Plant Genes, Genomes and Genetics

Book Preface

The word “plant” has many meanings

One goal of this book is to highlight the aspects of molecular biology that are unique to plants, and that represent mechanisms that cannot be understood simply by studying animals, yeast or bacteria.We therefore need to spend some time discussing what we mean by the word “plant”, which, perhaps surprisingly, does not have a simple or universally accepted definition.

When most people think of a plant, they generally immediately come up with an image of a tomato plant, or a petunia, or corn. A scientist might think of Arabidopsis thaliana, the tiny weed that has been domesticated by molecular biologists. All these are examples of flowering plants (angiosperms), which are the dominant forms of land plants on Earth today. The flowering plants represent a large group that originated in the early Cretaceous (∼140 million years ago, although the exact date is subject to much current debate); the group has subsequently diversified to produce most trees, shrubs, and herbs. The flowering plants include more than 300 000 species; only a few thousand are cultivated, and surprisingly, only a few of these – fewer than twenty – produce the vastmajority of the food for all of humanity.

The term “plant” is often used to mean “land plant”, amuch larger group that includes the flowering plants, but also the gymnosperms, ferns, lycophytes, mosses, hornworts and liverworts. This large group is monophyletic, a term that refers to all being descendants of a common ancestor, and is often called the Embryophytes because all members produce embryos retained on the parent plant. A phylogeny of the Embryophyta is presented in Figure 1, which is assembled on the basis of the main characteristics that define the major groups of plants. Clades (or groups) within the land plants include the seed plants (flowering plants plus gymnosperms, distinguished by how they bear their seeds) and other vascular plants [ferns (pteridophytes) and lycophytes], in which the streptophytes green plants (Viridiplantae) land plants (Embryophyta) vascular plants seed plants red algae Coleochaete other green algae glaucophytes Chara mosses lycophytes angiosperms gymnosperms ferns hornworts liverworts organisms with primary endosymbionts Figure 1 Phylogeny of organisms that originated with the primary endosymbiosis, in which a eukaryote acquired a symbiotic cyanobacterium. Superimposed on the phylogeny is a Venn diagram of major groups. While the green plants (Viridiplantae) and streptophytes are sometimes called “plants”, in this book we will use the term “plant” to refer to the land plants, the group shaded in green. Subgroups within the land plants are also indicated. diploid sporophyte forms on the independent gametophyte, and dispersal occurs via spores. In contrast, the non-vascular plants (hornworts and liverworts) are distinguished not only by the absence of phloem and xylem vessels, but by having a dominant gametophytic (haploid) stage of life and only a short lived sporophytic (diploid) stage.

Contents

PART I: PLANT GENOMES AND GENES

• Chapter 1 Plant genetic material
• Chapter 2 The shifting genomic landscape
• Chapter 3 Transposable elements
• Chapter 4 Chromatin, centromeres and telomeres
• Chapter 5 Genomes of organelles

PART II: TRANSCRIBING PLANT GENES

• Chapter 6 RNA
• Chapter 7 The plant RNA polymerases
• Chapter 8 Making mRNAs – Control of transcription by RNA polymerase II
• Chapter 9 Transcription factors interpret cis-regulatory information
• Chapter 10 Control of transcription factor activity
• Chapter 11 Small RNAs
• Chapter 12 Chromatin and gene expression

PART III: FROM RNA TO PROTEINS

• Chapter 13 RNA processing and transport
• Chapter 14 Fate of RNA
• Chapter 15 Translation of RNA
• Chapter 16 Protein folding and transport
• Chapter 17 Protein degradation