3.7 Putative signatures of selection
The 99th percentile threshold
values of the F ST and |XP-EHH|
were used to detect the putative signatures of selective sweeps between
invasive and source populations. These thresholds were 0.300 and 2.399
for diploids, and 0.021 and 2.021 for triploids, respectively (Figure
8). For diploids, 324 overlapping outlier windows between the two
methods were detected on 37 chromosomes, with most outliers on Chr24
(66) followed by Chr13 (38), Chr9 (34) and Chr30 (29) (Table S2). A
total of 16,754 SNPs were observed within these outlier regions, among
which 4.16% and 52.75% were annotated to the exonic and intronic
regions, respectively, with the percentages being higher than those
found in the whole genome (2.51% and 49.56%). The nucleotide diversity
within these outliers in the source range was more than two times higher
than that in the invasive range. The SNPs within exonic and intronic
regions were annotated to 191 genes (Table S3). GO enrichment of these
genes revealed one enriched cluster namely ‘mannosyl-oligosaccharide
mannosidase activity’ (Pvalue < 0.01 and Qvalue <
0.05) involving in three genes (Endoplasmic reticulum
mannosyl-oligosaccharide 1,2-alpha-mannosidase ,Mannosyl-oligosaccharide 1,2-alpha-mannosidase IB andAlpha-mannosidase 2 ). Other enriched clusters with Pvalue
< 0.01 but Qvalue > 0.05 were mainly involved in
mannosidase and embryo development (Table S4).
For triploids, 244 overlapping outliers between the two methods were
observed on 40 chromosomes. However, these outliers only formed visual
peaks on Chr14, Chr15, Chr18 and Chr35. Among 2,543 SNPs within these
outliers, 3.54% and 33.23% were annotated to exonic and intronic
regions, respectively, with the percentages being lower than those found
in the whole genome (3.85% and 49.31%). These SNPs were annotated to
60 genes with enriched GO terms related to metabolic process and immune
response (Table S4). Interestingly, one enriched GO term was
‘development of secondary sexual characteristics’ with two involved
genes (Beta-1,4-galactosyltransferase 1 and Signal
transducer and activator of transcription 5B ). When comparing outliers
for diploids and triploids, only four were overlapped on Chr2 and Chr18
with all SNPs being annotated to intergenic regions.