Prevalent Exon-Intron Structural Changes in the APETALA1/FRUITFULL, SEPALLATA, AGAMOUS-LIKE6, and FLOWERING LOCUS C MADS-Box Gene Subfamilies Provide New Insights into Their Evolution

Abstract

AP1/FUL, SEP, AGL6, and FLC subfamily genes play important roles in flower development. The phylogenetic relationships among them, however, have been controversial, which impedes our understanding of the origin and functional divergence of these genes. One possible reason for the controversy may be the problems caused by changes in the exon-intron structure of genes, which, according to recent studies, may generate non-homologous sites and hamper the homology-based sequence alignment. In this study, we first performed exon-by-exon alignments of these and three outgroup subfamilies (SOC1, AG, and STK). Phylogenetic trees reconstructed based on these matrices show improved resolution and better congruence with species phylogeny. In the context of these phylogenies, we traced evolutionary changes of exon-intron structures in each subfamily. We found that structural changes have occurred frequently following gene duplication and speciation events. Notably, exons 7 and 8 (if present) suffered more structural changes than others. With the knowledge of exon-intron structural changes, we generated more reasonable alignments containing all the focal subfamilies. The resulting trees showed that the SEP subfamily is sister to the monophyletic group formed by AP1/FUL and FLC subfamily genes and that the AGL6 subfamily forms a sister group to the three abovementioned subfamilies. Based on this topology, we inferred the evolutionary history of exon-intron structural changes among different subfamilies. Particularly, we found that the eighth exon originated before the divergence of AP1/FUL, FLC, SEP, and AGL6 subfamilies and degenerated in the ancestral FLC-like gene. These results provide new insights into the origin and evolution of the AP1/FUL, FLC, SEP, and AGL6 subfamilies.

Keywords: AGAMOUS-LIKE6; APETALA1/FRUITFULL; FLOWERING LOCUS C; SEPALLATA; exon-intron structural change.

Figure 1

Evolution of exon-intron structure in the AP1/FUL subfamily. (A–C) Representative structural change events occurred in the euFUL lineage of Solanaceae (A), the OsMADS15 lineage of Poaceae (B), and AP1/FUL-like genes of Liliales (C). (D) Exon-intron structural changes at several key nodes on the AP1/FUL phylogenetic tree. “Anc” (for Ancestor) is prefixed to the name of each gene lineage. Details are shown in Figure S1. Exons and introns are represented by boxes and curved lines, respectively. The length of each exon is shown above the box. Shared structural change events are linked by gray lines. Different mechanisms responsible for structural changes are marked on corresponding branches of the phylogenetic tree. Stars indicate structural changes involving non-triplet sequences.

Figure 2

Evolution of exon-intron structure in the SEP1 subfamily. (A–C) Representative structural change events occurred in SEP1/2 (A) and SEP4 (B) lineages of Brassicaceae, and the OsMADS34 lineage of Poaceae (C). (D) Exon-intron structural changes at several key nodes on the SEP1 phylogenetic tree. Details are shown in Figure S2. The symbols describing structural changes are the same as those in Figure 1.

Figure 3

Evolution of exon-intron structure in the SEP3 subfamily. (A–C) Representative structural change events occurred in SEP3-like genes of Fabaceae (A), Brassicaceae (B), and Poaceae (C). (D) Exon-intron structural changes at several key nodes on the SEP3 phylogenetic tree. Details are shown in Figure S3. The symbols describing structural changes are the same as those in Figure 1.

Figure 4

Evolution of exon-intron structure in the AGL6 subfamily. (A–C) Representative structural change events occurred in AGL6-like genes of Brassicaceae (A), Ranunculaceae (B), and Poaceae (C). (D) Exon-intron structural changes at several key nodes on the AGL6 phylogenetic tree. Details are shown in Figure S4. The symbols describing structural changes are the same as those in Figure 1.

Figure 5

A phylogenetic tree showing relationships of the AP1/FUL, FLC, SEP, and AGL6 subfamilies. The bootstrap values (>50%) obtained from maximum likelihood analysis and the posterior probabilities (>0.5) estimated by Bayesian inference are shown next to the nodes.

Figure 6

Evolution of exon-intron structures of the AP1/FUL, FLC, SEP, and AGL6 subfamilies. The simplified tree is from Figure 5 and Figure S8. Show here is the ancestral exon-intron structure of each subfamily in the MRCA of extant angiosperms and in the MRCA of extant gymnosperms (if applicable). The MADS domain, I region, K domain, and C-terminal region are indicated below exons, and the MADS and K domains are highlighted with gray boxes. “ang” is the abbreviation for “angiosperms,” and “gym” for “gymnosperms.” The symbols describing structural changes are the same as those in Figure 1.