@article{fdi:010095975,
  title = {{I}dentification of transposable elements and satellite {DNA} in the {N}eotropical species {D}rosophila amaguana from the {E}cuadorian {A}ndean {F}orests},
  author = {{C}oba-{M}ales, {M}. {A}. and {O}rozco-{A}rias, {S}. and {G}uyot, {R}omain and {V}ela, {D}.},
  editor = {},
  language = {{ENG}},
  abstract = {{G}enome size variation in eukaryotic species is largely influenced by repetitive {DNA} sequences such as transposable elements ({TE}s), simple repeats, and satellite {DNA}s (sat{DNA}s), which do not necessarily correlate with organismal complexity. {I}n insects, {TE}s are crucial to evolutionary processes and are correlated with variations in genome size. {I}n this study, we describe, for the first time, the mobilome and satellitome of {D}rosophila amaguana, an {E}cuadorian {N}eotropical species with a large, unexplored genome size, to assess the contribution of these repetitive {DNA} sequences to its genome composition. {U}sing a draft genome assembly of approximately 455.5 {M}b, generated from {I}llumina short-read sequences obtained from 10 wild specimens of {D}. amaguana collected at the {R}efugio de {V}ida {S}ilvestre {P}asochoa, we employed a de novo approach to create a manually curated {TE} library of 737 consensus sequences. {W}e identified 716 novel {TE} families that had not been previously described, 20 {TE}s previously characterized in other {D}rosophila species, and one {DNA} transposon previously described in the {L}epeophtheirus genus. {T}he total {TE} content in the {D}. amaguana genome was 21.54%, distributed as follows: 6.35% {H}elitrons (1 superfamily), 5.13% {LTR} retrotransposons (5 superfamilies), 3.63% {TIR}s (9 superfamilies), 3.61% {LINE}s (7 superfamilies), 1.17% {MITE}s, 0.94% {M}averick, 0.67% {PLE}, 0.02% {SINE}s, and 0.01% {DIRS}. {W}e also identified 11.8% of simple repeats. {A}dditionally, we estimated the sat{DNA} content using {I}llumina raw reads and identified 16 sat{DNA} families, all unique to the {D}rosophila genus, which comprise 4.90% of the genome. {O}verall, our results based on short-read data suggest that the large genome size of {D}. amaguana may not be the consequence of a high amount of {TE}s or sat{DNA}s. {I}nstead, its large genome size could be attributed to other factors (e.g., noncoding {DNA} occupying substantial portions of the genome or a high percentage of duplicated genes) that remain to be determined or explored in future studies using long-reads to overcome short-reads limitations. {T}hese findings may currently offer valuable insights into the adaptative and evolutionary processes of the mesophragmatica species group in the {A}ndean forests.},
  keywords = {{EQUATEUR} ; {ANDES}},
  booktitle = {},
  journal = {{PL}o{S} {O}ne},
  volume = {20},
  numero = {12},
  pages = {e0337390 [22 p.]},
  year = {2025},
  DOI = {10.1371/journal.pone.0337390},
  URL = {https://www.documentation.ird.fr/hor/fdi:010095975},
}