TE annotation and statistical analysis
Thede novo repeat libraries were built using
RepeatModeler
(http://www.repeatmasker.org/RepeatModeler/,
open-1.0.11) and were filtered using species-specific protein annotation
files. Then,
‘chalcidoidea’
TE library was extracted using the perl script queryRepeatDarabase.pl.
We
then combined the filtered de novo repeat libraries and
‘chalcidoidea’ TE library to obtain local species-specific TE libraries.
RepeatMasker
(http://www.repeatmasker.org,
open-v4.0.7) was used to mask the genomes. The parameters ‘-lib -s
-nolow -norna -no_is -cutoff 250 -gff -align’ were applied. To
summarize the TEs annotation results, parseRM.pl
(https://github.com/4ureliek/Parsing-RepeatMasker-Outputs/)
script was used. Spearman corration and Mann-Whitney U test were carried
out using
SPSS
software.