Large-scale analyses of angiosperm Flowering Locus T genes reveal duplication and functional divergence in monocots

Abstract

FLOWERING LOCUS T (FT) are well-known key genes for initiating flowering in plants. Delineating the evolutionary history and functional diversity of FT genes is important for understanding the diversification of flowering time and how plants adapt to the changing surroundings. We performed a comprehensive phylogenetic analysis of FT genes in 47 sequenced flowering plants and the 1,000 Plant Transcriptomes (1KP) database with a focus on monocots, especially cereals. We revealed the evolutionary history of FT genes. The FT genes in monocots can be divided into three clades (I, II, and III), whereas only one monophyletic group was detected in early angiosperms, magnoliids, and eudicots. Multiple rounds of whole-genome duplications (WGD) events followed by gene retention contributed to the expansion and variation of FT genes in monocots. Amino acid sites in the clade II and III genes were preferentially under high positive selection, and some sites located in vital domain regions are known to change functions when mutated. Clade II and clade III genes exhibited high variability in important regions and functional divergence compared with clade I genes; thus, clade I is more conserved than clade II and III. Genes in clade I displayed higher expression levels in studied organs and tissues than the clade II and III genes. The co-expression modules showed that some of the FT genes might have experienced neofunctionalization and subfunctionalization, such as the acquisition of environmental resistance. Overall, FT genes in monocots might form three clades by the ancient gene duplication, and each clade was subsequently subjected to different selection pressures and amino acid substitutions, which eventually led to different expression patterns and functional diversification. Our study provides a global picture of FT genes' evolution in monocots, paving a road for investigating FT genes' function in future.

Keywords: Flowering locus T (FT); functional divergence; gene duplication; monocots; positive selection.

Figure 1

The phylogenetic tree of all FT genes in angiosperms. The phylogenetic tree was constructed using the ML method. The FT genes are from the 47-species-genome database (2 early angiosperms, 17 monocots, and 28 eudicots) and the 1KP database including early angiosperm, magnoliids, Caryophyllales, ranunculids, Santalales, Saxifragales, asterids, and core rosids.

Figure 2

The phylogenetic relationship of the FT genes in monocots. The phylogenetic tree was constructed using the Bayes methods. The P. abies FT-like gene (JN039333) was set as the outgroup. The FT members from monocots are classified into three clades based on the tree; clade I is marked in green, II in blue, and III in pink. The stars mark the WGD event that occurred in monocots: green star, τ WGD; red star, ρ WGD; and purple star, σ WGD. Pa, P. abies; Zma, Zostera marina; Zmu, Zostera muelleri; Sp, Spirodela polyrhiza; Pd, Phoenix dactylifera; Ma, Musa acuminata; Pe, Phalaenopsis equestris; Aco, Ananas comosus; Bd, Brachypodium distachyon; Sb, Sorghum bicolor; Os, Oryza sativa; ZCN, Zea mays..

Figure 3

Pruned trees consisting of clade I and II (or III) and branch and branch site model tests. (A) Branch and branch site test using clade I as background and clade II as foreground. (B) Branch and branch site test using clade I as background and clade III as foreground. Green star, τ WGD; red star, ρ WGD; and purple star, σ WGD. ω denotes dN/dS values; sites indicate positive selection sites, P means p-value (probability). Digits in the branches are bootstrap values.

Figure 4

Sequence conservation and variation among three FT clades in monocots. (A). Multiple-sequence alignment of the FT gene family. (B) Homology modeling of the FT gene family shows the conservation degrees (displayed in different colors) of different regions. (C) Conservation differences among three monocot FT gene clades using ribbon diagrams. Positive selection sites (BEB value >0.9) also marked in three clades. All the figures were generated using the PyMol script with the output of ConSurf as input. Blue marks represent positive selection sites with clade I Red marks represent positive selection sites in clade I-1, magenta marks represent positive selection sites in clade I-2, and coffee marks represent positive selection sites in clade II-1a.

Figure 5

Characterization of sequences in three FT clades. (A) Exon and intron structures among three FT clades. (B) Logos representing motifs conserved within three clades. (C) Frequency of candidate amino acid residues responsible for function divergence between clade I vs. II. (D) Frequency of candidate amino acid residues responsible for function divergence between I vs. III. Red arrows represent positive selection sites in clade II, and green arrows represent positive selection sites in clade III.

Figure 6

The expression patterns of the three clades’ FT gene in two monocot species including (A) Oryza sativa and (B) Zea mays.

Figure 7

Expression patterns of FT and their co-expression genes in Oryza sativa and Zea mays. (A) Expression patterns of OsFTL1 and its co-expression genes in anther, leaf, panicle, root, seed, and shoot; different MADS-box classes labeled in different color lines. (B) Expression patterns of osFTL11 and its co-expression genes in anther, leaf, panicle, root, seed and shoot; different MADS-box class labeled in different color line. (C) Expression patterns of ZCN14 and its co-expression genes in kernel, leaf, shoot, stem, and tassel; different MADS-box classes labeled in different color lines.