Genetic basis of differentiation in floral development and rhizome growth between Orinus and Cleistogenes
To gain insights into why dimorphic flowers fail to develop inOrinus , we examined and compared the ABCDE model genes (AMGs) inO. sativa , O. kokonorica and C. songorica . Using 21 AMGs in O. sativa as references, we found that, after the shared allotetraploidy event, many copies were lost in O. kokonorica(31), while C. songorica gained more copies (46) (Figure 4A). Based on transcriptomic data of C. songorica flowers, we found that 36.96% (17) of AMGs showed significant higher expression (two-fold change) in CLs compared with that in CHs (Table S18). Two orthologs of these AMGs were lost in O. kokonorica , and multiple SVs, such as deletions or insertions upstream, intron or even exon regions of genes, were detected in the remaining 15 AMGs between the two species (Figure 4B, C). For examples, two deletions were detected in the exon regions ofOko006142 compared with its ortholog (CsA201468 ) inC. songorica . Another gene Oko019761 gained two MYB-binding domains compared with its ortholog in O. kokonorica . These SVs detected in the orthologous AMG pairs may affect their expression and contribute to the differentiation of floral development in the two genera.
Based on A. thaliana and O. sativa BOP genes, we identified 7, 6, and 3 BOP genes in O. kokonorica ,C. songorica , and O. thomaeum , respectively, and found that each BOP in O. thomaeum had synteny to two in the former two species, except one extra tandem copy in O. kokonorica(Oko044410 and Oko044411 ; Figure 5A, B). All 7 BOPgenes were highly expressed in rhizomes and rhizome tips of O. kokonorica , especially the two copies of BOP1 (Oko010623and Oko007168 ; Figure 5C), which may promote the growth of rhizomes in this species. In addition, we also detected extensive SVs in the BOP orthologous pairs between the two species (Table S19).