Meloidogyne enterolobii assemblies

We present the assembly of Meloidogyne enterolobii's genomes using the high-fidelity long-read sequencing method developed by Pacific Biosciences. Initially, we filtered out very low-quality reads ( < Q9, parameter --min-rq=0.88 ) and produced a draft consensus sequence with CCS (v6.4.0) and ACTC (v0.2.0). To correct for errors introduced by the PacBio Sequel II system, we aligned the subreads against the draft consensus sequence with a gap-aware sequence transformer, DeepConsensus (v1.1.0, Baid et al., 2023). This yielded 2,449,079 cleaned reads with an average Qscore of 34.04 for M. enterolobii. Following QC, the genome assembly was carried out using Peregrine-2021 (v0.4.11, Chin, J. ,2023). The number of best overlaps for each initial graph was increased to the default setting (parameter --bestn8). For the mitochondrial genome sequence, we used the ALADIN package (v1.1) with a complete M. enterolobii mitochondrion previously downloaded from the GenBank database (BioProject: PRJNA927338) as a reference seed sequence. The resulting nuclear genome assembly spans a total length of 273 Mbp and comprises 556 contigs, a GC% of 30 and an N50 value of 2.11 Mb (longest contig = 8,284,238 bp). The circular assembly of the mitochondrion spans 19,193 bp in length with a GC content of 17.2%.