milRNApredictor: Genome-free prediction of fungi milRNAs by incorporating k-mer scheme and distance-dependent pair potential

Yao, Yuangen; Zhang, Huiyu; Deng, Haiyou

doi:10.1016/j.ygeno.2019.12.019

Cited by 7 publications

(7 citation statements)

References 42 publications

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“…Competitive endogenous RNAs, such as pseudogene transcripts, are capable of regulating the expression levels of their parental genes at various levels (An et al, 2017). Although knowledge about small regulatory RNAs, such as miRNA-like RNAs (milRNAs), remains scarce for fungi (Yao et al, 2020), it cannot be ruled out that this could be the case for Complex IV due to its particular importance in metabolism and oxidative stress (Srinivasan & Avadhani, 2012). In line with its central importance in different cellular processes, mitochondrial genomes could be used to improve the production of secondary metabolites and the control of pathogenic fungi (Fonseca et al, 2021).…”

Section: Discussionmentioning

confidence: 99%

Assembly and comparative genome analysis of a Patagonian Aureobasidium pullulans isolate reveals unexpected intraspecific variation

Parra

Libkind

Hittinger

et al. 2023

Yeast

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Aureobasidium pullulans is a yeast‐like fungus with remarkable phenotypic plasticity widely studied for its importance for the pharmaceutical and food industries. So far, genomic studies with strains from all over the world suggest they constitute a genetically unstructured population, with no association by habitat. However, the mechanisms by which this genome supports so many phenotypic permutations are still poorly understood. Recent works have shown the importance of sequencing yeast genomes from extreme environments to increase the repertoire of phenotypic diversity of unconventional yeasts. In this study, we present the genomic draft of A. pullulans strain from a Patagonian yeast diversity hotspot, re‐evaluate its taxonomic classification based on taxogenomic approaches, and annotate its genome with high‐depth transcriptomic data. Our analysis suggests this isolate could be considered a novel variant at an early stage of the speciation process. The discovery of divergent strains in a genomically homogeneous group, such as A. pullulans, can be valuable in understanding the evolution of the species. The identification and characterization of new variants will not only allow finding unique traits of biotechnological importance, but also optimize the choice of strains whose phenotypes will be characterized, providing new elements to explore questions about plasticity and adaptation.

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Section: Discussionmentioning

confidence: 99%

Assembly and comparative genome analysis of a Patagonian Aureobasidium pullulans isolate reveals unexpected intraspecific variation

Parra

Libkind

Hittinger

et al. 2023

Yeast

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“…Many tools exist for sRNA-annotation, with most focusing on miRNAs in animals and plants [35][36][37]. In fungi, at least one tool has been developed for milRNA identification [55], but uses a genome free approach and doesn't address other categories of loci. The lack of reporting quality and differences in methods between species and studies shows a need for systematic analyses in fungal sRNA loci as has been performed for plants [56] to more clearly grasp the actual types of loci produced in this clade.…”

Section: Discussionmentioning

confidence: 99%

Comprehensive re-analysis of hairpin RNAs in fungi reveals ancestral links

Johnson

Larrondo

Álvarez

et al. 2022

Preprint

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RNA interference is an ancient mechanism with many regulatory roles in eukaryotic genomes, with small RNAs acting as their functional element. While there is a wide array of classes of small-RNA-producing loci, those resulting from stem-loop structures (hairpins) have received profuse attention. Such is the case of microRNAs (miRNAs), which have distinct roles in plants and animals. Fungi also produce small RNAs, and several publications have identified miRNAs and miRNA-like (mi/milRNA) hairpin RNAs in diverse fungal species using deep sequencing technologies. Despite this relevant source of information, relatively little is known about mi/milRNA-like features in fungi, mostly due to a lack of established criteria for their annotation. To systematically assess mi/miRNA-like characteristics and annotation confidence, we searched for publications describing mi/milRNA loci and re-assessed the annotations for 40 fungal species. We extracted and normalized the annotation data for 1,677 reported mi/milRNA-like loci and determined their abundance profiles, concluding that less than half of the reported loci passed basic standards used for hairpin RNA discovery. We found that fungal mi/milRNA are generally more similar in size to animal miRNAs and were frequently associated with protein-coding genes. The compiled genomic analyses identified 18 mi/milRNA loci conserved in multiple species. Our pipeline allowed us to build a general hierarchy of locus quality, identifying around 200 loci with high-quality annotations. We provide a centralized annotation of identified mi/milRNA hairpin RNAs in fungi which will serve as a resource for future research and advance in understanding the characteristics and functions of mi/milRNAs in fungal organisms.

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“…The recognition characteristic of k-mer and the advantages of distance-specific pair potential distinguishing between natural and non-natural structures were well combined. Furthermore, knowledge-based energy features have been firmly demonstrated to have very high discriminatory power [21,29,30]. Most recently, knowledge-based energy features have been further optimized and developed to consider position-specific information.…”

Section: Datasets and Feature Setmentioning

confidence: 99%

“…To do this, we developed plantMirP into plantMirP2. Firstly, we incorporated and optimized knowledge-based energy features, which are firstly proposed in plantMirP and further developed in our recent studies (i.e., riceMirP [29] and milRNApredictor [30]). Secondly, the parameters of the SVM model and the algorithm are optimized, and the independent dataset is updated according to the latest version of the miRBase database.…”

Section: Introductionmentioning

confidence: 99%

PlantMirP2: An Accurate, Fast and Easy-To-Use Program for Plant Pre-miRNA and miRNA Prediction

Fan

Yao

2021

Genes

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MicroRNAs (miRNAs) are a kind of short non-coding ribonucleic acid molecules that can regulate gene expression. The computational identification of plant miRNAs is of great significance to understanding biological functions. In our previous studies, we have put firstly forward and further developed a set of knowledge-based energy features to construct two plant pre-miRNA prediction tools (plantMirP and riceMirP). However, these two tools cannot be used for miRNA prediction from NGS (Next-Generation Sequencing) data. In addition, for further improving the prediction performance and accessibility, plantMirP2 has been developed. Based on the latest dataset, plantMirP2 achieves a promising performance: 0.9968 (Area Under Curve, AUC), 0.9754 (accuracy), 0.9675 (sensitivity) and 0.9876 (specificity). Additionally, the comparisons with other plant pre-miRNA tools show that plantMirP2 performs better. Finally, the webserver and stand-alone version of plantMirP2 are available.

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milRNApredictor: Genome-free prediction of fungi milRNAs by incorporating k-mer scheme and distance-dependent pair potential

Cited by 7 publications

References 42 publications

Assembly and comparative genome analysis of a Patagonian Aureobasidium pullulans isolate reveals unexpected intraspecific variation

Assembly and comparative genome analysis of a Patagonian Aureobasidium pullulans isolate reveals unexpected intraspecific variation

Comprehensive re-analysis of hairpin RNAs in fungi reveals ancestral links

PlantMirP2: An Accurate, Fast and Easy-To-Use Program for Plant Pre-miRNA and miRNA Prediction

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