Functional and evolutionary analysis of the AP1/SEP/AGL6 superclade of MADS-box genes in the basal eudicot Epimedium sagittatum

Abstract

This study provides a description of EsFUL-like, EsAGL2-1, EsAGL2-2 and EsAGL6-like function divergence and conservation in comparison with a selection of model core eudicots. The study also highlights how organization in genomic segments containing A and E class genes in sequenced model species has resulted in similar topologies of AP1 and SEP-like gene trees.

Phylogenomic Synteny Network Analysis of MADS-Box Transcription Factor Genes Reveals Lineage-Specific Transpositions, Ancient Tandem Duplications, and Deep Positional Conservation

“…For instance, floral organ identity is controlled largely by MADS-box genes, as explained by the ABC(DE) model ( Figure 1A) (Coen and Meyerowitz, 1991;Ditta et al, 2004) with, for example, the floral A-, B-, and E-function genes being required for petal identity (Figures 1A and 1B). Synteny data of the MADS-box genes have been used to infer the ancestral genetic composition of the B-and C-function (Causier et al, 2010), and the A-and E-function genes (Ruelens et al, 2013;Sun et al, 2014). However, these studies analyzed only a small number of species (fewer than 10) and the results were displayed as parallel coordinate plots (as in Figure 1C).…”

“…The relationships between the major clades of the plant MADS-box genes have already largely been inferred in various phylogenetic and evolutionary studies (Becker and Theissen, 2003;Martinez-Castilla and Alvarez-Buylla, 2003;Nam et al, 2003Nam et al, , 2004Nam et al, , 2005Gramzow et al, 2012Gramzow et al, , 2014Smaczniak et al, 2012;Ruelens et al, 2013;Sun et al, 2014;Yu et al, 2016b) (Figure 1B). However, these studies cannot fully resolve some of the deepest nodes of the MADS-box gene tree.…”

Phylogenomic Synteny Network Analysis Reveals an Ancient MADS-Box Transcription Factor Tandem Duplication and Lineage-Specific Transpositions

“…The function and evolution of MADS-box genes have been extensively studied, especially the MIKC C -types (for review see Smaczniak et al, 2012). Synteny data of MADS-box genes has partially been utilized to investigate the ancestral genetic composition of the B- and C-function (Causier et al, 2010) and the A- and E-function genes (Ruelens et al, 2013; Sun et al, 2014). However, these studies included limited set of species (<10) in their synteny comparisons, the results were displayed as linear pair-wise comparisons (as exampled in Figure 1a), and more importantly, complete syntenic data for the entire MADS-box gene family yet not feasible in one study.…”

Synteny-based phylogenomic networks for comparative genomics

“…For instance, floral organ identity is controlled largely by MADS-box genes, as explained by the ABC(DE) model (Figure 1a) (Coen and Meyerowitz, 1991;Ditta et al, 2004) with, for example, the floral A-, B-, and E-function genes being required for petal identity ( Figures 1a and 1b). Synteny data of the MADS-box genes have been used to infer the ancestral genetic composition of the B-and C-function (Causier et al, 2010), and the A-and Efunction genes (Ruelens et al, 2013;Sun et al, 2014). However, these studies analyzed only a small number of species (fewer than 10) and the results were displayed as parallel coordinate plots (as in Figure 1c).…”

“…The relationships between the major clades of the plant MADS-box genes have already largely been inferred in various phylogenetic and evolutionary studies (Becker and Theissen, 2003;Martinez-Castilla and Alvarez-Buylla, 2003;Nam et al, 2003;Nam et al, 2004;Nam et al, 2005;Gramzow et al, 2012;Smaczniak et al, 2012;Ruelens et al, 2013;Gramzow et al, 2014;Sun et al, 2014;Yu et al, 2016b) ( Figure 1b). However, these studies cannot fully resolve some of the deepest nodes of the MADS-box gene tree.…”