The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence

Abstract

BackgroundThe yellow potato cyst nematode, Globodera rostochiensis, is a devastating plant pathogen of global economic importance. This biotrophic parasite secretes effectors from pharyngeal glands, some of which were acquired by horizontal gene transfer, to manipulate host processes and promote parasitism. G. rostochiensis is classified into pathotypes with different plant resistance-breaking phenotypes.ResultsWe generate a high quality genome assembly for G. rostochiensis pathotype Ro1, identify putative effectors and horizontal gene transfer events, map gene expression through the life cycle focusing on key parasitic transitions and sequence the genomes of eight populations including four additional pathotypes to identify variation. Horizontal gene transfer contributes 3.5 % of the predicted genes, of which approximately 8.5 % are deployed as effectors. Over one-third of all effector genes are clustered in 21 putative ‘effector islands’ in the genome. We identify a dorsal gland promoter element motif (termed DOG Box) present upstream in representatives from 26 out of 28 dorsal gland effector families, and predict a putative effector superset associated with this motif. We validate gland cell expression in two novel genes by in situ hybridisation and catalogue dorsal gland promoter element-containing effectors from available cyst nematode genomes. Comparison of effector diversity between pathotypes highlights correlation with plant resistance-breaking.ConclusionsThese G. rostochiensis genome resources will facilitate major advances in understanding nematode plant-parasitism. Dorsal gland promoter element-containing effectors are at the front line of the evolutionary arms race between plant and parasite and the ability to predict gland cell expression a priori promises rapid advances in understanding their roles and mechanisms of action.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-016-0985-1) contains supplementary material, which is available to authorized users.

Analysis of survival and hatching transcriptomes from potato cyst nematodes, Globodera rostochiensis and G. pallida

“…rostochiensis reference transcriptome has 14,309 contigs 32 and the G . pallida reference transcriptome has 16,417 contigs 30 .…”

“…pallida 30 and G . rostochiensis 32 reference transcriptomes. Both reference transcriptomes were obtained with the gene prediction software Augustus 78 .…”

Alienness: Rapid Detection of Candidate Horizontal Gene Transfers across the Tree of Life

“…To further measure the ability of Alienness to recall highly supported candidate HGT, we tested whether previously reported cases of HGT, supported by careful manual phylogenetic analysis were We retrieved the PFAM domains [65] present in the corresponding proteins and scanned these domains against the proteomes of the root-knot nematode M. incognita [37] and of the cyst nematode G. rostochiensis [19]. We found corresponding protein-coding genes for 13 and 19 of these HGT cases in the proteomes of M. incognita and G. rostochiensis, respectively.…”

“…This AI method was used again to assess the total contribution of genes of non-metazoan origin in the whole genome of the bdelloid rotifer once it was sequenced [18]. Using custom Perl scripts, our laboratory and collaborators also used AI to identify candidate HGT of non-metazoan origin in the genome of the plant-parasitic nematode Globodera rostochiensis [19], in the genomes of several panagrolaimid nematodes [20] as well as in the transcriptomes of the nematodes Nacobbus aberrans [21], Xiphinema index and other as yet unpublished genomes. Calculation of Alien Index scores for whole proteomes had previously been implemented in a software called AlienG [22].…”

Potato resistance to quarantine diseases

“…Результаты полногеномного секвенирования G. rostochiensis (Evesvan den Akker et al, 2016) показали, что у нее, как у других эукариотических фитопатогенов, например Phytophthora infestans (Raf faele, Kamoun, 2012), геныэффекторы не случайным об разом распределены в геноме паразита, а локализованы в особых районах генома. Таким образом, на G. rostochiensis в полной мере распространяется модель «двухскоростно го генома», объясняющая быструю эволюцию фитопато генов и преодоление ими генов устойчивости растений хозяев.…”