The MADS-box floral homeotic gene lineages predate the origin of seed plants: Phylogenetic and molecular clock estimates

Purugganan, Michael D.

doi:10.1007/pl00006244

Cited by 96 publications

(75 citation statements)

References 17 publications

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“…This hypothesis is also consistent with the molecular clock hypothesis that the diversification of AGL2/AGL6/SQUA (or AP1/AGL9) clade occurred 373 MYA [35]. However, only AGL6 subfamily genes have been found in both gymnosperms and angiosperms, while close AGL6 homologs of SEP and SQUA clades have so far been only found in extant angiosperms (Supplementary information, Figure S4) [30,36].…”

Section: Agl6-like Genes Are Closely Related To Sep-and Ap1-like Genessupporting

confidence: 86%

The AGL6-like gene OsMADS6 regulates floral organ and meristem identities in rice

et al. 2009

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Although AGAMOUS-LIKE6 (AGL6) MADS-box genes are ancient with wide distributions in gymnosperms and angiosperms, their functions remain poorly understood. Here, we show the biological role of the AGL6-like gene, OsMADS6, in specifying floral organ and meristem identities in rice (Oryza sativa L.). OsMADS6 was strongly expressed in the floral meristem at early stages. Subsequently, OsMADS6 transcripts were mainly detectable in paleas, lodicules, carpels and the integument of ovule, as well as in the receptacle. Compared to wild type plants, osmads6 mutants displayed altered palea identity, extra glume-like or mosaic organs, abnormal carpel development and loss of floral meristem determinacy. Strikingly, mutation of a SEPALLATA (SEP)-like gene, OsMADS1 (LHS1), enhanced the defect of osmads6 flowers, and no inner floral organs or glume-like structures were observed in whorls 2 and 3 of osmads1-z osmads6-1 flowers. Furthermore, the osmads1-z osmads6-1 double mutants developed severely indeterminate floral meristems. Our finding, therefore, suggests that the ancient OsMADS6 gene is able to specify "floral state" by determining floral organ and meristem identities in monocot crop rice together with OsMADS1.

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Section: Agl6-like Genes Are Closely Related To Sep-and Ap1-like Genessupporting

confidence: 86%

The AGL6-like gene OsMADS6 regulates floral organ and meristem identities in rice

et al. 2009

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“…Hence, phylogenetic analyses of MADS-box genes are useful guides for studying their roles in plant evolution. Plant MADS-box gene phylogeny resolution, especially at its basal nodes, has been hindered by incomplete data and by limitations of inference methods (14,15). Here we show resolved gene phylogenies of the Arabidopsis MADS-box genes.…”

mentioning

confidence: 79%

Adaptive evolution in the Arabidopsis MADS-box gene family inferred from its complete resolved phylogeny

Martínez-Castilla

Álvarez-Buylla²

2003

Proc. Natl. Acad. Sci. U.S.A.

131

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Gene duplication is a substrate of evolution. However, the relative importance of positive selection versus relaxation of constraints in the functional divergence of gene copies is still under debate. Plant MADS-box genes encode transcriptional regulators key in various aspects of development and have undergone extensive duplications to form a large family. We recovered 104 MADS sequences from the Arabidopsis genome. Bayesian phylogenetic trees recover type II lineage as a monophyletic group and resolve a branching sequence of monophyletic groups within this lineage. The type I lineage is comprised of several divergent groups. However, contrasting gene structure and patterns of chromosomal distribution between type I and II sequences suggest that they had different evolutionary histories and support the placement of the root of the gene family between these two groups. Site-specific and sitebranch analyses of positive Darwinian selection (PDS) suggest that different selection regimes could have affected the evolution of these lineages. We found evidence for PDS along the branch leading to flowering time genes that have a direct impact on plant fitness. Sites with high probabilities of having been under PDS were found in the MADS and K domains, suggesting that these played important roles in the acquisition of novel functions during MADS-box diversification. Detected sites are targets for further experimental analyses. We argue that adaptive changes in MADSdomain protein sequences have been important for their functional divergence, suggesting that changes within coding regions of transcriptional regulators have influenced phenotypic evolution of plants.ene duplication provides a substrate for evolution, and understanding the fate of duplicates is fundamental to clarifying mechanisms of genetic redundancy and the link between gene family diversification and phenotypic evolution (1). Several empirical studies have evaluated the roles of duplication in adaptation and diversification (2), but the evolutionary forces at play during functional divergence of duplicates are still under debate (3, 4). Genomic studies are revealing that eukaryotes harbor large families of genes that have arisen during evolution through duplication and have persisted for longer periods of time than expected by classical models (5). Models that incorporate positive selection (6, 7) provide alternative explanations for the persistence of duplicates.Empirical studies to test models on the fate of duplicates and the evolutionary forces driving their functional divergence will need complete and resolved gene family phylogenies. Several studies suggest that positive Darwinian selection (PDS) might have been important in protein evolution. However, most previous studies have involved few members of a gene family from various species (8,9). In this article, we annotate, align, and analyze the complete MADS-box gene family of the plant model system Arabidopsis thaliana and provide resolved phylogenies as a basis to infer the role of PDS in protein ...

