PMID- 34129357
OWN - NLM
STAT- MEDLINE
DCOM- 20220224
LR  - 20220224
IS  - 0031-949X (Print)
IS  - 0031-949X (Linking)
VI  - 112
IP  - 2
DP  - 2022 Feb
TI  - Genomic Reconstruction of the Introduction and Diversification of Golden Potato 
      Cyst Nematode Populations in Indonesia.
PG  - 396-403
LID - 10.1094/PHYTO-04-21-0150-R [doi]
AB  - Potato cyst nematodes (PCNs), the umbrella term for Globodera rostochiensis and 
      G. pallida, coevolved with their Solanaceous hosts in the Andean Mountain region. 
      From there, PCN proliferated worldwide to virtually all potato production areas. 
      PCN is a major factor limiting the potato production in Indonesia. In our survey, 
      only G. rostochiensis was found. Fourteen field populations were collected on 
      Java and Sumatra, and unique variants were called by mapping resequencing data on 
      a G. rostochiensis reference genome. A phylogenetic tree based on 1.4 million 
      unique variants showed a genotypic separation between the outgroup, a Scottish 
      Ro1 population, and all Indonesian populations. This separation was comparable in 
      size with the genotypic distinction between the Javanese and the Sumatran PCN 
      populations. Next, variants within PCN effector gene families SPRYSEC, 1106, 
      4D06, and venom allergen-like protein (VAL) that all interfere with the host 
      innate immune system were compared. Distinct selective pressures acted on these 
      effector families; while SPRYSECs (4,341 single-nucleotide polymorphisms 
      [SNPs]/insertions or deletions of bases [indels]) behaved like neutral genes, the 
      phylogenetic trees of 1106, 4D06, and VAL proteins (235, 790, and 150 
      SNPs/indels, respectively) showed deviating topologies. Our data suggest that PCN 
      was introduced on Java not too long after the introduction of potato in the 
      middle of the eighteenth century. Soon thereafter, the pathogen established on 
      Sumatra and started to diversify independently. This scenario was corroborated by 
      diversification patterns of the effector families 1106, 4D06, and VAL. Our data 
      demonstrate how genome resequencing data from a nonindigenous pathogen can be 
      used to reconstruct the introduction and diversification process.
FAU - Handayani, Nurul Dwi
AU  - Handayani ND
AD  - Indonesian Agricultural Quarantine Agency, Ministry of Agriculture, Ragunan, 
      Jakarta 12550, Indonesia.
AD  - Laboratory of Nematology, Wageningen University, 6708 PB Wageningen, The 
      Netherlands.
AD  - Nematology Research Unit, Department of Biology, Ghent University, 9000 Ghent, 
      Belgium.
FAU - Lestari, Prabowo
AU  - Lestari P
AD  - Indonesian Agricultural Quarantine Agency, Ministry of Agriculture, Ragunan, 
      Jakarta 12550, Indonesia.
AD  - Laboratory of Nematology, Wageningen University, 6708 PB Wageningen, The 
      Netherlands.
AD  - Nematology Research Unit, Department of Biology, Ghent University, 9000 Ghent, 
      Belgium.
FAU - van As, Wouter
AU  - van As W
AD  - Laboratory of Nematology, Wageningen University, 6708 PB Wageningen, The 
      Netherlands.
FAU - Holterman, Martijn
AU  - Holterman M
AD  - Laboratory of Nematology, Wageningen University, 6708 PB Wageningen, The 
      Netherlands.
AD  - Solynta, 6703 HA Wageningen, The Netherlands.
FAU - van den Elsen, Sven
AU  - van den Elsen S
AD  - Laboratory of Nematology, Wageningen University, 6708 PB Wageningen, The 
      Netherlands.
FAU - Dikin, Antarjo
AU  - Dikin A
AD  - Directorate General of Estate Crops, Ministry of Agriculture, Ragunan, Jakarta 
      12550, Indonesia.
FAU - Bert, Wim
AU  - Bert W
AD  - Nematology Research Unit, Department of Biology, Ghent University, 9000 Ghent, 
      Belgium.
FAU - Helder, Johannes
AU  - Helder J
AUID- ORCID: 0000-0003-0408-3985
AD  - Laboratory of Nematology, Wageningen University, 6708 PB Wageningen, The 
      Netherlands.
FAU - Van Steenbrugge, Joris J M
AU  - Van Steenbrugge JJM
AD  - Laboratory of Nematology, Wageningen University, 6708 PB Wageningen, The 
      Netherlands.
LA  - eng
PT  - Journal Article
DEP - 20220201
PL  - United States
TA  - Phytopathology
JT  - Phytopathology
JID - 9427222
SB  - IM
MH  - Animals
MH  - Genomics
MH  - Indonesia
MH  - Phylogeny
MH  - Plant Diseases
MH  - *Solanum tuberosum/genetics
MH  - *Tylenchoidea/genetics
OTO - NOTNLM
OT  - disease control and pest management
OT  - evolution
OT  - genomics
OT  - host-parasite interactions
OT  - nematodes
OT  - pathogen effectors
EDAT- 2021/06/16 06:00
MHDA- 2022/02/25 06:00
CRDT- 2021/06/15 17:11
PHST- 2021/06/16 06:00 [pubmed]
PHST- 2022/02/25 06:00 [medline]
PHST- 2021/06/15 17:11 [entrez]
AID - 10.1094/PHYTO-04-21-0150-R [doi]
PST - ppublish
SO  - Phytopathology. 2022 Feb;112(2):396-403. doi: 10.1094/PHYTO-04-21-0150-R. Epub 
      2022 Feb 1.