Comparative genomics of two inbred lines of the potato cyst nematode Globodera rostochiensis reveals disparate effector family-specific diversification patterns

This work was funded as part of a grant by the Netherlands Organization for Scientific Research (NWO) as part of the Applied and Technical Science domain (TTW) under grant no. 14708. PT: bioinformatics and computational biology analyses were supported by the University of St Andrews Bioinformatics Unit (AMD3BIOINF), funded by Wellcome Trust ISSF award 105621/Z/14/Z.Background: Potato cyst nematodes belong to the most harmful pathogens in potato, and durable management of these parasites largely depends on host-plant resistances. These resistances are pathotype specific. The current Globodera rostochiensis pathotype scheme that defines five pathotypes (Ro1 - Ro5) is both fundamentally and practically of limited value. Hence, resistant potato varieties are used worldwide in a poorly informed manner. Results : We generated two novel reference genomes of G. rostochiensis inbred lines derived from a Ro1 and a Ro5 population. These genome sequences comprise 173 and 189 scaffolds respectively, marking a ≈ 24-fold reduction in fragmentation as compared to the current reference genome. We provide copy number variations for 19 effector families. Four dorsal gland effector families were investigated in more detail. SPRYSECs, known to be implicated in plant defence suppression, constitute by far the most diversified family studied herein with 60 and 99 variants in Ro1 and Ro5 distributed over 18 and 26 scaffolds. In contrast, CLEs, effectors involved in feeding site induction, show strong physical clustering. The 10 and 16 variants cluster on respectively 2 and 1 scaffolds. Given that pathotypes are defined by their effectoromes, we pinpoint the disparate nature of the contributing effector families in terms of sequence diversification and loss and gain of variants. Conclusions : Two novel reference genomes allow for nearly complete inventories of effector diversification and physical organisation within and between pathotypes. Combined with insights we provide on effector family-specific diversification patterns, this constitutes a basis for an effectorome-based virulence scheme for this notorious pathogen.Publisher PDFPeer reviewe

Comparative genomics among cyst nematodes reveals distinct evolutionary histories among effector families and an irregular distribution of effector-associated promoter motifs

JvS, MH and SvdE were supported by a grant from the Applied and Technical Science domain (TTW) of the Netherlands Organization for Scientific Research (NWO) under grant no. 14708. PT received support from the University of St Andrews Bioinformatics Unit (AMD3BIOINF), funded by Wellcome Trust ISSF award 105621/Z/14/Z. MS benefitted from funding by a VENI grant (17282) from the NWO domain Applied and Engineering Sciences.Potato cyst nematodes (PCNs), an umbrella term used for two species, Globodera pallida and G. rostochiensis, belong worldwide to the most harmful pathogens of potato. Pathotype-specific host plant resistances are an essential handle for PCN control. However, the poor delineation of G. pallida pathotypes hampers the efficient use of available host plant resistances. Long-read sequencing technology allowed us to generate a new reference genome of G. pallida population D383 and, as compared to the current reference, the new genome assembly is 42 times less fragmented. For comparison of diversification patterns of six effector families between G. pallida and G. rostochiensis, an additional reference genome was generated for an outgroup, the beet cyst nematode Heterodera schachtii (IRS population). Large evolutionary contrasts in effector family topologies were observed. While VAPs diversified before the split between the three cyst nematode species, the families GLAND5 and GLAND13 only expanded in PCN after their separation from the genus Heterodera. Although DNA motifs in the promoter regions thought to be involved in the orchestration of effector expression ('DOG boxes') were present in all three cyst nematode species, their presence is not a necessity for dorsal gland-produced effectors. Notably, DOG box dosage was only loosely correlated with expression level of individual effector variants. Comparison of the G. pallida genome with those of two other cyst nematodes underlined the fundamental differences in evolutionary history between effector families. Re-sequencing of PCN populations with deviant virulence characteristics will allow for the linking of these characteristics with the composition of the effector repertoire as well as for the mapping of PCN diversification patterns resulting from extreme anthropogenic range expansion.Publisher PDFPeer reviewe

Nematodes as evolutionary commuters between marine, freshwater and terrestrial habitats

Nematodes are the only major metazoan group which is persistently abundant and diverse across marine, freshwater and terrestrial ecosystems. This could be the result of a few major habitat transitions followed by extensive diversification, or numerous habitat transitions followed by moderate diversification. To pinpoint habitat transitions, we superposed nematode habitat associations on an available phylum-wide phylogenetic tree based on small subunit ribosomal DNA sequences (≈2730 SSU rDNA sequences covering ≈1750 nematode taxa). Our analysis revealed at least 30 major habitat transitions within the phylum Nematoda. These transitions as well as their directionality were unevenly spread over the 12 major clades. Most transitions reside in Clades 1–6, and these transitions are bidirectional. Members of Clades 8–12 showed five full transitions, and these took place exclusively from terrestrial to marine systems. We relate our results to the distinct secretory–excretory systems in Clades 1–6 and Clades 8–12, as well as to differences in water permeability of the nematode cuticle. Hence, the phylum Nematoda is characterized by a relatively large number of habitat transitions followed by moderate diversification. The identification of multiple habitat transitions at a low taxonomic level will facilitate future investigations into the mechanisms underlying this unusual ecological flexibility

