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Root-knot nematodes (genus Meloidogyne) are plant parasites causing huge economic loss in the agricultural industry and affecting severely numerous developing countries. Control methods against these plant pests are sparse, the preferred one being the deployment of plant cultivars bearing resistance genes against Meloidogyne species. However, M. enterolobii is not controlled by the resistance genes deployed in the crop plants cultivated in Europe. The recent identification of this species in Europe is thus a major concern. Here, we sequenced the genome of M. enterolobii using short and long-read technologies. The genome assembly spans 240 Mbp with contig N50 size of 143 kbp, enabling high-quality annotations of 59,773 coding genes, 4,068 non-coding genes, and 10,944 transposable elements (spanning 8.7% of the genome). We validated the genome size by flow cytometry and the structure, quality and completeness by bioinformatics metrics. This ensemble of resources will fuel future projects aiming at pinpointing the genome singularities, the origin, diversity, and adaptive potential of this emerging plant pest., Measurement(s) genome • sequence_assembly • sequence feature annotation Technology Type(s) DNA sequencing assay • sequence assembly process • sequence annotation Sample Characteristic - Organism Meloidogyne enterolobii Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.12410363

Applying high-throughput DNA sequencing technologies to the ancient DNA molecules preserved in subfossil material can provide genetic information from past individuals, populations, and communities at the genomic scale. The combination of dedicated statistical techniques and specific molecular tools aimed at reducing the impact of post-mortem DNA damage can also help recover epigenetic data from ancient individuals. However, the capacity of different sequence aligners to identify ultrashort and deaminated ancient DNA templates and their impact on the characterization of ancient methylomes remain overlooked. In this study, we use both simulated and real ancient DNA sequence data to benchmark the performance of the read alignment tools most commonly used in ancient DNA research. We identify a read alignment strategy making use of the Bowtie2 aligner that substantially reduce computational times but shows increased sensitivity relative to previous recommendations based on the BWA aligner. This strategy significantly improves the genome coverage especially when DNA templates are shorter than 90 bp, as is typically the case for ancient DNA. It also impacts on ancient DNA methylation estimates as it maximizes coverage improvement within CpG dinucleotide contexts, which hold the vast majority of DNA methylation marks in mammals. Our work contributes to improve the accuracy of DNA methylation maps and to maximize the amount of recoverable genetic information from archeological and subfossil material. As the molecular complexity of ancient DNA libraries is generally limited, the mapping strategy recommended here is essential to limit both sequencing costs and sample destruction.

Root-knot nematodes (genusMeloidogyne) are plant parasitic species that cause huge economic loss in the agricultural industry and affect the prosperity of communities in developing countries. Control methods against these plant pests are sparse and the current preferred method is deployment of plant cultivars bearing resistance genes againstMeloidogynespecies. However, some species such asM. enterolobiiare not controlled by the resistance genes deployed in the most important crop plants cultivated in Europe. The recent identification of this species in Europe is thus a major concern. Like the other most damaging Meloidogyne species (e.g.M. incognita,M. arenariaandM. javanica),M. enterolobiireproduces by obligatory mitotic parthenogenesis. Genomic singularities such as a duplicated genome structure and a relatively high proportion of transposable elements have previously been described in the above mentioned mitotic parthenogenetic Meloidogyne.To gain a better understanding of the genomic and evolutionary background we sequenced the genome ofM. enterolobiiusing high coverage short and long read technologies. The information contained in the long reads helped produce a highly contiguous genome assembly ofM. enterolobii, thus enabling us to perform high quality annotations of coding and non-coding genes, and transposable elements.The genome assembly and annotation reveals a genome structure similar to the ones described in the other mitotic parthenogenetic Meloidogyne, described as recent hybrids. Most of the genome is present in 3 different copies that show high divergence. Because most of the genes belong to these duplicated regions only few gene losses took place, which suggest a recent polyploidization. The most likely hypothesis to reconcile high divergence between genome copies despite few gene losses and translocations is also a recent hybrid origin. Consistent with this hypothesis, we found an abundance of transposable elements at least as high as the one observed in the mitotic parthenogenetic nematodesM. incognitaandM. javanica.