Genome assembly and annotation of Meloidogyne enterolobii, an emerging parthenogenetic root-knot nematode

Abstract

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.

Comparative Genomics Reveals Novel Target Genes towards Specific Control of Plant-Parasitic Nematodes

“…The only support values lower than 0.9 concerned the relative branching order of the RKN within clade I, sensu De Ley ( M. arenaria , M. enterolobii , M. floridensis , M. incognita and M. javanica ). This observation is not particularly surprising, as these RKN species underwent complex hybridization and polyploidization events, with a probable same common or very similar maternal origin and distinct paternal progenitors [ 23 , 24 , 29 , 78 ]. As a result, some genome regions are highly similar between these species, while copies of the region are highly divergent within a same species.…”

“…Describing more thoroughly the effector protein repertoire and dissecting their functions is therefore important for the development of novel nematode control strategies. Over the years, the availability of several RKN genomes provided new resources for the identification of complete sets of candidate effectors in these species [ 20 , 21 , 22 , 23 , 24 , 25 , 26 , 27 , 28 , 29 ]. Although nematode effectors are very diverse, many share common features with other secreted animal proteins, such as the presence of N-terminal signal peptides for secretion, or the absence of transmembrane domains.…”

“…Even if original, the comparative genomics study published in 2013 [ 32 ] was limited to the only two genomes for plant-parasitic species available at the time (two RKN). Since this initial comparative genomics study, the availability of genome sequences for additional RKN species [ 24 , 26 , 27 , 28 , 29 ], as well as for other plant-parasitic nematode species, including cyst nematodes [ 15 , 34 , 35 ], stem and bulb nematodes [ 36 , 37 ], or the more distantly related pine wilt disease nematode [ 38 ], has now greatly expanded the diversity of genomes for plant-parasitic nematode species. Similar genome sequencing efforts were also accomplished in the other nematode clades, including in animal parasites and free-living species, offering a novel opportunity for nematode comparative genomics.…”

Comparative Genomics Reveals Novel Target Genes Towards Specific Control of Plant-Parasitic Nematodes

“…Over the years, the availability of several RKN genomes provided new resources for the identification of complete sets of candidate effectors in these species [20][21][22][23][24][25][26][27][28][29]. Although nematode effectors are very diverse, many share some common features with other secreted animal proteins, such as the presence of N-terminal signal peptides for secretion, or the absence of transmembrane domains.…”

“…Furthermore, the M. incognita genome employed in this original study [20] was later shown to be partially incomplete, with an improved version published afterwards [23]. Meanwhile, the availability of genome sequences for additional RKN species [24,[26][27][28][29], as well as for other plant-parasitic nematode species, including cyst nematodes [15,34,35], stem and bulb nematodes [36,37], or the more distantly related pine wilt disease nematode [38], greatly expanded the diversity of genomes for plant-parasitic nematode species. Similar genome sequencing efforts were also accomplished in the other nematode clades, including in animal parasites and free-living species, offering a novel opportunity for nematode comparative genomics.…”