Regnum Vegetabile Next Generation Sequencing In Plant Systematics

Cheap and plentiful genome sequence data is transforming biology, and will surely transform systematics. This volume explores how.

In the five years since the publication of Molecular Systematics of Plants, the field of molecular systematics has advanced at an astonishing pace. This period has been marked by a volume of new empirical data and advances in theoretical and analytical issues related to DNA. Comparative DNA sequencing, facilitated by the amplification of DNA via the polymerase chain reaction (PCR), has become the tool of choice for molecular systematics. As a result, large portions of the Molecular Systematics of Plants have become outdated. Molecular Systematics of Plants II summarizes these recent achievements in plant molecular systematics. Like its predecessor, this completely revised work illustrates the potential of DNA markers for addressing a wide variety of phylogenetic and evolutionary questions. The volume provides guidance in choosing appropriate techniques, as well as appropriate genes for sequencing, for given levels of systematic inquiry. More than a review of techniques and previous work, Molecular Systematics of Plants II provides a stimulus for developing future research in this rapidly evolving field. Molecular Systematics of Plants II is not only written for systematists (faculty, graduate students, and researchers), but also for evolutionary biologists, botanists, and paleobotanists interested in reviewing current theory and practice in plant molecular systematics.

Phylogenetics often uncovers contradicting hypotheses regarding the relationships within the same group of organisms, a phenomenon known since the beginning of the molecular systematics era. While, historically, single marker-based analyses produced discordance, nowadays entire cellular genomes or portions of the same genomic compartment conflict with others or the rest, respectively. In contrast to the beginning of the molecular systematics era, when adding markers and taxa offered a way out of systematic errors, genome inference-based incongruences cannot be addressed and explained easily. Disagreeing phylogenomic hypotheses might originate from various evolutionary processes, including but not limited to hybridization or incomplete lineage sorting, thereby leading to gene tree-versus species tree-associated discrepancies. Today, this can be expanded to genome discordance, where phylogenomic signals of organellar genomes (plastid, mitochondrial) and the nuclear genome disagree due to intrinsically different coalescent paths or phenomena like organelle capture.

The application of molecular techniques is rapidly transforming the study of plant systematics. The precision they offer enables researchers to classify plants that have not been subject to rigorous classification before and thus allows them to obtain a clearer picture of evolutionary relationships. Plant Molecular Systematics is arranged both conceptually and phylogenetically to accommodate the interests not only of general systematists, but also those of people interested in a particular plant family. The first part discusses molecular sequencing; the second reviews restriction site analysis and the sequencing of mitochondrial DNA. A third section details the analysis of ribosomal DNA and chloroplast DNA. The following section introduces model studies involving well-studied families such as the Onagraceae, Compositae and Leguminosae. The book concludes with a section addressing theoretical topics such as data analysis and the question of morphological vs. molecular data.

This Research Topic is part of the Mobile Elements and Plant Genome Evolution, Comparative Analyses and Computational Tools series: Mobile Elements and Plant Genome Evolution, Comparative Analyses and Computational Tools Transposable elements are very common mobile genetic elements that are composed of several classes and make up the majority of eukaryotic genomes. The movement and accumulation of mobile genetic elements have been a major force in the formation of the genes and genomes of nearly all organisms. As dispersed and ubiquitous mobile elements, their life cycle of replicative transposition leads to genome rearrangements affecting cellular function. Transposable elements are important drivers of species diversity, and they exhibit great variety in structure, size, and mechanisms of transposition, making them important putative actors in genome evolution.

Molecular Systematics and Plant Evolution discusses the diversity and evolution of plants with a molecular approach. It looks at population genetics, phylogeny (history of evolution) and developmental genetics, to provide a framework from which to understand evolutionary patterns and relationships amongst plants. The international panel of contributors are all respected systematists and evolutionary biologists, who have brought together a wide range of topics from the forefront of research while keeping the text accessible to students. It has been written for senior undergraduates, postgraduates and researchers in the fields of botany, systematics, population / conservation genetics, phylogenetics and evolutionary biology.

Plastid Genome Evolution, Volume 85 provides a summary of recent research on plastid genome variation and evolution across photosynthetic organisms. It covers topics ranging from the causes and consequences of genomic changes, to the phylogenetic utility of plastomes for resolving relationships across the photosynthetic tree of life. This newly released volume presents thorough, up-to-date information on coevolution between the plastid and nuclear genomes, with chapters on plastid autonomy vs. nuclear control over plastid function, establishment and genetic integration of plastids, plastid genomes in alveolate protists, plastid genomes of glaucophytes, the evolution of the plastid genome in chlorophyte and streptophyte green algae, and more. Provides comprehensive coverage of plastid genome variation by leading researchers in the field Presents a broad range of taxonomic groups, ranging from single and multicellular algae, to the major clades of land plants Includes thorough, up-to-date information on coevolution between the plastid and nuclear genomes