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

Background Free-living nematodes such as Caenorhabditis elegans and Pristionchus pacificus are 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. Results In this work, we generated a near chromosome-scale genome assembly of the nematode Rhabditoides inermis which had previously been proposed as the sister group of the family Diplogastridae to which P. pacificus belongs. The genome was assembled from a complex microbial community that consists of multiple bacteria and a fungus of the genus Vanrija . The R. inermis genome has five chromosomes that likely arose from recent fusions of different Nigon elements. Phylogenomic analysis grouped R. inermis within a clade including C. elegans , Mesorhabditis belari and other rhabditids and thus, did not support a sister group relationship between R. inermis and the family Diplogastridae. Comparative genomic analyses identified abundant lineage-specific orthogroups which reveal evidence for parallel expansions of environmentally responsive gene families. Conclusions Our work demonstrates the value of the R. inermis genome as a resource for future phylogenomic analysis and for studying gene family evolution.