Phylogeny of Agavaceae Based on ndhF, rbcL, and its Sequences

Great advances have been made in our understanding of the phylogeny and classification of Agavaceae in the last 20 years. In older systems Agavaceae were paraphyletic due to overemphasis of ovary position or habit. Discovery of a unique bimodal karyotype in Agave and Yucca eventually led to a reexamination of concepts and relationships in all the lilioid monocots, which continues to the present day. Developments in cytogenetics, microscopy, phylogenetic systematics, and most recently DNA technology have led to remarkable new insights. Large-scale rbcL sequence studies placed Agavaceae with the core Asparagales and identified closely related taxa. Analysis of cpDNA restriction sites, rbcL, and ITS nrDNA sequences all supported removal of Dracaenaceae, Nolinaceae, and clarified relationships. Agavaceae s.s. presently consists of Agave, Beschorneria, Furcraea, Hesperaloe, Hesperoyucca, Manfreda, Polianthes, Prochnyanthes, and Yucca. In this paper we analyze recently obtained ndhF sequence data from Agavaceae and Asparagales and discuss the implications for classification. Parsimony analysis of ndhF data alone resolves most genera of Agavaceae and supports the inclusion of Camassia, Chlorogalum, Hesperocallis, and Hosta within Agavaceae s.l. Analysis of combined ndhF and rbcL data sets of selected Asparagales results in better resolution and stronger bootstrap support for many relationships. Combination of all available ndhF, rbcL, and ITS data in a single analysis results in the best resolution currently available for Agavaceae s.l. Implications for classification schemes past and present are discussed

Effect of transgene introgression site on gene migration from transgenic b. napus to b. rapa [abstract]

Abstract only availableThere is a growing concern of the possible transgenic introgression from GM plants into agricultural weeds, which has stimulated research in the process of crop to weed gene flow. Crop to weed gene flow often involves the hybridization of a polyploidy crop to a diploid weed. An example is canola (Brassica napus with AACC genomes) which can hybridize with B. rapa (AA) to produce fertile triploid F1 hybrids (ACC) in the wild. It is hypothesized that there are "safe sites" on the C genome because the C genome is likely to be lost from wild populations after a few generations of repeated backcrossing with B. rapa. However, there is homoeology between the A and C genomes of Brassica, which allows potential recombination between genomes and the movement of transgenes from the C to A genomes by chromosomal rearrangements. Recent advances in molecular markers and fluorescent in situ hybridization (FISH) now allow us to observe the frequency of homoeologous exchanges following hybridization. Our research is focused on finding safe sites within the B. napus genome which are least likely to be transferred into B. napus and B. rapa hybrids and their progeny. To test this, we have crossed a transgenic B. napus with a natural B. rapa three times to make three different F1events. Then we backcrossed each of the three F1 three times with B. rapa. We are measuring the germination rate of each generation and using transgene specific PCR primers to check the presence or absence of the transgene in hybrids. We will also use molecular cytogenetics (FISH) to count chromosome numbers. This study will help determine the possibilities of a "safe" site in B. napus and offer insight in the mechanisms of crop to weed transgene introgression in B. napus x B. rapa hybrids.MU Monsanto Undergraduate Research Fellowshi

Escape from Preferential Retention Following Repeated Whole Genome Duplications in Plants

The well supported gene dosage hypothesis predicts that genes encoding proteins engaged in dose–sensitive interactions cannot be reduced back to single copies once all interacting partners are simultaneously duplicated in a whole genome duplication. The genomes of extant flowering plants are the result of many sequential rounds of whole genome duplication, yet the fraction of genomes devoted to encoding complex molecular machines does not increase as fast as expected through multiple rounds of whole genome duplications. Using parallel interspecies genomic comparisons in the grasses and crucifers, we demonstrate that genes retained as duplicates following a whole genome duplication have only a 50% chance of being retained as duplicates in a second whole genome duplication. Genes which fractionated to a single copy following a second whole genome duplication tend to be the member of a gene pair with less complex promoters, lower levels of expression, and to be under lower levels of purifying selection. We suggest the copy with lower levels of expression and less purifying selection contributes less to effective gene-product dosage and therefore is under less dosage constraint in future whole genome duplications, providing an explanation for why flowering plant genomes are not overrun with subunits of large dose–sensitive protein complexes

