Subgenome dominance and differentiation in homoeolog expression
patterns
Unequal expression of homoeologous genes in allopolyploids can be an
important feature and consequence of polyploidization. We investigated
homoeolog expression bias in five different tissues and under three
stress treatments. Of 11,861 identified homoeologous gene pairs between
subgenomes A and B, 11,409 had homoeologous expression bias (HEB) in at
least one tissue or treatment, and 1,160 had biased expression in all
sampled tissues and treatments. Pairwise comparisons between syntenic
gene pairs support a slight bias in expression toward the B subgenome
across all five tissues and three treatments (Figure S10). Roughly
26.6% (3,155) of the 11,861 pairwise comparisons across the five
tissues and three stress treatments showed biased expression toward
homoeologs in the B subgenome. Each tissue and treatment have
approximately 6,000 homoeologous gene pairs with significant
differential expression, including 52.16% biased toward the B subgenome
(Figure S10).
To investigate the differentiation in homoelog expression patterns
between O. kokonorica and C. songorica , we first performed
transcriptomic analysis under the same stress treatments (i.e., light
drought, cold, heat) in both shoots and roots of O. kokonorica as
conducted for C. songorica . Hierarchical cluster analysis of
transcriptomic data showed clustering of the four repeats for the shoot
or root at each treatment, except for one root and shoot sample in the
cold treatment group and one shoot sample in control group (Figure S11),
which were discarded for downstream analysis. Differentially expressed
genes (DEGs) were identified under different treatments by comparison
with the control group. A total of 1,246 and 631 DEGs in shoots and
roots, respectively, were identified under cold stress with 2-fold
changes compared with the control sample. 2,316 DEGs in shoots and 338
DEGs in roots were identified under heat stress. However, under light
drought stress, much lower DEGs (11 in shoots; 420 in roots) were
detected compared to the other two treatments (Figure S12). The DEGs in
roots were about 57 times greater than in shoots, indicating that
drought stress in early stages does not considerably affect the shoots
of O. kokonorica .
Next, we downloaded transcriptomic data under the same stress treatments
for C. songorica and identified DEGs using the same method as
described for O. kokonorica . To reduce bias resulting from the
two experiments, we only focused on the orthologous genes that were both
DEGs in the two species (either in shoots, roots, or both) under each
treatment. A total of 533, 99, 350 orthologous DEG pairs were identified
under cold, drought, and heat treatments, respectively (Figure 3B;
Tables S15-S17). We examined the differential expression pattern of two
orthologous copies in each pair. We found that 53% (52) of orthologous
genes had conserved functions in the two species under light drought
treatment, consistent with the fact that both are drought resistance
species. However, only ~2% and ~11% of
orthologous genes under cold and heat treatments, respectively, had
similar expression patterns in the two species (Figure 3B, C). Most
orthologous genes were differentially expressed either in different
tissues or in different ways (i.e. up- vs. down-regulation) or both,
which may be related to the significant distinct altitudinal
distributions of the two species.