TheAphelenchoidesgenomes reveal substantial horizontal gene transfers in the last common ancestor of free-living and major plant parasitic nematodes

Abstract

AbstractAphelenchoides besseyiis a plant-parasitic nematode (PPN) in the Aphelenchoididae family capable of infecting more than 200 plant species.A. besseyiis also a species complex with strains exhibiting varying pathogenicity to plants. We present the genome and annotations of sixAphelenchoidesspecies, four of which belonged to theA. besseyispecies complex. MostAphelenchoidesgenomes have a size of 44.7-47.4 Mb and are amongst the smallest in clade IV, with the exception ofA. fujianensis, which has a size of 143.8 Mb and is the largest. Phylogenomic analysis successfully delimited the species complex intoA. oryzaeandA. pseudobesseyiand revealed a reduction of transposon elements in the last common ancestor ofAphelenchoides. Synteny analyses between reference genomes indicated that three chromosomes inA. besseyiwere derived from fission and fusion events. A systematic identification of horizontal gene transfer (HGT) genes across 27 representative nematodes allowed us to identify two major episodes of acquisition corresponding to the last common ancestor of clade IV or major PPNs, respectively. These genes were mostly lost and differentially retained between clades or strains. Most HGT events were acquired from bacteria, followed by fungi, and also from plants; plant HGT was especially prevalent inBursaphelenchus mucronatus. Our results comprehensively improve the understanding of horizontal gene transfer in nematodes.