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“…The two loci are members of the MADS-box family of plant transcriptional activators, many of which are known to regulate floral and inflorescence development in angiosperms (25). Phylogenetic analysis indicates that the ASAP3͞TM6 gene is a member of the AP3 floral homeotic gene group, and appears to be an orthologue of the Lycopersicon TM6 locus (26,27). The ASAP1 gene is an orthologue of the Arabidopsis AP1 locus.…”

Section: Regulatory and Structural Genes In The Hawaiian And North Ammentioning

confidence: 99%

Accelerated regulatory gene evolution in an adaptive radiation

Barrier

Robichaux

Purugganan

2001

Proc. Natl. Acad. Sci. U.S.A.

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181

110

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The disparity between rates of morphological and molecular evolution remains a key paradox in evolutionary genetics. A proposed resolution to this paradox has been the conjecture that morphological evolution proceeds via diversification in regulatory loci, and that phenotypic evolution may correlate better with regulatory gene divergence. This conjecture can be tested by examining rates of regulatory gene evolution in species that display rapid morphological diversification within adaptive radiations. We have isolated homologues to the Arabidopsis APETALA3 (ASAP3͞TM6) and APETALA1 (ASAP1) floral regulatory genes and the CHLOROPHYLL A͞B BINDING PROTEIN9 (ASCAB9) photosynthetic structural gene from species in the Hawaiian silversword alliance, a premier example of plant adaptive radiation. We have compared rates of regulatory and structural gene evolution in the Hawaiian species to those in related species of North American tarweeds. Molecular evolutionary analyses indicate significant increases in nonsynonymous relative to synonymous nucleotide substitution rates in the ASAP3͞TM6 and ASAP1 regulatory genes in the rapidly evolving Hawaiian species. By contrast, no general increase is evident in neutral mutation rates for these loci in the Hawaiian species. An increase in nonsynonymous relative to synonymous nucleotide substitution rate is also evident in the ASCAB9 structural gene in the Hawaiian species, but not to the extent displayed in the regulatory loci. The significantly accelerated rates of regulatory gene evolution in the Hawaiian species may reflect the influence of allopolyploidy or of selection and adaptive divergence. The analyses suggest that accelerated rates of regulatory gene evolution may accompany rapid morphological diversification in adaptive radiations.floral regulatory loci ͉ MADS-box ͉ CAB9 ͉ Hawaiian silversword alliance R ates of morphological evolution are generally not correlated with rates of molecular evolution. This paradoxical observation was highlighted early by Wilson and coworkers (1-3), and subsequent molecular studies in species groups that have undergone recent adaptive radiations, such as African rift lake cichlids (4), columbines (5), and the Hawaiian silversword alliance (6), have documented marked incongruities in rates of morphological and molecular evolution. A proposed resolution to this paradox has been the conjecture that evolutionary changes in regulatory genes, rather than large-scale diversification in structural genes, may be responsible for interspecific variation in organismal morphologies (1)(2)(3)(7)(8)(9). This conjecture is reinforced by molecular developmental studies that indicate that dramatic shifts in organismal structure may arise from mutations at key regulatory loci (7-9). One test of this conjecture is to examine whether there is a significant acceleration in rates of regulatory gene evolution in species that display rapid morphological diversification within adaptive radiations.The Hawaiian silversword alliance (Asteraceae: Heliantheae-Madiinae) is...

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The MADS-box floral homeotic gene lineages predate the origin of seed plants: Phylogenetic and molecular clock estimates

Cited by 96 publications

References 17 publications

The AGL6-like gene OsMADS6 regulates floral organ and meristem identities in rice

The AGL6-like gene OsMADS6 regulates floral organ and meristem identities in rice

Adaptive evolution in the Arabidopsis MADS-box gene family inferred from its complete resolved phylogeny

Accelerated regulatory gene evolution in an adaptive radiation

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