The role of transposable elements on gene expression regulation in maize and its response to drought
Abstract
Transposable elements (TEs) are major constituents of plant genomes and contribute
to their dynamics and evolution. The extent to which they contribute to local adaptation
nevertheless remains to be fully elucidated. To better characterize the potential role of TEs
in maize local adaptation, we aim at characterizing TE polymorphisms in a set of 7 maize
inbred lines of contrasted origins. We have de novo assembled the genome sequences of these
maize lines, and are now focusing on TE annotation and polymorphism discovery.
Several softwares and pipelines are available to de novo annotate TEs in genomes. They rely
on (i) approaches that use characteristic structural features of TE super-families to detect
complete copies and/or (ii) approaches that use the repetitiveness of TE copies across the
genome. These approaches are often completed by the detection of coding domains to clas-
sify of TEs into families. Existing softwares have proven useful for TE annotation of small
genomes of a few hundreds of megabases, but remain challenging to apply on larger genomes,
mainly due to the amount of genomic data to analyze and to the structural complexity of
these genomes.
With a ˜2.1 Gb genome, 85% of which is occupied by TE sequences that are often nested
within one another, maize is a typical average diploid angiosperm genome. Improving tools
for maize TE genome annotation will therefore leverage TE annotation for a large amount of
plant species. After reviewing existing approaches to de novo annotate TEs, we will discuss
their advantages and limits to annotate TEs in the maize genome. We will then suggest
ways to improve de novo TE annotations in such a genome
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