@phdthesis{fdi:010087015,
  title = {Étude du paysage des {\'e}l{\'e}ments transposables sous forme d'{ADN} circulaire extrachromosomique et dans l'assemblage des g{\'e}nomes de plantes {\`a} l'aide du s{\'e}quen{\c{c}}age en lectures longues},
  author = {{Z}hang, {P}anpan},
  editor = {},
  language = {{ENG}},
  abstract = {{T}ransposable elements ({TE}s) are repetitive {DNA} sequences with the intrinsic ability to move and amplify in genomes. {A}ctive transposition of {TE}s is linked to the formation of extrachromosomal circular {DNA} (ecc{DNA}). {H}owever, the complete landscape of this ecc{DNA} compartment and its interactions with the genome were not well defined. {I}n addition, at the beginning of my thesis, there were no bioinformatics tools available to identify ecc{DNA}s from long-read sequencing data.{T}o address these questions during my {P}h{D}, we first developed a tool, called ecc_finder, to automate ecc{DNA} detection from long-read sequencing and optimized detection from short-read sequences to characterize {TE} mobility. {B}y applying ecc_finder to {A}rabidopsis, human and wheat ecc{DNA}-seq data (with genome sizes ranging from 120 {M}b to 17 {G}b), we documented the broad applicability of ecc_finder as well as optimization of computational time, sensitivity and accuracy.{I}n the second project, we developed a meta-assembly tool called {SASAR} to reconcile the results of different genome assemblies from long-read sequencing data. {F}or different plant species, {SASAR} obtained high quality genome assemblies in an efficient time and resolved structural variations caused by {TE}s.{I}n the last project, we used {SASAR}-assembled genome and ecc_finder-detected ecc{DNA} to characterize ecc{DNA}-genome interactions. {I}n {A}rabidopsis hypomethylated epigenetic mutants, we highlighted the role of the epigenome in protecting genome stability not only from {TE} mobility but also from genomic rearrangements and gene chimerism. {O}verall, our findings on ecc{DNA}, genome assembly and their interactions, as well as the development of tools, offer new insights into the role of {TE}s in the adaptive evolution of plants to rapid environmental change.},
  keywords = {},
  address = {{M}ontpellier},
  publisher = {{IRD}},
  pages = {181  multigr.},
  year = {2022},
  URL = {https://www.documentation.ird.fr/hor/fdi:010087015},
}