Inpactor2: a software based on deep learning to identify and classify LTR-retrotransposons in plant genomes.

LTR-retrotransposons are the most abundant repeat sequences in plant genomes and play an important role in evolution and biodiversity. Their characterization is of great importance to understand their dynamics. However, the identification and classification of these elements remains a challenge today. Moreover, current software can be relatively slow (from hours to days), sometimes involve a lot of manual work and do not reach satisfactory levels in terms of precision and sensitivity. Here we present Inpactor2, an accurate and fast application that creates LTR-retrotransposon reference libraries in a very short time. Inpactor2 takes an assembled genome as input and follows a hybrid approach (deep learning and structure-based) to detect elements, filter partial sequences and finally classify intact sequences into superfamilies and, as very few tools do, into lineages. This tool takes advantage of multi-core and GPU architectures to decrease execution times. Using the rice genome, Inpactor2 showed a run time of 5 minutes (faster than other tools) and has the best accuracy and F1-Score of the tools tested here, also having the second best accuracy and specificity only surpassed by EDTA, but achieving 28% higher sensitivity. For large genomes, Inpactor2 is up to seven times faster than other available bioinformatics tools.

Automatic curation of LTR retrotransposon libraries from plant genomes through machine learning.

Transposable elements are mobile sequences that can move and insert themselves into chromosomes, activating under internal or external stimuli, giving the organism the ability to adapt to the environment. Annotating transposable elements in genomic data is currently considered a crucial task to understand key aspects of organisms such as phenotype variability, species evolution, and genome size, among others. Because of the way they replicate, LTR retrotransposons are the most common transposable elements in plants, accounting in some cases for up to 80% of all DNA information. To annotate these elements, a reference library is usually created, a curation process is performed, eliminating TE fragments and false positives and then annotated in the genome using the homology method. However, the curation process can take weeks, requires extensive manual work and the execution of multiple time-consuming bioinformatics software. Here, we propose a machine learning-based approach to perform this process automatically on plant genomes, obtaining up to 91.18% F1-score. This approach was tested with four plant species, obtaining up to 93.6% F1-score (Oryza granulata) in only 22.61 s, where bioinformatics methods took approximately 6 h. This acceleration demonstrates that the ML-based approach is efficient and could be used in massive sequencing projects.

K-mer-based machine learning method to classify LTR-retrotransposons in plant genomes.

Every day more plant genomes are available in public databases and additional massive sequencing projects (i.e., that aim to sequence thousands of individuals) are formulated and released. Nevertheless, there are not enough automatic tools to analyze this large amount of genomic information. LTR retrotransposons are the most frequent repetitive sequences in plant genomes; however, their detection and classification are commonly performed using semi-automatic and time-consuming programs. Despite the availability of several bioinformatic tools that follow different approaches to detect and classify them, none of these tools can individually obtain accurate results. Here, we used Machine Learning algorithms based on k-mer counts to classify LTR retrotransposons from other genomic sequences and into lineages/families with an F1-Score of 95%, contributing to develop a free-alignment and automatic method to analyze these sequences.

InpactorDB: A Classified Lineage-Level Plant LTR Retrotransposon Reference Library for Free-Alignment Methods Based on Machine Learning.

Long terminal repeat (LTR) retrotransposons are mobile elements that constitute the major fraction of most plant genomes. The identification and annotation of these elements via bioinformatics approaches represent a major challenge in the era of massive plant genome sequencing. In addition to their involvement in genome size variation, LTR retrotransposons are also associated with the function and structure of different chromosomal regions and can alter the function of coding regions, among others. Several sequence databases of plant LTR retrotransposons are available for public access, such as PGSB and RepetDB, or restricted access such as Repbase. Although these databases are useful to identify LTR-RTs in new genomes by similarity, the elements of these databases are not fully classified to the lineage (also called family) level. Here, we present InpactorDB, a semi-curated dataset composed of 130,439 elements from 195 plant genomes (belonging to 108 plant species) classified to the lineage level. This dataset has been used to train two deep neural networks (i.e., one fully connected and one convolutional) for the rapid classification of these elements. In lineage-level classification approaches, we obtain up to 98% performance, indicated by the F1-score, precision and recall scores.