| Autor: |
Ou, Shujun, Scheben, Armin, Collins, Tyler, Qiu, Yinjie, Seetharam, Arun S., Menard, Claire C., Manchanda, Nancy, Gent, Jonathan I., Schatz, Michael C., Anderson, Sarah N., Hufford, Matthew B., Hirsch, Candice N. |
| Zdroj: |
Genome Research; 2024, Vol. 34 Issue: 8 p1140-1153, 14p |
| Abstrakt: |
Much of the profound interspecific variation in genome content has been attributed to transposable elements (TEs). To explore the extent of TE variation within species, we developed an optimized open-source algorithm, panEDTA, to de novo annotate TEs in a pangenome context. We then generated a unified TE annotation for a maize pangenome derived from 26 reference-quality genomes, which reveals an excess of 35.1 Mb of TE sequences per genome in tropical maize relative to temperate maize. A small number (n= 216) of TE families, mainly LTR retrotransposons, drive these differences. Evidence from the methylome, transcriptome, LTR age distribution, and LTR insertional polymorphisms reveals that 64.7% of the variability is contributed by LTR families that are young, less methylated, and more expressed in tropical maize, whereas 18.5% is driven by LTR families with removal or loss in temperate maize. Additionally, we find enrichment for Young LTR families adjacent to nucleotide-binding and leucine-rich repeat (NLR) clusters of varying copy number across lines, suggesting TE activity may be associated with disease resistance in maize. |
| Databáze: |
Supplemental Index |
| Externí odkaz: |
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