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.

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.

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

The growing scale of plant-based chemicals for industrial use has generated considerable interest in developing methods to meet their desired production levels. Among various available strategies for their production, the development of Agrobacterium rhizogenes mediated hairy root cultures (HRCs) is generally considered the most feasible approach. Additionally, several proof-of-principle experiments have demonstrated the practical feasibility of HRCs in the plant-based remediation of environment pollutants, biotransformation of important compounds, and production of therapeutic proteins. Given that hairy root biotechnology has now been recognized as a promising and highly dynamic research area, this book offers a timely update on recent advances, and approaches hairy roots as a multifaceted biological tool for various applications. Further, it seeks to investigate the loopholes in existing methodologies, identify remaining challenges and find potential solutions by presenting well thought-out scientific discussions from various eminent research groups working on hairy root biotechnology. This book provides detailed conceptual and practical information on HRC-based research, along with relevant case studies. The content is divided into three broad sections, namely (i) Hairy Roots and Secondary Metabolism, (ii) Progressive Applications, and (iii) Novel Approaches and Future Prospects. By informing the research and teaching community about the major strides made in HRC-based interventions in plant biology and their applications, the book is sure to spark further research in this fascinating field.

Potatoes are a staple crop around the world. Covering all aspects of botany, production and uses, this book presents a comprehensive discussion of the most important topics for potato researchers and professionals. It assesses the latest research on plant growth such as tuber development, water use and seed production, covers all aspects of pest management and reviews postharvest issues such as storage, global markets, and of course, nutritional value and flavour.