Assigning confidence scores to homoeologs using fuzzy logic.

Natasha M Glover,Adrian Altenhoff,Christophe Dessimoz

doi:10.7717/peerj.6231

Abstract

In polyploid genomes, homoeologs are a specific subtype of homologs, and can be thought of as orthologs between subgenomes. In Orthologous MAtrix, we infer homoeologs in three polyploid plant species: upland cotton (Gossypium hirsutum), rapeseed (Brassica napus), and bread wheat (Triticum aestivum). While we can typically recognize the features of a “good” homoeolog prediction (a consistent evolutionary distance, high synteny, and a one-to-one relationship), none of them is a hard-fast criterion. We devised a novel fuzzy logic-based method to assign confidence scores to each pair of predicted homoeologs. We inferred homoeolog pairs and used the new and improved method to assign confidence scores, which ranged from 0 to 100. Most confidence scores were between 70 and 100, but the distribution varied between genomes. The new confidence scores show an improvement over our previous method and were manually evaluated using a subset from various confidence ranges.

Highlights

Polyploidy is an important and widespread phenomenon within the plant kingdom (De Bodt, Maere & Van De Peer, 2005), and redundancy at the level of chromosomes implies redundancy at the level of genes
We evaluated our homoeolog predictions by comparing the confidence scores to other data aggregated from Orthologous MAtrix (OMA), and by manually assessing a subset of the predictions
In the OMA pipeline, homoeologs are predicted as orthologs between subgenomes, the genes have to be annotated as belonging to a particular subgenome in order to infer homoeology

Summary

Introduction

Polyploidy is an important and widespread phenomenon within the plant kingdom (De Bodt, Maere & Van De Peer, 2005), and redundancy at the level of chromosomes implies redundancy at the level of genes. Homoeologs are defined as genes which originated by a speciation event, diverged, and came back together some time later via allopolyploidization (Glover, Redestig & Dessimoz, 2016). (See Table 1 for definitions of terms related to polyploidy.) The homoeologous relationships between subgenomes of a polyploid can be used in order to determine the structural, genetic, and evolutionary results of polyploidization. Since 2015 we have included pairwise homoeolog predictions between subgenomes in Orthologous MAtrix (OMA), which is a method and database for inferring evolutionary relationships (Altenhoff et al, 2015). Homoeologs are usually predicted using a best bidirectional hit approach, sometimes in combination with an added requirement of positional conservation, that is, synteny (Dewey, 2011). How to cite this article Glover NM, Altenhoff A, Dessimoz C.

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