Complete genome sequencing and the mitochondrial genome analysis of Tylenchulus semipenetrans, an important Tylenchulidae nematode causing citrus slow decline disease

Abstract Tylenchulus semipenetrans, is considered to be the most devastating nematode pest of citrus, causing significant damage to all citrus-producing regions of the world. The present study, the T. semipenetrans from the rhizosphere of Citrus grandis was sequenced using Illumina and Oxford Nanopore technologies, yielding a high-contiguity 68.9 Mb assembly (N50 = 670.6 kb). The genes were predicted using RNA-seq data, resulting in 11,068 protein-coding genes been annotated. This assembly represents the first long-reads assembled genome for the Criconematoidea superfamily. A total of 424 genes were identified as horizontal gene transfer (HGT) candidates, with 269 from bacteria, 117 from archaea, 22 from other eukaryota, and 16 from varidnaviria. We identified two GH5_2 cellulase paralogs that were clustered together with insects, but distinct from other nematodes. The GH18 (g7408.t1) chitinase gene was placed as early-diverging Tylenchida clade, supporting its vertical inheritance from a common Tylenchida ancestor. Spanning 23,157 bp, the T. semipenetrans has one of largest known mitochondrial genomes in Nematoda. This genome contains 56% non-coding regions, limiting protein-coding sequences to 44% yet encoding 12 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs) and 2 ribosomal RNAs (rRNAs). The genome highlights evolutionary adaptations driven by horizontally acquired CAZymes, such as GH5 family cellulases, that facilitate plant cell wall degradation for parasitic success.