Duplication and diversification of the LEAFY HULL STERILE1 and Oryza sativa MADS5 SEPALLATA lineages in graminoid Poales

<p>Abstract</p> <p>Background</p> <p>Gene duplication and the subsequent divergence in function of the resulting paralogs via subfunctionalization and/or neofunctionalization is hypothesized to have played a major role in the evolution of plant form. The <it>LEAFY HULL STERILE1 (LHS1) SEPALLATA </it>(<it>SEP</it>) genes have been linked with the origin and diversification of the grass spikelet, but it is uncertain 1) when the duplication event that produced the <it>LHS1 </it>clade and its paralogous lineage <it>Oryza sativa MADS5 (OSM5) </it>occurred, and 2) how changes in gene structure and/or expression might have contributed to subfunctionalization and/or neofunctionalization in the two lineages.</p> <p>Methods</p> <p>Phylogenetic relationships among 84 <it>SEP </it>genes were estimated using Bayesian methods. RNA expression patterns were inferred using <it>in situ </it>hybridization. The patterns of protein sequence and RNA expression evolution were reconstructed using maximum parsimony (MP) and maximum likelihood (ML) methods, respectively.</p> <p>Results</p> <p>Phylogenetic analyses mapped the <it>LHS1/OSM5 </it>duplication event to the base of the grass family. MP character reconstructions estimated a change from cytosine to thymine in the first codon position of the first amino acid after the <it>Zea mays MADS3 </it>(<it>ZMM3</it>) domain converted a glutamine to a stop codon in the <it>OSM5 </it>ancestor following the <it>LHS1/OSM5 </it>duplication event. RNA expression analyses of <it>OSM5 </it>co-orthologs in <it>Avena sativa, Chasmanthium latifolium, Hordeum vulgare, Pennisetum glaucum</it>, and <it>Sorghum bicolor </it>followed by ML reconstructions of these data and previously published analyses estimated a complex pattern of gain and loss of <it>LHS1 </it>and <it>OSM5 </it>expression in different floral organs and different flowers within the spikelet or inflorescence.</p> <p>Conclusions</p> <p>Previous authors have reported that rice OSM5 and LHS1 proteins have different interaction partners indicating that the truncation of OSM5 following the <it>LHS1/OSM5 </it>duplication event has resulted in both partitioned and potentially novel gene functions. The complex pattern of <it>OSM5 </it>and <it>LHS1 </it>expression evolution is not consistent with a simple subfunctionalization model following the gene duplication event, but there is evidence of recent partitioning of <it>OSM5 </it>and <it>LHS1 </it>expression within different floral organs of <it>A. sativa, C. latifolium, P. glaucum </it>and <it>S. bicolor</it>, and between the upper and lower florets of the two-flowered maize spikelet.</p

Early inflorescence development in the grasses (Poaceae)

The shoot apical meristem of grasses produces the primary branches of the inflorescence, controlling inflorescence architecture and hence seed production. Whereas leaves are produced in a distichous pattern, with the primordia separated from each other by an angle of 180°, inflorescence branches are produced in a spiral in most species. The morphology and developmental genetics of the shift in phyllotaxis have been studied extensively in maize and rice. However, in wheat, Brachypodium, and oats, all in the grass subfamily Pooideae, the change in phyllotaxis does not occur; primary inflorescence branches are produced distichously. It is unknown whether the distichous inflorescence originated at the base of Pooideae, or whether it appeared several times independently. In this study, we show that Brachyelytrum, the genus sister to all other Pooideae has spiral phyllotaxis in the inflorescence, but that in the remaining 3000+ species of Pooideae, the phyllotaxis is two-ranked. These two-ranked inflorescences are not perfectly symmetrical, and have a clear “front” and “back;” this developmental axis has never been described in the literature and it is unclear what establishes its polarity. Strictly distichous inflorescences appear somewhat later in the evolution of the subfamily. Two-ranked inflorescences also appear in a few grass outgroups and sporadically elsewhere in the family, but unlike in Pooideae do not generally correlate with a major radiation of species. After production of branches, the inflorescence meristem may be converted to a spikelet meristem or may simply abort; this developmental decision appears to be independent of the branching pattern

Data from: Allopolyploidy, diversification, and the Miocene grassland expansion

The role of polyploidy, particularly allopolyploidy, in plant diversification is a subject of debate. Whole-genome duplications precede the origins of many major clades (e.g., angiosperms, Brassicaceae, Poaceae), suggesting that polyploidy drives diversification. However, theoretical arguments and empirical studies suggest that polyploid lineages may actually have lower speciation rates and higher extinction rates than diploid lineages. We focus here on the grass tribe Andropogoneae, an economically and ecologically important group of C4 species with a high frequency of polyploids. A phylogeny was constructed for ca. 10% of the species of the clade, based on sequences of four concatenated low-copy nuclear loci. Genetic allopolyploidy was documented using the characteristic pattern of double-labeled gene trees. At least 32% of the species sampled are the result of genetic allopolyploidy and result from 28 distinct tetraploidy events plus an additional six hexaploidy events. This number is a minimum, and the actual frequency could be considerably higher. The parental genomes of most Andropogoneae polyploids diverged in the Late Miocene coincident with the expansion of the major C4 grasslands that dominate the earth today. The well-documented whole-genome duplication in Zea mays ssp. mays occurred after the divergence of Zea and Sorghum. We find no evidence that polyploidization is followed by an increase in net diversification rate; nonetheless, allopolyploidy itself is a major mode of speciation

Alignments of Orthologous and Paralogous Isolates for Allopolyploidy Identification in Andropogoneae

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