Genomic basis of differentiation in floral development and
rhizome growth between Orinus and Cleistogenes
Floral development is effectively
explained by the ABCDE model (Ó’Maoiléidigh et al., 2014), and many
ABCDE genes had higher expression in cleistogamous flowers (CLs)
compared with that in chasmogamous flowers (CHs) in C. songorica(Zhang et al., 2021a). These genes may play an important role in the
development of CLs. To investigate the genomic basis of differentiation
in floral development between O. kokonorica and C.
songorica , we identified genes related to floral development (ABCDE
model genes) in these two species based on the ABCDE models of A.
thaliana and O. sativa . ABCDE genes of A. thaliana andO. sativa were downloaded from TAIR and RICEDATA, respectively.
All genes of O. kokonorica and C. songorica were searched
against the A. thaliana and O. sativa ABCDE model genes
using BLASTP with an E-value cut-off of 1e-5. We then identified domains
of candidate genes using HMMER v3.2.1 (Finn et al., 2011) by searching
the Pfam database (Punta et al., 2011). Phylogenetic analysis was
performed based on the ABCDE genes identified in O. kokonorica, C.
songorica, and in A. thaliana and O. sativa . Only genes
grouped with A. thaliana or O. sativa in the same clade
were selected as orthologs.
Rhizomes are modified stems that grow horizontally underground in
various perennial species, a growth habit that is advantageous for
vigorous asexual proliferation. O. kokonorica and C.
songorica differ in rhizome growth with the former having elongated
rhizomes. The suppression of leaf blade development is necessary for the
underground growth of rhizomes, and BLADE-ON-PETIOLE (BOP )
homologs are important in the regulation of rhizome growth (Toriba et
al., 2020). We searched BOP genes in O. kokonorica ,C. songorica , and O. thomaeum using the same strategy
mentioned above with A. thaliana and O. sativa BOP genes.
Domain confirmation and phylogenetic analyses were performed to identify
orthologs.