Introduction

What is the primary problem that plants face? They are not triffids (Wyndham, 1951); that is, they cannot move their place of residence if it becomes less than ideal, except through seed dispersal. In addition to being unable to move, plants can be extremely long-lived, and they are generally autotrophic so need only minerals, light, water, and air to grow. Thus, the genome must encode the enzymes that support the whole range of necessary metabolic processes, including photosynthesis, respiration, intermediary metabolism, mineral acquisition, and the synthesis of fatty acids, lipids, amino acids, nucleotides, and cofactors, many of which, in contrast, animals acquire through their diet. Although genomics studies, which take a global view of genomic information and how it is used to define the form and function of an organism, have a common thread that can be applied to almost any system, the diversity of plants means that, here, a single model cannot suffice. Plant genomics builds on centuries of observations and experiments designed to describe and understand many plant processes, which provides the basis for applying genomics and proteomics techniques to understand how plants grow and develop. However, the use of the suite of "-omics" methods must be considered experimental approaches with important limitations and challenges. These methods must be used in conjunction with other complementary techniques, such as microscopy, genetics, biochemistry, physiology, and cell biology, in order to acquire a more complete knowledge of plant biology. Much of the experimental detail and observations in plant biology have been made in very diverse plant material by using the plant that was most convenient in which to study the phenomena, rather than all the information being available in a convenient single model organism. Thus, algae may be appropriate models for photosynthesis and provide useful pointers as to which genes are involved but, conversely, cannot be useful for understanding, for example, how stresses in the roots might affect the same photosynthetic processes in a plant growing under drought or saline conditions. These historical experimental observations that span very diverse plant material are being recreated into model organisms with the application of the -omics techniques, as can be seen with the enormous data compilations from plants such as Arabidopsis as a model organism and rice, maize, and wheat as major agricultural crops. However, the availability of sequence information for a reasonable cost now means that the DNA sequence data is no longer restricted to these well-supported systems, even if the transcriptomic and proteomic data will be more difficult to obtain. Overall, the genomics approaches to plant biology will enhance knowledge of gene structure, function, and variability in plants. There are also areas in which work in plant biology has made unique contributions to genetics and genomics, from the description of transposable elements to ribonucleic acid (RNA) interference. The identification that small RNAs that are ubiquitous and can affect an enormously broad range of biological processes stems from work in plants. The linking of small interfering RNAs and DNA methylation on a whole-genome scale was made through plant genomics, although, as with many such discoveries, its wide importance has only been recognized following its application to human cells. Applying the -omics knowledge will lead to new methods of improving crop productivity, which is necessary for developing climate-resilient crops to meet the challenges of sustaining our food supply.

Deciphering entire plant genomes has become a reality with the advancements in high-throughput sequencing technologies. However, higher plants are a group of organisms with great variation in genome size, spanning more than 1500-fold variation. Because of this variation, there is not a single example that can be considered as the typical plant nuclear genome. However, the general organizational principle of the interspersion of low-copy number sequences with repetitive elements generally holds. Genome size does not necessarily correlate with the perceived complexity of a species. Some of the most intricate and morphologically complex plant species have relatively modest genome sizes, while seemingly simpler plants may contain surprisingly large genomic landscapes. Therefore, a typical plant genome is difficult to define because the contribution of additional DNA may have phenotypic effects independent of the actual sequence present. The adaptive advantages and constraints imposed by genome size can also be viewed through examples of polyploidization events that have frequently occurred during plant evolution. These genome duplications are followed by a restructuring of the resulting polyploid genome, which provides illustrations of the dynamic nature of plant genomes in response to their ecological niches. The gene duplications that result add a complication for both genome assembly and genetics, the extent of which is governed by the divergence of the duplicated segments and whether they can compensate for the inactivation of one in the case of a tetraploid.

The mosaic of genetic variation within plant genomes extends from the extensive rearrangements of structural variations to the potentially silent variations of single nucleotide polymorphisms (SNPs) that do not change the protein sequence encoded, giving a kaleidoscope of the role genetic diversity plays in shaping the robustness of plant populations. However, it is important when considering two sequences that encode the same polypeptide not to equate apparent identity of the final product with identity of the functionality of the two encoding sequences. This became readily apparent in the experiments with expression of foreign genes in the first transgenic plants, where the selection of codon usage was a vital factor in obtaining high expression of the introduced transgene.

The technologies for sequencing and assembling plant genomes have progressed from obtaining a few hundred bases from a cloned fragment to high-throughput sequencing by synthesis, with the length of each sequencing read increasing from tens of bases to many kilobases per read. With proximity ligation and optical mapping, the longer sequence reads can now result in the completion of telomere-to-telomere assemblies of plant genomes. Sequencing platforms and bioinformatics tools applied to plant genomes provide insights into the details of sequencing projects, from DNA isolation to, under optimal circumstances, telomere-to-telomere assemblies of any plant sample. The accuracy of sequencing platforms is increasing, and the costs of all the stages of a genome project are reducing so that a whole-genome assembly of any plant is now within reach. Where the initial aim of a genome sequencing project used to be the development of a reference genome against which all other examples would be compared, now it is possible to provide assembled genomes of the genotypes of interest, so important regions that are not present in the initial exemplar of the species are not overlooked.

Thus, the challenges of obtaining and assembling the data from the large range of nuclear DNA contents (genome sizes) that occur in the plant kingdom, even between closely related species, have steadily been overcome with the different sequencing techniques and bioinformatic assembly programs. The upshot of all this data is the concept of the pangenome, the sum of all the sequences that are present in all the members of a species, which is far greater than that found in any individual. This pangenome within a crop species, or extended to its wild relatives, is vital as it may contain the genetic information needed to provide the crops with appropriate resilience to the effects of global climate change.

Sequencing technologies also provide information about the modifications of the DNA sequence, such as the methylation of the cytosine and adenine residues, termed the epigenome. These epigenetic marks are important for the control of gene expression and possible transgenerational inheritance of stress adaptation. Thus, both the genome and the epigenome are important players in the overall control of plant form, function, and resilience.

The assembly of a plant genome is only the first step in understanding the translation of the genomic information into the plant phenotype. The transcriptome is the part of the genome that is transcribed into RNA. This compartment of knowledge is more difficult to ascertain since, unlike the genome, which is essentially constant throughout all cells in the plant, the transcriptome is cell- and environment-dependent. Here, model systems that were most amenable for study have provided the basis for understanding many complex developmental processes. An example would be the Zinnia tracheids, which are especially valuable in elucidating the cellular events that govern wood formation since Zinnia mesophyll cells can be synchronously induced to form these tracheary elements in vitro. This synchrony permits the establishment and chronology of the molecular and biochemical events associated with the differentiation of the cells to a specific fate and the identification of the genes involved in the differentiation of xylem. The study of Zinnia tracheids has provided a wealth of knowledge about the intricacies of wood formation, offering a model system for investigating cellular differentiation, programmed cell death, lignification, environmental responses, and genetic regulation, with the insights gained...