Maize Genomics and Genetics 2024, Vol.15, No.4, 182-190 http://cropscipublisher.com/index.php/mgg 184 in gene content, genome structure, and DNA methylation across different maize accessions. By leveraging whole-genome sequencing (WGS) and whole genome bisulfite sequencing (WGBS), researchers have investigated the adaptive and phenotypic consequences of methylation variations in maize populations, providing insights into the evolutionary forces acting on DNA methylation patterns (Xu et al., 2020). These population genomics studies are essential for understanding the extent and impact of gene flow in maize. Figure 1 Pan-genome analysis of the gene space (Adopted from Hufford et al., 2021) Image caption: (A) Pan-genes categorized by annotation method and phylostrata; Genes annotated with evidence have mRNA support, whereas ab initio genes are predicted on the basis of DNA sequence alone; Genes within progressing phylostrata [species Z. mays (maize), tribe Andropogoneae, family Poaceae, kingdom Viridiplantae] are more conserved; (B) Number of pan-genes added with each additional genome assembly. Order of genomes being added into the pan-genome was bootstrapped 1000 times. Tropical lines include CML52, CML69, CML103, CML228, CML247, CML277, CML322, CML333, Ki3, Ki11, NC350, NC358, and Tzi8; temperate lines include B73, B97, Ky21, M162W, Ms71, Oh43, Oh7B, HP301, P39, and Il14H. (C) Proportion of pan-genes in the core, near-core, dispensable, and private fractions of the pan-genome. For (B) and (C), tandem duplicates were considered as a single pan-gene and coordinates were filled in when a gene was not annotated, but an alignment with>90% coverage and 90% identity was present within the correct homologous block; (D) Number of tissues with expression (reads per kilobase per million reads>1) for each gene in each genome on the basis of their pan-genome classification. Tissues in this analysis include root, shoot, V11 base, V11 middle, V11 tip, anther, tassel, and ear (Adopted from Hufford et al., 2021) 3.3 Phylogeographic approaches Phylogeographic approaches combine phylogenetic and geographic data to study the historical processes that have shaped the genetic structure of maize populations. Phylogenetic analysis based on complete genome sequences has been used to reveal evolutionary relationships among MDMV isolates, highlighting the divergence of isolates from different regions (Wijayasekara et al., 2021). Such analyses help trace the movement and spread of genetic variants across geographical landscapes, providing a historical context for gene flow events. By integrating phylogenetic data with geographic information, researchers can infer the origins and migration patterns of maize populations, thereby elucidating the evolutionary dynamics of gene flow.
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