Corrigendum: A Worm's World: Ecological Flexibility Pays off for Free-Living Nematodes in Sediments and Soils

In a recent article (doi:10.1093/biosci/biz086), the name of the second author was misspelled in the byline. It should have read Martijn Holterman. It is spelled correctly throughout the remainder of the manuscript.</p

A Worm's World: Ecological Flexibility Pays Off for Free-Living Nematodes in Sediments and Soils

Free-living nematodes, an ancient animal phylum of unsegmented microscopic roundworms, have successfully adapted to nearly every ecosystem on Earth: from marine and freshwater to land, from the polar regions to the tropics, and from the mountains to the ocean depths. They are globally the most abundant animals in sediments and soils. In the present article, we identify the factors that collectively explain the successful ecological proliferation of free-living nematodes and demonstrate the impact they have on vital sediment and soil processes. The ecological success of nematodes is strongly linked to their ability to feed on various food sources that are present in both sediments and soils, and to proliferate rapidly and survive in contrasting environmental conditions. The adaptations, roles, and behaviors of free-living nematodes have important implications for the resilience of sediments and soils, and for emergent animal communities responding to human alterations to ecosystems worldwide

Corrigendum: A Worm's World: Ecological Flexibility Pays off for Free-Living Nematodes in Sediments and Soils

In a recent article (doi:10.1093/biosci/biz086), the name of the second author was misspelled in the byline. It should have read Martijn Holterman. It is spelled correctly throughout the remainder of the manuscript.</p

Characterisation of Ditylenchus paraoncogenus n. sp. (Nematoda : Anguinidae), a new stem nematode parasitising tumble thistle

During a survey, three populations of a new stem nematode were isolated from galls on the shoots of tumble thistle (Gundelia tournefortii) plants in Fars province, Iran, and identified. Ditylenchus paraoncogenus n. sp. is described based on morphometric and morphological characters. It is characterised by having long-sized females, 1252 (943-1628) μm long, narrow lateral fields with six incisures, rather developed stylet 9.9 (9.0-11.3) μm long with round knobs, usually elongate and offset from intestine basal pharyngeal bulb, oocytes in two rows in distal part of ovary, V = 83.3 (80.3-86.2), post-vulval uterine sac 68.1 (46.9-86.1)% of vulva to anus distance long, bursa covering 63.2 (33.3-74.4)% of tail length, spicules 24.7 (21.0-27.9) μm long with minute processes at the base of its manubrium and anteriorly pointed cuticle parts within the lamina, and thick conical tail, usually with a pointed terminus. In addition, the ITS and 18S rDNA sequences of 17 populations of D. destructor, D. dipsaci, D. medicaginis, D. myceliophagus, D. paraoncogenus n. sp., Ditylenchus sp. and Nothotylenchus geraerti plus one population of Anguinidae sp. were analysed. The results showed a close relationship between D. paraoncogenus n. sp. and the stem nematodes D. oncogenus, D. gigas, D. weischeri and D. dipsaci. Ditylenchus species were divided into two clades, one clade comprising stem nematodes and gall-forming nematodes of the family Anguinidae, and the other clade containing fungivorous species. Observations showed that the second-stage juvenile is the dormant stage of D. paraoncogenus n. sp. and can survive in anhydrobiotic condition for at least 4 years

Analyses of morphological and molecular characteristics of Telotylenchinae from Iran point at the validity of the genera Bitylenchus and Sauertylenchus

To investigate relationships within the subfamily Telotylenchinae, more than 500 soil samples were collected from various natural and agricultural habitats in several localities of Iran. Individuals of seven known species, including Bitylenchus dubius, B. parvus, B. serranus, Sauertylenchus maximus, Tylenchorhynchus clarus, T. microconus and Trophurus ussuriensis, were recovered and characterized based on morphological and morphometric characters. Furthermore, phylogenetic relationships within representatives of the subfamily Telotylenchinae were explored using 13 sequences from the D2-D3 expansion regions of 28S ribosomal (r) DNA and 13 sequences for the partial 18S rDNA genes obtained in the present study. Analyses based on the relatively conserved 18S rDNA gene underlined the polyphyletic status of Tylenchorhynchus sensu lato, as three clusters representing Tylenchorhynchus, Bitylenchus and Sauertylenchus were well separated, and interspersed by, e.g., representatives of the Macrotrophurinae. Analysis of the more variable D2-D3 28S rDNA sequences suggested at least four clades within the subfamily Telotylenchinae: two clades dominated by Tylenchorhynchus species; a third clade harbouring representatives of Sauertylenchus, Bitylenchus, and Paratrophurus in distinct but unresolved branches;and a fourth clade dominated by Trophurus species. Although no molecular information was available from a number of genera that were originally gathered under Tylenchorhynchus sensu lato, we concluded that both Bitylenchus and Sauertylenchus should be seen as valid Telotylenchinae genera related to, but distinct from Tylenchorhynchus