The genome assembly ofRhabditoides inermisfrom a complex microbial community reveals further evidence for parallel gene family expansions across multiple nematodes

Abstract

AbstractBackgroundFree-living nematodes such asCaenorhabditis elegansandPristionchus pacificusare powerful model systems for linking specific traits to their underlying genetic basis. To trace the evolutionary history of a candidate gene, a robust phylogenomic framework is indispensable.ResultsIn this work, we generated a near chromosome-scale genome assembly of the nematodeRhabditoides inermiswhich had previously been proposed as the sister group of the family Diplogastridae to whichP. pacificusbelongs. The genome was assembled from a complex microbial community that consists of multiple bacteria and a fungus of the genusVanrija. TheR. inermisgenome has five chromosomes that likely arose from recent fusions of different Nigon elements. Phylogenomic analysis groupedR. inermiswithin a clade includingC. elegans,Mesorhabditis belariand other rhabditids and thus, did not support a sister group relationship betweenR. inermisand the family Diplogastridae. Comparative genomic analyses identified abundant lineage-specific orthogroups which reveal evidence for parallel expansions of environmentally responsive gene families.ConclusionsOur work demonstrates the value of theR. inermisgenome as a resource for future phylogenomic analysis and for studying gene family evolution.