BMC Genomics volume 21, Article number: 428 (2020) doi: 10.1186/s12864-020-06824-
Summary
Maize, sorghum, and foxtail millet are each leading crop plants from the Panacoid family of grass plants. The goal of this work was to identify genes important for regulation of daily activities in these plants. The working hypothesis was critical regulatory features will be retained through evolution and, therefore, these will be discovered by finding aspects of the genomes shared between these plants. Of particular interest was understanding how plants anticipate and prepare for changes in the environment throughout the day-night cycle. With several comparative computational biology approaches, this study found probable key regulatory genes and sets of genes with shared expression that are predicted to be involved in common physiological processes. Also discovered within these three grass species were short DNA sequences, called motifs, near genes with the same expression pattern. This is typical of DNA regions used to control gene expression. By analysis of the DNA sequence of these genomic regions, it was clear these represented both previously known motifs with described activity and novel, previously undiscovered motifs with unknown activity. Overall, this study provides an overview of the divergence and conservation of daily expression patterns and associated DNA sequence motifs amongst related genes in three crop grass species of the same family.
Interspecific analysis of diurnal gene regulation in panicoid grasses identifies known and novel regulatory motifs
X. Lai, C. Bendix, L. Yan, Y. Zhang, J. Schnable & F. Harmon
BMC Genomics volume 21, Article number: 428 (2020) doi: 10.1186/s12864-020-06824-3
X. Lai, C. Bendix, L. Yan, Y. Zhang, J. Schnable & F. Harmon
BMC Genomics volume 21, Article number: 428 (2020) doi: 10.1186/s12864-020-06824-
Summary
Maize, sorghum, and foxtail millet are each leading crop plants from the Panacoid family of grass plants. The goal of this work was to identify genes important for regulation of daily activities in these plants. The working hypothesis was critical regulatory features will be retained through evolution and, therefore, these will be discovered by finding aspects of the genomes shared between these plants. Of particular interest was understanding how plants anticipate and prepare for changes in the environment throughout the day-night cycle. With several comparative computational biology approaches, this study found probable key regulatory genes and sets of genes with shared expression that are predicted to be involved in common physiological processes. Also discovered within these three grass species were short DNA sequences, called motifs, near genes with the same expression pattern. This is typical of DNA regions used to control gene expression. By analysis of the DNA sequence of these genomic regions, it was clear these represented both previously known motifs with described activity and novel, previously undiscovered motifs with unknown activity. Overall, this study provides an overview of the divergence and conservation of daily expression patterns and associated DNA sequence motifs amongst related genes in three crop grass species of the same family.
Maize, sorghum, and foxtail millet are each leading crop plants from the Panacoid family of grass plants. The goal of this work was to identify genes important for regulation of daily activities in these plants. The working hypothesis was critical regulatory features will be retained through evolution and, therefore, these will be discovered by finding aspects of the genomes shared between these plants. Of particular interest was understanding how plants anticipate and prepare for changes in the environment throughout the day-night cycle. With several comparative computational biology approaches, this study found probable key regulatory genes and sets of genes with shared expression that are predicted to be involved in common physiological processes. Also discovered within these three grass species were short DNA sequences, called motifs, near genes with the same expression pattern. This is typical of DNA regions used to control gene expression. By analysis of the DNA sequence of these genomic regions, it was clear these represented both previously known motifs with described activity and novel, previously undiscovered motifs with unknown activity. Overall, this study provides an overview of the divergence and conservation of daily expression patterns and associated DNA sequence motifs amongst related genes in three crop grass species of the same family.