Abstract
Anthocyanin is the main pigment forming floral diversity. Several transcription factors that regulate the expression of anthocyanin biosynthetic genes belong to the R2R3-MYB family. Here we examined the transcriptomes of inflorescence buds of Scutellaria species (skullcaps), identified the expression R2R3-MYBs, and detected the genetic signatures of positive selection for adaptive divergence across the rapidly evolving skullcaps. In the inflorescence buds, seven R2R3-MYBs were identified. MYB11 and MYB16 were detected to be positively selected. The signature of positive selection on MYB genes indicated that species diversification could be affected by transcriptional regulation, rather than at the translational level. When comparing among the background lineages of Arabidopsis, tomato, rice, and Amborella, heterogeneous evolutionary rates were detected among MYB paralogs, especially between MYB13 and MYB19. Significantly different evolutionary rates were also evidenced by type-I functional divergence between MYB13 and MYB19, and the accelerated evolutionary rates in MYB19, implied the acquisition of novel functions. Another paralogous pair, MYB2/7 and MYB11, revealed significant radical amino acid changes, indicating divergence in the regulation of different anthocyanin-biosynthetic enzymes. Our findings not only showed that Scutellaria R2R3-MYBs are functionally divergent and positively selected, but also indicated the adaptive relevance of regulatory genes in floral diversification.
Highlights
Plant diversity is usually characterized by morphological variation [1,2]
Seven R2R3-MYBs were identified from the expressed sequence tag (EST) contig library of inflorescence bud transcriptomes of Scutellaria, including MYB2/7, MYB8, MYB11, MYB13, MYB15, MYB16, and MYB19, corresponding with Arabidopsis AtMYB68 (S14), AtMYB90 (S6), AtMYB36 (S14), AtMYB5, AtMYB20, AtMYB65 (S18), and AtMYB5, respectively (Table 3)
The closer groupings of these R2R3-MYBs expressing in inflorescence buds suggest that the paralogous relationships of these genes could be due to recent duplication in genus Scutellaria
Summary
Plant diversity is usually characterized by morphological variation [1,2]. Adaptive divergence is one of the most important mechanisms for the high divergence of morphological traits among phylogenetically closely related species [3]. We further performed type-I and type-II functional divergence analyses for the paralogous pair. MYB13 and MYB19 and another paralogous pair, MYB2/7 and MYB11 Both a Z-score test (p < 0.00001) and LRT (p = 0.00002) for the estimated θI showed significant type-I functional divergence between MYB13 and MYB19, but not for the paralogous pair MYB2/7 and MYB11. The significant type-I divergence between the paralogous pair MYB13 and MYB19, which indicates heterogeneous evolutionary rates after duplication, is consistent with the estimated ω of MYB13 (ω ≪ 1) and MYB19 (ω ≫ 1) by clade model. The type-II functional divergence analysis showed significant divergence between MYB2/7 and MYB11 by Z-score test (p = 0.042) but not for the paralogous pair MYB13 and MYB19 (p = 0.073) (Table 7). If the indels were not considered, two of 55 aligned amino acid sites (3.64%) of the R2 and R3 domains received a ratio score >9 (i.e., posterior probability > 0.9 or false positive rate < 10%) while seven of 55 alignments (12.73%) received a ratio score >2.33 (i.e., posterior probability > 0.7) specifying cluster-specific radical changes between
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