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.