PMID- 30045782
OWN - NLM
STAT- MEDLINE
DCOM- 20190807
LR  - 20190807
IS  - 1465-2099 (Electronic)
IS  - 0022-1317 (Linking)
VI  - 99
IP  - 9
DP  - 2018 Sep
TI  - Baculovirus Kimura two-parameter species demarcation criterion is confirmed by 
      the distances of 38 core gene nucleotide sequences.
PG  - 1307-1320
LID - 10.1099/jgv.0.001100 [doi]
AB  - Kimura two-parameter nucleotide distance comparisons based on polyhedrin/granulin 
      (polh/gran), late expression factor 8 (lef-8) and late expression factor 9 
      (lef-9) are a widely applied method for species demarcation for 
      lepidopteran-specific baculoviruses. Baculoviruses are considered to belong to 
      the same species when a pairwise distance threshold of 0.015 is not exceeded and 
      are considered as possibly belonging to the same species with a distance of up to 
      0.050. In the present work this method was revised and extended for 172 entirely 
      sequenced lepidopteran, hymenopteran and dipteran baculovirus genomes by applying 
      the nucleotide sequences of all 38 known baculovirus core genes for pairwise 
      distance calculations. On the basis of this large dataset, the previously 
      established standard thresholds for baculovirus species demarcation were adjusted 
      for pairwise nucleotide distances estimated from the alignments of all 38 core 
      genes. With the newly applied thresholds for the 38 core-gene dataset, a more 
      sophisticated Kimura two-parameter method was established, avoiding the possible 
      influence of the chimerical polh gene of the Autographa californica multiple 
      nucleopolyhedrovirus. Based on the new dataset, the present classification of 
      baculovirus species was confirmed. Thereby the Kimura two-parameter method for 
      baculovirus demarcation was extended to include the information from all 38 
      Baculoviridae core genes, which represent the established standard information 
      for baculovirus phylogeny to date.
FAU - Wennmann, Jorg T
AU  - Wennmann JT
AD  - 1​Julius Kuhn Institute, Federal Research Centre for Cultivated Plants, Institute 
      for Biological Control, Heinrichstrasse 243, 64287 Darmstadt, Germany.
FAU - Keilwagen, Jens
AU  - Keilwagen J
AD  - 2​Julius Kuhn Institute, Federal Research Centre for Cultivated Plants, Institute 
      for Biosafety and Plant Biotechnology, Erwin-Bauer-Strasse 27, 06484 Quedlinburg, 
      Germany.
FAU - Jehle, Johannes A
AU  - Jehle JA
AD  - 1​Julius Kuhn Institute, Federal Research Centre for Cultivated Plants, Institute 
      for Biological Control, Heinrichstrasse 243, 64287 Darmstadt, Germany.
LA  - eng
PT  - Journal Article
DEP - 20180727
PL  - England
TA  - J Gen Virol
JT  - The Journal of general virology
JID - 0077340
RN  - 0 (DNA, Viral)
MH  - Baculoviridae/classification/*genetics
MH  - Base Sequence
MH  - DNA, Viral/genetics
MH  - *Genome, Viral
MH  - Phylogeny
MH  - Sequence Alignment
MH  - Species Specificity
OTO - NOTNLM
OT  - Baculoviridae
OT  - Kimura two-parameter
OT  - barcoding
OT  - molecular phylogeny
OT  - species demarcation
OT  - whole genome sequencing
EDAT- 2018/07/27 06:00
MHDA- 2019/08/08 06:00
CRDT- 2018/07/27 06:00
PHST- 2018/07/27 06:00 [pubmed]
PHST- 2019/08/08 06:00 [medline]
PHST- 2018/07/27 06:00 [entrez]
AID - 10.1099/jgv.0.001100 [doi]
PST - ppublish
SO  - J Gen Virol. 2018 Sep;99(9):1307-1320. doi: 10.1099/jgv.0.001100. Epub 2018 Jul 
      27.