Cerri, R. | Search bioRxiv

bioRxiv2021

Draft genome of the Brazilian railroad worm Phrixothrix hirtus E.Olivier (Phengodidae: Coleoptera)

The Neotropical region is the richest in bioluminescent Coleoptera species, however, its bioluminescence megadiversity is still underexplored in terms of genomic organization and evolution, mainly within the Phengodidae family. The railroad worm Phrixothrix hirtus is an important biological model and symbolic species due to its bicolor bioluminescence, being the only organism that produces true red light among bioluminescent terrestrial species. Here, we performed the partial genome assembly of P. hirtus, combining short and long reads generated with Illumina sequencing, providing an important source of genomic information and a framework for comparative genomic analyses for the evaluation of the bioluminescent system in Elateroidea. The estimated genome size has [~]3.4Gb, 32% of GC content, and 67% of repetitive elements, being the largest genome described in the Elateroidea superfamily. Several events of gene family expansions associated with anatomical development and morphogenesis, as well as distinct odorant-binding receptors and retrotransposable elements were found in this genome. Similar molecular functions and biological processes are shared with other studied species of Elateriformia. Common genes putatively associated with bioluminescence production and control, including two luciferase genes that displayed 7 exons and 6 introns, and genes that could be involved in luciferin biosynthesis were found, indicating that there are no clear differences about the presence or absence of gene families associated with bioluminescence in Elateroidea. In P. hirtus the conversion of L- to D-luciferin seems to involve additional steps using a Palmitoyl-CoA thioesterase instead of an Acyl-CoA synthetase, which was found in Lampyridae species. HighlightsO_LIFirst draft genome assembly of Phengodidae, the largest one described in Coleoptera; C_LIO_LIGene family expansions associated with anatomical development and morphogenesis; C_LIO_LIBioluminescent control and luciferin biosynthesis genes are common within Elateroidea; C_LIO_LIDespite similar bioluminescent system, metabolic routes may have evolved independently; C_LI

genomics↗

bioRxiv2020

Investigating Feedforward Neural Networks for Classification of Transposon-Derived piRNAs

PIWI-Interacting RNAs (piRNAs) form an important class of non-coding RNAs that play a key role in the genome integrity through the silencing of transposable elements. However, despite their importance and the large application of deep learning in computational biology for classification tasks, there are few studies of deep learning and neural networks for piRNAs prediction. Therefore, this paper presents an investigation on deep feedforward networks models for classification of transposon-derived piRNAs. We analyze and compare the results of the neural networks in different hyperparameters choices, such as number of layers, activation functions and optimizers, clarifying the advantages and disadvantages of each configuration. From this analysis, we propose a model for human piRNAs classification and compare our method with the state-of-the-art deep neural network for piRNA prediction in the literature and also traditional machine learning algorithms, such as Support Vector Machines and Random Forests, showing that our model has achieved a great performance with an F-measure value of 0.872, outperforming the state-of-the-art method in the literature.

bioinformatics↗