest-growing flowering plants. Many of these aquatic monocotyledonous plants can grow all over the world, in a variety of climates. Given their simplified and neotenous morphology, duckweeds have been researched for several decades as a model species for plant physiology and ecotoxicological research, contributing to our understanding e.g. of flowering response, plant circadian systems, sulfur assimilation pathways and auxin biosynthesis. In addition, duckweed-based treatment has been a favorite and feasible means, especially in developing countries, of removing phosphorus and pharmaceutical chemicals from sewage and wastewater. With a dry annual mass yield per hectare of up to 80 tonnes (equivalent to 10 tonnes of protein), duckweed is also a promising aquatic crop in new modern and sustainable agriculture. Besides being an excellent primary or supplemental feedstock for the production of livestock and fish, duckweed biomass can be utilized as a potential resource for human nutrition, biofuel, or bioplastics, depending on water quality as well as protein or starch accumulating procedures. These academic and commercial interests have led to international efforts to sequence the Spirodela polyrhiza genome, the smallest and most ancient genome in the family.




Genomics and Transcriptomics of the Greater Duckweed, Spirodela Polyrhiza, a Model for Aquatic Biology


Book Description

My thesis provides the first whole genome analysis of an aquatic plant, Spirodela polyrhiza and a reference genome for a new order among the monocotelydonous angiosperms. The Lemnoideae belong to the order of the Alismatales and are commonly known as duckweeds, the smallest, fastest growing, and simplest of aquatic plants, thus telling them apart is not a trivial task. Whereas a simple and accessible protocol has been established for land plants by the Consortium for the Barcode of Life with seven universal DNA barcoding markers, we found that atpF-atpH noncoding spacer is the most promising marker for duckweed species-level identification. Furthermore, our assembly and annotation of the Spirodela chloroplast and mitochondrial genomes open an opportunity of population-level classification. A key to our understanding of the evolution of a species and its potential use is the gene content of the organism. Therefore, we sequenced Spirodela polyrhiza 7498 that has one of the smallest genomes with 158 Mb within this subfamily of species. The genome contains 19,623 predicted protein-coding genes, sharing a total of 8,255 common gene families with Arabidopsis, tomato, banana, and rice despite a significantly reduced gene number. Reduced gene families and missing genes reflect changes consistent with its compact and reduced morphogenesis or forever-young life style, aquatic suspension, and suppression of juvenile-to-adult transition. Spirodela exhibits a remarkable phenotypic plasticity to adapt to cold weather in winter. We identified and functionally annotated 362 differentially expressed genes, which open a major step towards understanding the molecular network underlying vegetative frond dormancy. Moreover, the expression data for lipid and starch biosynthesis together with the turion-specific transcriptional genes from our RNA-Seq data could be ideal targets to develop duckweeds into oil crops. Thanks to its unique and fascinating biology, applications of duckweed in water remediation and as a renewable energy source are predicted to have a bright future. The genome sequence of Spirodela provides the first step to identify, understand, and improve relevant traits for specific target applications.







Plant Genomes


Book Description

Recent major advances in the field of comparative genomics and cytogenomics of plants, particularly associated with the completion of ambitious genome projects, have uncovered astonishing facets of the architecture and evolutionary history of plant genomes. The aim of this book was to review these recent developments as well as their implications in our understanding of the mechanisms which drive plant diversity. New insights into the evolution of gene functions, gene families and genome size are presented, with particular emphasis on the evolutionary impact of polyploidization and transposable elements. Knowledge on the structure and evolution of plant sex chromosomes, centromeres and microRNAs is reviewed and updated. Taken together, the contributions by internationally recognized experts present a panoramic overview of the structural features and evolutionary dynamics of plant genomes.This volume of Genome Dynamics will provide researchers, teachers and students in the fields of biology and agronomy with a valuable source of current knowledge on plant genomes.







Plant Comparative Genomics


Book Description

This detailed book presents recent methodologies for the task of inspecting the genomic world of plants, extracting valuable information, and presenting it in a readable way. With a focus on bioinformatics tools, the volume explores phylogenetics and evolution, Omics analysis, as well as experimental procedures for trait characterization. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of vital expert implementation advice that will lead to successful results. Authoritative and practical, Plant Comparative Genomics serves as an ideal resource for researchers looking to implement comparative tools in order to explore their genomic data for their daily scientific work.




Handbook of Glycosyltransferases and Related Genes


Book Description

The so-called postgenomic research era has now been launched, and the field of gly cobiology and glycotechnology has become one of the most important areas in life science because glycosylation is the most common post-translational modification reaction of proteins in vivo. On the basis of Swiss-Prot data, over 50% proteins are known to undergo glycosylation, but in fact the actual functions of most of the sugar chains in the glycoconjugates remain unknown. The complex carbohydrate chains of glycoproteins, glycolipids, and proteoglycans represent the secondary gene products formed through the reactions of glycosyl transferases. The regulation of the biosynthesis of sugar chains is under the control of the expression of glycosyltransferases, their substrate specificity, and their local ization in specific tissue sites. There is a growing body of evidence to suggest that these enzymes play pivotal roles in a variety of important cellular differentiation and developmental events, as well as in disease processes. Over 300 glycosyltransferases appear to exist in mammalian tissues. If the genes that have been purified and cloned from various species such as humans, cattle, pigs, rats and mice are counted as one, approximately 110 glycogenes that encode glycosyltransferases and related genes have been cloned at present, and this number continues to grow each day. However, most of the functions of the glycosyltransferase genes and related genes are unknown. This fact has stimulated numerous new and interesting approaches in molecular biologi cal investigations.




Genetics and Genomics of Pineapple


Book Description

This book is the first comprehensive volume on the genetics and genomics of pineapple and provides an overview of the current state of pineapple research. Pineapple [Ananas comosus (L.) Merr.] is the second most important tropical fruit after banana in term of international trade. Its features are advantageous for genomic research: it has a small genome of 527 Mb which is diploid and vegetatively propagated; it is monocot, closely related to the grass family that includes major cereal crops, wheat, rice, corn, sorghum, and millet; and it serves as an out group for genetic and genomic research in grasses. In addition to exploring the evolution and improvement of pineapple, this work examines the pineapple genome with respect to genome structure and organization, comparative analyses with other angiosperm genomes, transcription factors, disease resistance, and circadian clock regulation of CAM related genes. With chapters covering botanical, genetic, genomic, and applied aspects of pineapple, this text also encourages the application of genomic technologies and suggests future prospects.







The Molecular Biology of Plant Cells


Book Description

Plant cell structure and function; Gene expression and its regulation in plant cells; The manipulation of plant cells.