Differences in activity and stability drive transposable element variation in tropical and temperate maize

Ou, Shujun, Collins, Tyler, Qiu, Yinjie, Seetharam, Arun, Menard, Claire, Manchanda, Nancy, Gent, Jonathan, Schatz, Michael, Anderson, Sarah, Hufford, Matthew, Hirsch, Candice (2022) Differences in activity and stability drive transposable element variation in tropical and temperate maize. (Submitted)

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Abstract

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 pan-genome context. We then generated a unified TE annotation for a maize pan-genome derived from 26 reference-quality genomes, which revealed 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 revealed that 64.7% of the variability was contributed by LTR families that were young, less methylated, and more expressed in tropical maize, while 18.5% was driven by LTR families with removal or loss in temperate maize. This study demonstrates the use of a comprehensive pan-TE annotation to reveal the driving role of TEs in within-species genomic variation via their ongoing amplification and purging.

Item Type:	Paper
Subjects:	bioinformatics bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification bioinformatics > genomics and proteomics > genetics & nucleic acid processing bioinformatics > genomics and proteomics organism description > plant > maize organism description > plant bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > transposons
CSHL Authors:	Schatz, Michael C.
Communities:	CSHL labs > Schatz lab
SWORD Depositor:	CSHL Elements
Depositing User:	CSHL Elements
Date:	2022
Date Deposited:	13 Oct 2023 13:51
Last Modified:	16 Jan 2024 20:55
Related URLs:	Publisher
URI:	https://repository.cshl.edu/id/eprint/41222

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