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 evidence-based pipeline we developed to predict gene structures from alignments of RNA-Seq data. The BIND pipeline integrates ab initio predictions of BRAKER and Direct inference; MIND combines Direct Inference and MAKER predictions. We use highly-curated Arabidopsis and yeast annotations as gold-standard benchmarks, and cross-validate in rice. Each pipeline under-predicts orphan genes (as few as 11 percent, under one prediction scenario). Increasing RNA-Seq diversity greatly improves prediction efficacy. The combined methods (BIND and MIND) yield best predictions overall, BIND identifying 68% of annotated orphan genes, 99% of ancient genes, and give the highest sensitivity score regardless dataset in Arabidopsis. We provide a light weight, flexible, reproducible, and well-documented solution to improve gene prediction.

Origins, evolution, and physiological implications of de novo genes in yeast

“…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.…”

A happy accident: a novel turfgrass reference genome

“…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).…”

“…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.…”

Research Advances and Prospects of Orphan Genes in Plants

“…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).…”