Elizabeth A. Kellogg

Reference Genome Sequence Of The Model Plant Setaria

We generated a high-quality reference genome sequence for foxtail millet (Setaria italica). The ∼400-Mb assembly covers ∼80% of the genome and >95% of the gene space. The assembly was anchored to a 992-locus genetic map and was annotated by comparison with >1.3 million expressed sequence tag reads. We produced more than 580 million RNA-Seq reads to facilitate expression analyses. We also sequenced Setaria viridis, the ancestral wild relative of S. italica, and identified regions of differential single-nucleotide polymorphism density, distribution of transposable elements, small RNA content, chromosomal rearrangement and segregation distortion. The genus Setaria includes natural and cultivated species that demonstrate a wide capacity for adaptation. The genetic basis of this adaptation was investigated by comparing five sequenced grass genomes. We also used the diploid Setaria genome to evaluate the ongoing genome assembly of a related polyploid, switchgrass (Panicum virgatum).

Foxtail Millet: A Sequence-Driven Grass Model System

Foxtail millet ( Setaria italica ) is a small diploid C4 panicoid crop species, whose genome is being sequenced by the Joint Genome Institute (JGI) of the Department of Energy. The rationale for sequencing foxtail millet is that it is closely related to the bioenergy grasses switchgrass ( Panicum

Reconstructing the evolutionary history of paralogous APETALA1/FRUITFULL-like genes in grasses (Poaceae).

Gene duplication is an important mechanism for the generation of evolutionary novelty. Paralogous genes that are not silenced may evolve new functions (neofunctionalization) that will alter the developmental outcome of preexisting genetic pathways, partition ancestral functions (subfunctionalization) into divergent developmental modules, or function redundantly. Functional divergence can occur by changes in the spatio-temporal patterns of gene expression and/or by changes in the activities of their protein products. We reconstructed the evolutionary history of two paralogous monocot MADS-box transcription factors, FUL1 and FUL2, and determined the evolution of sequence and gene expression in grass AP1/FUL-like genes. Monocot AP1/FUL-like genes duplicated at the base of Poaceae and codon substitutions occurred under relaxed selection mostly along the branch leading to FUL2. Following the duplication, FUL1 was apparently lost from early diverging taxa, a pattern consistent with major changes in grass floral morphology. Overlapping gene expression patterns in leaves and spikelets indicate that FUL1 and FUL2 probably share some redundant functions, but that FUL2 may have become temporally restricted under partial subfunctionalization to particular stages of floret development. These data have allowed us to reconstruct the history of AP1/FUL-like genes in Poaceae and to hypothesize a role for this gene duplication in the evolution of the grass spikelet.

barren inflorescence2 Encodes a Co-Ortholog of the PINOID Serine/Threonine Kinase and Is Required for Organogenesis during Inflorescence and Vegetative Development in Maize

Organogenesis in plants is controlled by meristems. Axillary meristems, which give rise to branches and flowers, play a critical role in plant architecture and reproduction. Maize (Zea mays) and rice (Oryza sativa) have additional types of axillary meristems in the inflorescence compared to Arabidopsis (Arabidopsis thaliana) and thus provide an excellent model system to study axillary meristem initiation. Previously, we characterized the barren inflorescence2 (bif2) mutant in maize and showed that bif2 plays a key role in axillary meristem and lateral primordia initiation in the inflorescence. In this article, we cloned bif2 by transposon tagging. Isolation of bif2-like genes from seven other grasses, along with phylogenetic analysis, showed that bif2 is a co-ortholog of PINOID (PID), which regulates auxin transport in Arabidopsis. Expression analysis showed that bif2 is expressed in all axillary meristems and lateral primordia during inflorescence and vegetative development in maize and rice. Further phenotypic analysis of bif2 mutants in maize illustrates additional roles of bif2 during vegetative development. We propose that bif2/PID sequence and expression are conserved between grasses and Arabidopsis, attesting to the important role they play in development. We provide further support that bif2, and by analogy PID, is required for initiation of both axillary meristems and lateral primordia.

Reinstatement and Emendation of Subfamily Micrairoideae (Poaceae)

Abstract Phylogenetic relationships among subfamilies of the well supported PACCAD clade of Poaceae remain uncertain. Several genera such as Micraira and Eriachne were considered incertae sedis in the most recent subfamilial classification of the grasses, but these two genera formed a well-supported clade in an analysis based on chloroplast and structural data. Another genus, Isachne, traditionally classified in the Panicoideae, also formed part of this well-supported clade. Despite strong molecular support for the clade, thus far no morphological synapomorphy has been found. Nevertheless, the strongly supported monophyly of this clade allowed us to suggest the recognition of a new subfamily within the PACCAD clade. Since there was already a name available, in this paper we propose the reinstatement and emendation of the circumscription of Micrairoideae. The reinstatement of Micrairoideae changes the acronym PACCAD to PACCMAD for this large clade of grasses.

