About this Research Topic
Highly contiguous reference genome sequences are a prerequisite for genomics research and for the optimal utilization of plant species. However, whole-genome duplication events and subsequent chromosomal rearrangements and losses shape the complex features and extensive diversity of plant genomes, and hinder their highly contiguous assembly. With the advent of single-molecule, long-read sequencing technologies, such as PacBio High-Fidelity (HiFi) and Oxford Nanopore Technologies (ONT), as well as Bionano genomics and high-throughput chromatin conformation capture (Hi-C), many highly complex chromosome-level genomes have been revealed, even with phased haplotypes. These advanced sequencing technologies, coupled with improvements in assembly methods, have greatly improved the quality of the assembled genomes.
Transcriptomics and metabolomics are playing an increasingly important role in research into genetic variation and functional genes, and enable their combination with other omics studies. For example, in studies of plant stress resistance, the application of transcriptomics and metabolomics technologies allows comprehensive and dynamic detection of the spatial and temporal changes in plant genes/metabolite expression under stress, enabling functional genes to be “mined” and the regulatory mechanism underlying stress responses to be analyzed, providing a molecular genetic basis for the breeding of stress-resistant varieties.
This research topic focuses on the latest advances in the field of genome sequence analysis. We particularly encourage studies in the following areas: (1) plant co-evolution, adaptive evolution, and gene function based on highly contiguous genome assembly, and (2) plant stress tolerance and morphological development based on new co-expression network algorithms.
We welcome submissions of original research articles, methods, reviews and mini-reviews on plant genome assembly and co-expression network algorithms. The topic covers, but is not limited to, the following themes:
• Highly contiguous genome assembly that sheds novel insights on plant evolution and adaptation.
• The evolution of functional genes and regulatory networks revealed by new plant genome assemblies.
• Multi-omics studies investigating the molecular mechanisms underlying plant responses to abiotic stresses, e.g., drought, extreme temperatures, and salt stress.
• Co-expression network algorithms to study key genes regulating the morphogenesis of important traits in plants.
Transcriptomics and metabolomics are playing an increasingly important role in research into genetic variation and functional genes, and enable their combination with other omics studies. For example, in studies of plant stress resistance, the application of transcriptomics and metabolomics technologies allows comprehensive and dynamic detection of the spatial and temporal changes in plant genes/metabolite expression under stress, enabling functional genes to be “mined” and the regulatory mechanism underlying stress responses to be analyzed, providing a molecular genetic basis for the breeding of stress-resistant varieties.
This research topic focuses on the latest advances in the field of genome sequence analysis. We particularly encourage studies in the following areas: (1) plant co-evolution, adaptive evolution, and gene function based on highly contiguous genome assembly, and (2) plant stress tolerance and morphological development based on new co-expression network algorithms.
We welcome submissions of original research articles, methods, reviews and mini-reviews on plant genome assembly and co-expression network algorithms. The topic covers, but is not limited to, the following themes:
• Highly contiguous genome assembly that sheds novel insights on plant evolution and adaptation.
• The evolution of functional genes and regulatory networks revealed by new plant genome assemblies.
• Multi-omics studies investigating the molecular mechanisms underlying plant responses to abiotic stresses, e.g., drought, extreme temperatures, and salt stress.
• Co-expression network algorithms to study key genes regulating the morphogenesis of important traits in plants.
Keywords: transcriptional regulation, plant genome assembly, multi-omics, genome evolution, gene co-expression network
Important Note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.
