TY  - JOUR
A1  - Ou, Shujun
A1  - Scheben, Armin
A1  - Collins, Tyler
A1  - Qiu, Yinjie
A1  - Seetharam, Arun S.
A1  - Menard, Claire C.
A1  - Manchanda, Nancy
A1  - Gent, Jonathan I.
A1  - Schatz, Michael C.
A1  - Anderson, Sarah N.
A1  - Hufford, Matthew B.
A1  - Hirsch, Candice N.
T1  - Differences in activity and stability drive transposable element variation in tropical and temperate maize
Y1  - 2024/08/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 1140 
EP  - 1153 
DO  - 10.1101/gr.278131.123 
VL  - 34 
IS  - 8 
UR  - http://genome.cshlp.org/content/34/8/1140.abstract 
N2  - 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. 
ER  -