Integrating Phylogeny into Studies of C4 Variation in the Grasses

C4 photosynthesis consists of morphological and biochemical novelties that create a CO2 pump that concentrates CO2 around Rubisco ([Kanai and Edwards, 1999][1]), which decreases photorespiration and the resulting energy waste. Consequently, C4 photosynthesis provides a competitive advantage in all

Evolution of reproductive structures in grasses (Poaceae) inferred by sister-group comparison with their putative closest living relatives, Ecdeiocoleaceae.

Despite much recent activity in the phylogeny and developmental genetics of grasses, the enigmatic homologies of their reproductive structures remain largely unresolved, partly because their highly derived morphology has resulted in a unique associated terminology. Outstanding questions include whether grass lodicules and stamens are derived from a single perianth or stamen whorl, respectively, whether the grass caryopsis is homologous with a nut, and how the scutellum evolved. We investigated the reproductive structures of the putative sister group of grasses, the southwestern Australian family Ecdeiocoleaceae, which includes two genera, Ecdeiocolea and Georgeantha. The zygomorphic arrangement of the four (rather than six) stamens in male flowers of Ecdeiocolea indicates that they may represent three outer stamens plus the adaxial inner stamen. Within Ecdeiocoleaceae, characters such as the highly unusual nucellus structure of Ecdeiocolea are autapomorphic. Sister-group comparisons indicate that some characteristic grass features, notably the scutellum, do not occur in their putative closest relatives and that more data are needed on early-diverging grass genera to resolve these issues. The grass caryopsis could represent one end of a transformation series embodied by the reduced gynoecial structure and indehiscent fruit of other Poales such as Flagellaria, Joinvillea, and Ecdeiocolea.

Molecular phylogeny of the moonseed family (Menispermaceae): implications for morphological diversification

We used the chloroplast gene ndhF to reconstruct the phylogeny of the moonseed family (Menispermaceae), a morphologically diverse and poorly known cosmopolitan family of dioecious, primarily climbing plants. This study includes a worldwide sample of DNA sequences for 88 species representing 49 of the 70 genera of all eight traditionally recognized tribes. Phylogenetic relationships were estimated, and the Shimodaira-Hasegawa test was used to compare the likelihood of alternative phylogenetic hypotheses and to evaluate the monophyly of tribes currently in use. The monospecific Indo-Malesian Tinomiscium is sister to the remaining members of the family, within which are two major clades. Within these two clades, well-supported clades correspond to four of the eight traditionally recognized tribes, while others, such as Menispermeae, are polyphyletic. Mapping of major morphological characters on the phylogeny indicates that the crescent-shaped seed is derived from a straight seed, the tree habit has arisen multiple times, endosperm has been lost many times, but unicarpellate flowers evolved only once. Morphological synapomorphies for Menispermaceae include the presence of a condyle, a large embryo, and druplets. The phylogeny provides for the first time a detailed molecular-based assessment of relationships in Menispermaceae and clarifies our understanding of morphological diversification within the family.

What happens to genes in duplicated genomes

Introductory textbooks tell us that humans (and other metazoa and all our agricultural plants) are diploid. They have two copies of each gene, one from each parent. Comparative genomic studies, however, suggest that we, along with yeast (Saccharomyces cerevisiae) (1), maize (2, 3), and Arabidopsis (4), may actually be ancient polyploids (5, 6) in which the chromosome complement doubled at some time in the past and then, through gene silencing, mutation, and loss, reverted to a diploid-like state.

A global database of C4 photosynthesis in grasses

C3, C4 or Crassulacean acid metabolism (CAM) photosynthetic pathways represent a fundamental axis of trait variation in plants, with importance at scales from genome to biome. Knowing the distribution of these pathways among wild species is a crucial first step in understanding the patterns and processes of photosynthetic evolution and its role in ecological processes at large scales (e.g. changes in the composition of biomes under global change). C4 photosynthesis is most prevalent in the Poaceae (grasses), which account for about half of allC4 species (Sage et al., 1999a).Research on the evolution and ecology of these plants has undergone a renaissance during the last 7 yr, catalyzed by phylogenetic analyses showing multiple parallel C4 origins (e.g. Christin et al., 2007; Vicentini et al., 2008; GPWG II, 2012), insights into the distribution of C4 species and assembly of the C4 grassland biome (Edwards & Still, 2008; Edwards & Smith, 2010; Edwards et al., 2010), and efforts to introduce the C4 pathway into rice (Hibberd et al., 2008; von Caemmerer et al., 2012). C4 photosynthesis is an excellent model for investigating complex trait evolution, because of the broad knowledge base describing its biochemical basis, evolutionary history, and ecological interactions (Christin et al., 2010).