Transposable elements contribute to dynamic genome content in maize

Abstract

Transposable elements (TEs) are ubiquitous components of eukaryotic genomes and can create variation in genome organization and content. Most maize genomes are composed of TEs. We developed an approach to define shared and variable TE insertions across genome assemblies and applied this method to four maize genomes (B73, W22, Mo17 and PH207) with uniform structural annotations of TEs. Among these genomes we identified approximately 400 000 TEs that are polymorphic, encompassing 1.6 Gb of variable TE sequence. These polymorphic TEs include a combination of recent transposition events as well as deletions of older TEs. There are examples of polymorphic TEs within each of the superfamilies of TEs and they are found distributed across the genome, including in regions of recent shared ancestry among individuals. There are many examples of polymorphic TEs within or near maize genes. In addition, there are 2380 gene annotations in the B73 genome that are located within variable TEs, providing evidence for the role of TEs in contributing to the substantial differences in annotated gene content among these genotypes. TEs are highly variable in our survey of four temperate maize genomes, highlighting the major contribution of TEs in driving variation in genome organization and gene content.

European maize genomes unveil pan-genomic dynamics of repeats and genes

“…The observation that lineage-specific transposable elements are more enriched in gene-rich regions towards the distal ends of the chromosomes, a genome environment that is usually lower in (fl-) TEs, and the observation that TE presence in the surrounding of genes frequently interferes with expression and functionality [27] thus allows to speculate that in part the lineage-specific TEs located in gene-rich regions might underlie functional and trait differences. Our results complement a similar recent comparison on the mobile genome content of four maize lines [28] and highlight the enormous dynamics of TE generation and purging which are already visible within the -in evolutionary time dimensions -very narrow time window after domestication and during the breeding process of maize and the spread along the Americas and towards Europe.…”

A Maize Practical Haplotype Graph Leverages Diverse NAM Assemblies

“…Processing the assemblies through the PHG pipeline allows us to identify homologous haplotypes among the included assemblies for most defined reference ranges. Previous analyses of variation in intergenic (Anderson et al, 2019) and genic regions (Sun et al, 2018) show a relatively similar pattern to the results observed in this maize PHG database, having regions essentially shared at ~80% rate, with a relatively small subset of them being mostly missing in the majority of taxa. This is only a first approach, as potentially a more complete gene model set, resulting in smaller reference ranges, might better reflect the presence/absence variation of more refined haplotypes.…”

“…More recent analyses have leveraged whole-genome assemblies, allowing a detailed view of the extent of the intraspecific changes between maize varieties. These have identified signals of gene reordering, copy number, and other structural variations (Sun et al, 2018), with some cases accounting for 1.6Gb (equivalent to ~50% of the genome of B73) of variable transposable element sequences (Anderson et al, 2019).…”

Variation and inheritance of small RNAs in maize inbreds and F1 hybrids

“…al (2012) observed differences in sRNA abundance between retrotransposon families. Here, armed with an updated annotation of maize TEs Anderson et al, 2019), we observed differences in the distribution of 22-nt and 24-nt sRNA between different TE orders with 22-nt around >90% LTRs while 24-nt sRNAs have a high composition from helitron and TIR DNA transposons, far greater than the genome space these TEs occupy; 2.9% and 3.0% respectively. This hints at differences in the potential roles of sRNAs in regulating different classes of TEs in maize.…”