Systematics of Xanthorrhoeaceae Sensu Lato, with an Emphasis on Bulbine

We provide here results of a combined analysis of plastid genes rbcL, matK, and ndhF for Xanthorrhoeaceae s.l., the Asphodelaceae/Xanthorrhoeaceae/Hemerocallidaceae clade, which are well supported by the DNA data. Xanthorrhoea (often treated as the sole member of Xanthorrhoeaceae) is sister to the hemerocallid clade (former Hemerocallidaceae); and the asphodelid clade (formerly Asphodelaceae) is sister to them both. For additional species of Bulbine and Jodrellia (both Asphodeloideae), we also collected rps16 intron and ITS nuclear ribosomal DNA sequences to better assess their relationships. Bulbine, with Jodrellia, embedded are sister to the collective genera of subfamily Alooideae in which all species are characterized by strongly bimodal and nearly identical karyotypes, whereas that of Bulbine is much more variable. Cytological studies have previously shown Bulbine to possess a range of karyotypes from graduated to clearly bimodal (although never exactly like the aloid genera) and point toward a lower level of bimodality in the Australian members, all of which are autotetraploid, than in the African members, all of which are diploid. Therefore, there have been two events of particular interest within Bulbine, a change in ploidy and a long-range dispersal event

Resolution of phylogenetic patterns within the angiosperm order Asparagales [abstract]

Abstract only availableThe angiosperm order Asparagales, is an economically important monocot order that includes onions (Allium), asparagus (Asparagus), and agaves (Agave). The core Asparagales includes ten families that form a monophyletic group (Agapanthaceae, Agavaceae, Alliacae, Amaryllidaceae, Aphyllantaceae, Asparagaceae, Hyacinthaceae, Laxmaniaceae, Ruscaceae, and Themidaceae). Phylogenetic studies based on four chloroplast gene regions leave numerous relationships among these families unresolved or inadequately supported. In addition, questions remain about the origin, patterns of morphological divergence, geographic diversification, and ecological radiation of this group. Our primary goal is to resolve indistinct relationships among Asparagales families by adding data based on DNA sequence variation of an additional chloroplast region. To date, we have screened six chloroplast gene regions across fifteen taxa representing seven core Asparagales families and outgroups, Iridaceae and Xanthorrhoeaceae to identify informative phylogenetic variation. A one kilobase region of the large ribosomal subunit protein (rpL14-rpL 36) shows variation between closely related families and we are now expanding our taxonomic sampling within each family. We will conduct independent phylogenetic analyses of this region and combine our new data with existing data from previous studies and from a low-copy nuclear gene (PHYC). This combined phylogeny will potentially provide the additional data needed to resolve the evolutionary relationships among families and help interpret patterns of morphological diversification among Asparagales lineages.NSF Undergraduate Mentoring in Environmental Biolog

Meeting report:Fungal genomics meets social media: Highlights of the 28th fungal genetics conference at asilomar

International audienc

Chromosomal evolution in Brassicacae: Allopolyploidy, aneuploidy and transgene transmission [abstract]

Abstract only availablePolyploidy is a eukaryotic phenomenon common to plants that serves as an evolutionary mechanism for speciation. Diploid species undergo polyploidization through single genome duplication (autopolyploidy) or by the hybridization of genomes from two or more distinct progenitor species (allopolyploidy). Aneuploidy can arise where offspring possess extra or fewer chromosomes than their progenitors. Over successive generations, changes in chromosomal number and rearrangement can lead to speciation or differentiation of ecotypes within a species. Using advanced molecular cytogenetics and fluorescent in situ hybridization (FISH), we can distinguish chromosomes and genomic markers among different ecotypes and species. In the agricultural industry where genetically modified organisms (GMOs) are used, aneuploidy and homoeologous recombination of transgenic elements presents a potential mechanism of moving transgenes from GMO crops into the genomes of wild diploids. These wild diploids then have the potential to become "superweeds" that can disrupt ecological systems. The goal of this study was to investigate the movement of a transgene from an allopolyploid to a diploid in controlled greenhouse crosses. Transgenic Brassica napus allopolyploid plants (AACC) were backcrossed to natural Brassica rapa (AA) recurrently over three generations. We examined each of the three backcross generations for chromosome number and gene transmission. Molecular cytogenetic analysis was performed on flower buds from each backcross, chromosome numbers were recorded and gene transmission was analyzed by PCR. As expected, we found aneuploidy in Brassica napus x Brassica rapa hybrids suggesting potential for homoeologous recombination of transgenes into non-transgenic diploid species. Surprisingly, despite aneuploidy, we also found a high rate of both germination and transmission of the transgene into wild Brassica rapa, suggesting the need to find safe sites in Brassica napus to insert transgenes

Biodiversity comparison among phylogenetic diversity metrics and between three North American prairies

