Highly Contiguous Plant Genome Assembly And Transcriptional Regulation

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.