Gene annotation
Repeat families were de novo identified and classified using the
RepeatModeler, subsequently genome was masked using RepeatMasker, and
protein-coding genes were annotated using the MAKER2 annotation pipeline
(Cantarel et al., 2008). Functional
annotation was performed by aligning protein sequences with the protein
database using BLAT (Kent, 2002)
(identity >30 %, and the E < 1e -5). The
detailed description in File S1.
Chromosome grouping and subgenome
recombination test
We first collected genome data of 4 poplars and Salix suchowensis(Dai et al., 2014), and de novotranscriptomes assembly of other white poplars (Table S2 ). Then
we performed gene family clustering using OrthoMCL on protein sequences,
and conducted further collinearity analysis using MCScanX
(Y. Wang et al., 2012) We chose 1,052
single copy and collinear orthologous genes to construct gene trees.
Subsequently, the total 38 chromosomes of P. tomentosa were
partitioned into two subgenomes (2 × 19 chromosomes) based on phylogenic
distance. To investigate potential recombinantion between homologus gene
pairs of the subgenomes, we compared the synonymous substitution rates
of parent and progeny alleles, assuming that recombination would lead to
higher substittion rates than in its absence. The detailed description
in File S1.