Protection of Earth’s ecosystems requires identification of geographical areas of greatest biodiversity. Assessment of biodiversity begins with knowledge of the evolutionary histories of species in a geographic area. Multiple phylogenetic diversity (PD) metrics have been developed to describe biodiversity beyond species counts, but sufficient empirical studies, particularly at fine phylogenetic scales, have not been conducted to provide conservation planners with evidence for incorporating PD metrics into selection of priority regions. We review notable studies that are contributing to a growing database of empirical results, we report on the effect of using high-throughput sequencing to estimate the phylogenies used to calculate PD metrics, and we discuss difficulties in selecting appropriate diversity indices. We focused on two of the most speciose angiosperm families in prairies—Asteraceae and Fabaceae—and compared 12 PD metrics and four traditional measures of biodiversity between three North American prairie sites. The varying results from the literature and from the current data reveal the wide range of applications of PD metrics and the necessity for many more empirical studies. The accumulation of results from further investigations will eventually lead to a scientific understanding upon which conservation planners can make informed decisions about where to apply limited preservation funds

Evolutionary relationships in Panicoid grasses based on plastome phylogenomics (Panicoideae; Poaceae)

Background: Panicoideae are the second largest subfamily in Poaceae (grass family), with 212 genera and approximately 3316 species. Previous studies have begun to reveal relationships within the subfamily, but largely lack resolution and/or robust support for certain tribal and subtribal groups. This study aims to resolve these relationships, as well as characterize a putative mitochondrial insert in one linage. Results: 35 newly sequenced Panicoideae plastomes were combined in a phylogenomic study with 37 other species: 15 Panicoideae and 22 from outgroups. A robust Panicoideae topology largely congruent with previous studies was obtained, but with some incongruences with previously reported subtribal relationships. A mitochondrial DNA (mtDNA) to plastid DNA (ptDNA) transfer was discovered in the Paspalum lineage. Conclusions: The phylogenomic analysis returned a topology that largely supports previous studies. Five previously recognized subtribes appear on the topology to be non-monophyletic. Additionally, evidence for mtDNA to ptDNA transfer was identified in both Paspalum fimbriatum and P. dilatatum, and suggests a single rare event that took place in a common progenitor. Finally, the framework from this study can guide larger whole plastome sampling to discern the relationships in Cyperochloeae, Steyermarkochloeae, Gynerieae, and other incertae sedis taxa that are weakly supported or unresolved.Fil: Burke, Sean V.. Northern Illinois University; Estados UnidosFil: Wysocki, William P.. Northern Illinois University; Estados UnidosFil: Zuloaga, Fernando Omar. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Botánica Darwinion. Academia Nacional de Ciencias Exactas, Físicas y Naturales. Instituto de Botánica Darwinion; ArgentinaFil: Craine, Joseph M.. Jonah Ventures; Estados UnidosFil: Pires, J. Chris. University of Missouri; Estados UnidosFil: Edger, Patrick P.. Michigan State University; Estados UnidosFil: Mayfield Jones, Dustin. Donald Danforth Plant Science Center; Estados UnidosFil: Clark, Lynn G.. Iowa State University; Estados UnidosFil: Kelchner, Scot A.. University of Idaho; Estados UnidosFil: Duvall, Melvin R.. Northern Illinois University; Estados Unido

Resolving deep relationships of PACMAD grasses: a phylogenomic approach

Background Plastome sequences for 18 species of the PACMAD grasses (subfamilies Panicoideae, Aristidoideae, Chloridoideae, Micrairoideae, Arundinoideae, Danthonioideae) were analyzed phylogenomically. Next generation sequencing methods were used to provide complete plastome sequences for 12 species. Sanger sequencing was performed to determine the plastome of one species, Hakonechloa macra, to provide a reference for annotation. These analyses were conducted to resolve deep subfamilial relationships within the clade. Divergence estimates were assessed to determine potential factors that led to the rapid radiation of this lineage and its dominance of warmer open habitats. Results New plastomes were completely sequenced and characterized for 13 PACMAD species. An autapomorphic ~1140 bp deletion was found in Hakonechloa macra putatively pseudogenizing rpl14 and eliminating rpl16 from this plastome. Phylogenomic analyses support Panicoideae as the sister group to the ACMAD clade. Complete plastome sequences provide greater support at deep nodes within the PACMAD clade. The initial diversification of PACMAD subfamilies was estimated to occur at 32.4 mya. Conclusions Phylogenomic analyses of complete plastomes provides resolution for deep relationships of PACMAD grasses. The divergence estimate of 32.4 mya at the crown node of the PACMAD clade coincides with the Eocene-Oligocene Transition (EOT). The Eocene was a period of global cooling and drying, which led to forest fragmentation and the expansion of open habitats now dominated by these grasses. Understanding how these grasses are related and determining a cause for their rapid radiation allows for future predictions of grassland distribution in the face of a changing global climate.This work was supported in part by the Plant Molecular Biology Center, the Department of Biological Sciences at Northern Illinois University and the National Science Foundation under Grant Numbers DEB-1120750 to LGC, DEB-1120856 to SAK and DEB-1120761 to MRD.This article is made openly accessible in part by an award from the Northern Illinois University Libraries’ Open Access Publishing Fund