@article{fdi:010085895,
  title = {{C}omposition and diversity of {LTR} retrotransposons in the coffee leaf rust genome ({H}emileia vastatrix)},
  author = {{O}rozco-{A}rias, {S}. and {C}andamil, {M}. {S}. and {J}aimes, {P}. {A}. and {C}ristancho, {M}. and {T}abares-{S}oto, {R}. and {G}uyot, {R}omain},
  editor = {},
  language = {{ENG}},
  abstract = {{C}offee leaf rust is the most damaging disease for coffee cultivation around the world. {I}t is caused by a fungal pathogen, {H}emileia vastatrix ({H}va), belonging to the phylum {B}asidiomycota. {C}offee leaf rust causes significant yield losses and increases costs related to its control, with evaluated losses of {USD} 1-2 billion annually. {I}t attacks both the cultivated coffee species {C}offea canephora ({R}obusta coffee) and {C}offea arabica ({A}rabica coffee). {N}ew races, or pathotypes, are constantly emerging with increased virulence, suggesting a rapid evolution of the pathogen. {P}revious genetic and genomic studies have indicated a limited nucleotide diversity of {H}va despite a high genetic diversity and large genome size estimated to be similar to 800 {M}b, with a high content of repeated sequences (>74%). {D}espite several genomic resources and the release of a recent partial genome sequence, the diversity of these repeated sequences and how they may impact the evolution of the leaf rust genome have not been investigated in detail. {I}n an attempt to characterize the transposable elements within the {H}va genomes, we report here new lineages of long terminal repeat ({LTR}) retrotransposons, called {CO}-{HUI}, {S}oroa, and {B}aco, which are classified into {G}ypsy, and and {L}abe and {M}api, which are classified as {C}opia. {T}he {CO}-{HUI} and {S}oroa elements represent the main part of all {H}va transposable elements, as well as approximately 37% of the available genome assemblies. {M}api and {CO}-{HUI} are the main expressed families in {RNA}-seq data. {A}lthough {S}oroa is the lineage showing more insertions into exons and genes, {M}api seems to be more frequently involved in co-expression with genes. {A}ll these new families are also present in the {P}ucciniales, suggesting that they dynamically participate in their genome evolution.},
  keywords = {{H}va ; transposable elements ; new lineages ; genome size ; {P}ucciniales ; {P}ucci{DB}},
  booktitle = {},
  journal = {{A}gronomy},
  volume = {12},
  numero = {7},
  pages = {1665 [17 p.]},
  year = {2022},
  DOI = {10.3390/agronomy12071665},
  URL = {https://www.documentation.ird.fr/hor/fdi:010085895},
}