Vitales sister to core rosids + Saxifragales
Our whole-genome microarray analysis of superrosids showed that
Saxifragales shared more synteny clusters with core rosids than Vitales
(Fig. 3 ), suggesting that it has a closer relationship with
core rosids. Similarly, Vitales and Saxifragales were supported as
successive sisters to the core rosids based on the phylogenetic analysis
of 122 nuclear putative single-copy genes with BS = 100% and PP = 1 in
the concatenation tree (Fig.
5 ). The same position of Vitales was also reconstructed using the
coalescent method with a 1.0 LPP support (Fig. 6 ). These
results agree with the coalescent analysis in the 1KP study (One
Thousand Plant Transcriptomes Initiative, 2019 ) and the coalescent and
concatenation analyses in Zeng et al. (2017) , both of which
relied on nuclear gene sequence data but do not agree with most other
studies that largely relied on plastid gene sequences. While Vitales and
Saxifragales are generally found to be closely associated with core
rosids, relationships among them are uncertain, and all three possible
relationships have been recovered (APG III, 2009; Moore et al.,
2010 ). The consensus relationship in APG IV (2016) , which is
different from that reported here, considers Saxifragales as sister to
the remaining superrosids (Vitales + core rosids). For example,Wang et al. (2009) recovered the relationship of Saxifragales
as sister to Vitales + core rosids (BS = 72%) using numerous genes
(primarily plastid), a topology that has also been recovered in
subsequent studies based on different molecular markers, for example, 17
loci including 11 plastid, two nuclear and four mitochondrial genes (BS
= 85%, Soltis et al., 2011 ), four loci including one
mitochondrial and three plastid genes (BS = 97%, Sun et al.,
2016 ), four mitochondrial genes (BS = 13%, Sun et al., 2015 ),
or even the entire protein-coding and rRNA genes of the plastid genome
(BS = 60%, Li et al., 2019a ). In other studies, Saxifragales
plus Vitales occasionally formed a clade sister to core rosids based on
plastid phylogenomic data (BS = 82%, Moore et al., 2010; BS =
73%, Sun et al., 2015; BS/PP = 91/0.99, Zhang et al.,
2016 ), or sister to a clade comprising Caryophyllales and the remaining
rosid species based on 5-gene nuclear sequences (PP=1, Zhang et
al., 2012 ; BS = 96%, Sun et al., 2015 ). The topology of
Vitales sister to Saxifragales + core rosids was first reported byMoore et al. (2011) based on the plastid inverted repeat
region. The same topology was also retrieved with strong support byShi et al. (2020) using 44 plastid genes (PP = 1) as well asZeng et al. (2017) and Wang et al. (2022b) based on
numerous nuclear genes.