Transposable elements (TEs) are significant genomic components which can be detected either through sequence homology against existing databases or de novo, with the latter potentially reducing the risk of underestimating TE abundance. Here, we describe the semi-automated generation of a de novo TE library using the newly developed EDTA pipeline and DeepTE classifier in a non-model teleost (Corydoras fulleri). Using both genomic and transcriptomic data, we assess this de novo pipeline's performance across four TE based metrics: (i) abundance, (ii) composition, (iii) fragmentation, and (iv) age distributions. We then compare the results to those found when using a curated teleost library (Danio rerio). We identify quantitative differences in these metrics and highlight how TE library choice can have major impacts on TE-based estimates in non-model species.

中文翻译：

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非模型物种中的转座因子注释：使用半自动 EDTA 和 DeepTE de novo 管道的物种特异性重复库的好处

转座因子 (TE) 是重要的基因组成分，可以通过与现有数据库的序列同源性或从头检测，后者可能降低低估 TE 丰度的风险。在这里，我们描述了在非模型硬骨鱼 ( Corydoras fulleri )中使用新开发的 EDTA 管道和 DeepTE 分类器半自动生成从头 TE 库。使用基因组和转录组数据，我们评估了这个从头管道在四个基于 TE 的指标上的性能：（i）丰度，（ii）组成，（iii）碎片化和（iv）年龄分布。然后，我们将结果与使用精选硬骨鱼库 ( Danio rerio）。我们确定了这些指标中的定量差异，并强调了 TE 库选择如何对非模型物种中基于 TE 的估计产生重大影响。