2021
DOI: 10.1093/nar/gkab1238
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Foster thy young: enhanced prediction of orphan genes in assembled genomes

Abstract: Proteins encoded by newly-emerged genes (‘orphan genes’) share no sequence similarity with proteins in any other species. They provide organisms with a reservoir of genetic elements to quickly respond to changing selection pressures. Here, we systematically assess the ability of five gene prediction pipelines to accurately predict genes in genomes according to phylostratal origin. BRAKER and MAKER are existing, popular ab initio tools that infer gene structures by machine learning. Direct Inference is an evide… Show more

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Cited by 17 publications
(26 citation statements)
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“…The issue lies, in part, in that there is no consensus operational definition of what constitutes a “gene” in the context of de novo gene birth, where the signatures of evolutionary conservation typically relied on to predict functionality are absent (Keeling et al, 2019). Further developments of computational methods for the detection of de novo‐originated genes are also much needed for the advancement of the field (Li et al, 2022). Such advances are more challenging to attain in the yeast lineage than in other eukaryotic lineages whose genomes tend to evolve more slowly.…”
Section: Methods For Inferring De Novo Originmentioning
confidence: 99%
“…The issue lies, in part, in that there is no consensus operational definition of what constitutes a “gene” in the context of de novo gene birth, where the signatures of evolutionary conservation typically relied on to predict functionality are absent (Keeling et al, 2019). Further developments of computational methods for the detection of de novo‐originated genes are also much needed for the advancement of the field (Li et al, 2022). Such advances are more challenging to attain in the yeast lineage than in other eukaryotic lineages whose genomes tend to evolve more slowly.…”
Section: Methods For Inferring De Novo Originmentioning
confidence: 99%
“…Gene prediction was carried out using a comprehensive method combining ab initio predictions (from BRAKER v2.1.6; Brůna et al . 2021) with direct evidence (inferred from transcript assemblies) using the BIND strategy (Li et al . 2021).…”
Section: Methodsmentioning
confidence: 99%
“…Gene prediction was carried out using a comprehensive method combining ab initio predictions (from BRAKER v2.1.6; Br ůna et al 2021) with direct evidence (inferred from transcript assemblies) using the BIND strategy (Li et al 2021). Briefly, 58 RNA-seq libraries were downloaded from NCBI (Supplement 5) and mapped to the genome using a STAR (v2.5.3a; Dobin et al 2013)-indexed genome and an iterative two-pass approach under default options to generate mapped BAM files.…”
Section: Genome Annotationmentioning
confidence: 99%
“…Taking into consideration the rice genome, in which 37 OGs were obtained under BLAST and BLAT (BLAST-Like Alignment Tool) programs (Jin et al, 2019). Other effective modules or programs include the SMOTE-ENN-XGBoost model (Synthetic Minority Over-sampling TEchnique-Edited Nearest Neighbors-eXtreme Gradient Boosting) (Gao et al, 2020), BIND (BRAK-ER-Inferred Directly), and MIND (MAKER-Inferred Directly) platforms (Li J. et al, 2021), ORFanFinder (Ekstrom and Yin, 2016), combined BLAST and Microarray-based genome hybridization methods (Li G. et al, 2019).…”
Section: Orphan Genes Identification and Its Fast Evolving Characteri...mentioning
confidence: 99%