PMID- 35560992
OWN - NLM
STAT- MEDLINE
DCOM- 20230309
LR  - 20240320
IS  - 1365-294X (Electronic)
IS  - 0962-1083 (Print)
IS  - 0962-1083 (Linking)
VI  - 32
IP  - 6
DP  - 2023 Mar
TI  - Comparative genomics among cyst nematodes reveals distinct evolutionary histories 
      among effector families and an irregular distribution of effector-associated 
      promoter motifs.
PG  - 1515-1529
LID - 10.1111/mec.16505 [doi]
AB  - 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 essential for PCN control. 
      However, the poor delineation of G. pallida pathotypes has hampered 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 (venom allergen-like proteins) diversified before the split 
      between the three cyst nematode species, the families GLAND5 and GLAND13 only 
      expanded in PCNs 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 the 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. Resequencing of PCN populations with different 
      virulence characteristics will allow for the linking of these characteristics to 
      the composition of the effector repertoire as well as for the mapping of PCN 
      diversification patterns resulting from extreme anthropogenic range expansion.
CI  - (c) 2022 The Authors. Molecular Ecology published by John Wiley & Sons Ltd.
FAU - van Steenbrugge, Joris J M
AU  - van Steenbrugge JJM
AUID- ORCID: 0000-0002-9961-2538
AD  - Laboratory of Nematology, Wageningen University & Research, Wageningen, The 
      Netherlands.
FAU - van den Elsen, Sven
AU  - van den Elsen S
AD  - Laboratory of Nematology, Wageningen University & Research, Wageningen, The 
      Netherlands.
FAU - Holterman, Martijn
AU  - Holterman M
AD  - Laboratory of Nematology, Wageningen University & Research, Wageningen, The 
      Netherlands.
AD  - Solynta, Wageningen, The Netherlands.
FAU - Lozano-Torres, Jose L
AU  - Lozano-Torres JL
AD  - Laboratory of Nematology, Wageningen University & Research, Wageningen, The 
      Netherlands.
FAU - Putker, Vera
AU  - Putker V
AD  - Laboratory of Nematology, Wageningen University & Research, Wageningen, The 
      Netherlands.
FAU - Thorpe, Peter
AU  - Thorpe P
AD  - School of Medicine, Medical & Biological Sciences, University of St. Andrews, St 
      Andrews, UK.
FAU - Goverse, Aska
AU  - Goverse A
AD  - Laboratory of Nematology, Wageningen University & Research, Wageningen, The 
      Netherlands.
FAU - Sterken, Mark G
AU  - Sterken MG
AD  - Laboratory of Nematology, Wageningen University & Research, Wageningen, The 
      Netherlands.
FAU - Smant, Geert
AU  - Smant G
AD  - Laboratory of Nematology, Wageningen University & Research, Wageningen, The 
      Netherlands.
FAU - Helder, Johannes
AU  - Helder J
AD  - Laboratory of Nematology, Wageningen University & Research, Wageningen, The 
      Netherlands.
LA  - eng
GR  - WT_/Wellcome Trust/United Kingdom
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20220601
PL  - England
TA  - Mol Ecol
JT  - Molecular ecology
JID - 9214478
RN  - 0 (Antioxidants)
SB  - IM
MH  - Animals
MH  - *Genomics
MH  - Sequence Analysis, DNA
MH  - Antioxidants
MH  - Promoter Regions, Genetic
MH  - *Nematoda
PMC - PMC10946958
OTO - NOTNLM
OT  - Globodera
OT  - Heterodera
OT  - DOG box
OT  - cyst nematodes
OT  - nematode effectors
COIS- All authors declare that they have no conflict of interest.
EDAT- 2022/05/14 06:00
MHDA- 2023/03/10 06:00
PMCR- 2024/03/18
CRDT- 2022/05/13 19:31
PHST- 2022/04/26 00:00 [revised]
PHST- 2021/11/02 00:00 [received]
PHST- 2022/05/04 00:00 [accepted]
PHST- 2022/05/14 06:00 [pubmed]
PHST- 2023/03/10 06:00 [medline]
PHST- 2022/05/13 19:31 [entrez]
PHST- 2024/03/18 00:00 [pmc-release]
AID - MEC16505 [pii]
AID - 10.1111/mec.16505 [doi]
PST - ppublish
SO  - Mol Ecol. 2023 Mar;32(6):1515-1529. doi: 10.1111/mec.16505. Epub 2022 Jun 1.