Pan-genomes reflect the structural variation and polymorphisms in genomes and facilitate in-depth comparisons of variation within species or wider taxonomic range. Pan-genomes are larger than any individual genome and composed of two parts: the core genome and the dispensable genome. Core genome has the maximum number of shared genes, whereas the dispensable genome has genomic variations associated with adaptation and survival in different environments, agronomic performance, disease resistance, and evolutionary processes. In crops, pan-genome analyses help understand gene conservation/loss during domestication and breeding and allow defining species-level differences in gene content. Plant genome variation processes such as tandem duplications, activity of transposable elements, insertion/deletions, genome rearrangement, and recombination can lead to gene presence/absence variation (PAV) and structural variation (SV). Genomic PAV reflects in the transcriptome ePAV (expression Presence and Absence Variation). ePAVs involve not only the gene content but also the genetic and epigenetic regulatory elements. Pan-transcriptome analyses help in the characterization of ePAV genes and their function.
The main goal of this Research Topic is to present the community with new methods and analytical solutions for breeding, crop improvement, and domestication. Pan-genome analyses develop the understanding of structural variation linked to phenotype, and complex polyploid genomes. Novel data-driven approaches enable phenotyping, identification of genes related to agronomically important traits, help develop a toolkit for breeders to include genetic diversity to increase crop yield. The other goal of this Research Topic is to decipher the GRNs that are supposed to involve in stress management and crop improvement. Genome-scale methods are the key to the identification of gene regulatory networks (GRNs). Various experimental and computational methods leveraging advanced technology and machine learning tools can be used for constructing GRNs. Here, we invite a broad discussion on different aspects to focus attention on the inferences drawn by GRNs.
Here, we propose a Research Topic to bring together the latest advances in the plant pan-genome, pan-transcriptome, and gene regulatory network (GRN) analyses. We will include contributions in themes such as but not limited to:
• Advance methods for whole-genome assembly, annotation, and in-depth analyses
• Latest techniques/tools for pan-genome, pan-transcriptome, variation graph construction, assembly, and visualization
• How pan-genome/pan-transcriptome analysis contribute to population genetics and crop improvement
• Applications, challenges, and opportunities of pan-genomics for crop improvement
• Methods for construction and analysis of GRNs
• Evolution of GRN regulating crop improvement and domestication
Pan-genomes reflect the structural variation and polymorphisms in genomes and facilitate in-depth comparisons of variation within species or wider taxonomic range. Pan-genomes are larger than any individual genome and composed of two parts: the core genome and the dispensable genome. Core genome has the maximum number of shared genes, whereas the dispensable genome has genomic variations associated with adaptation and survival in different environments, agronomic performance, disease resistance, and evolutionary processes. In crops, pan-genome analyses help understand gene conservation/loss during domestication and breeding and allow defining species-level differences in gene content. Plant genome variation processes such as tandem duplications, activity of transposable elements, insertion/deletions, genome rearrangement, and recombination can lead to gene presence/absence variation (PAV) and structural variation (SV). Genomic PAV reflects in the transcriptome ePAV (expression Presence and Absence Variation). ePAVs involve not only the gene content but also the genetic and epigenetic regulatory elements. Pan-transcriptome analyses help in the characterization of ePAV genes and their function.
The main goal of this Research Topic is to present the community with new methods and analytical solutions for breeding, crop improvement, and domestication. Pan-genome analyses develop the understanding of structural variation linked to phenotype, and complex polyploid genomes. Novel data-driven approaches enable phenotyping, identification of genes related to agronomically important traits, help develop a toolkit for breeders to include genetic diversity to increase crop yield. The other goal of this Research Topic is to decipher the GRNs that are supposed to involve in stress management and crop improvement. Genome-scale methods are the key to the identification of gene regulatory networks (GRNs). Various experimental and computational methods leveraging advanced technology and machine learning tools can be used for constructing GRNs. Here, we invite a broad discussion on different aspects to focus attention on the inferences drawn by GRNs.
Here, we propose a Research Topic to bring together the latest advances in the plant pan-genome, pan-transcriptome, and gene regulatory network (GRN) analyses. We will include contributions in themes such as but not limited to:
• Advance methods for whole-genome assembly, annotation, and in-depth analyses
• Latest techniques/tools for pan-genome, pan-transcriptome, variation graph construction, assembly, and visualization
• How pan-genome/pan-transcriptome analysis contribute to population genetics and crop improvement
• Applications, challenges, and opportunities of pan-genomics for crop improvement
• Methods for construction and analysis of GRNs
• Evolution of GRN regulating crop improvement and domestication