Floral gene resources from basal angiosperms for comparative genomics research

BACKGROUND: The Floral Genome Project was initiated to bridge the genomic gap between the most broadly studied plant model systems. Arabidopsis and rice, although now completely sequenced and under intensive comparative genomic investigation, are separated by at least 125 million years of evolutionary time, and cannot in isolation provide a comprehensive perspective on structural and functional aspects of flowering plant genome dynamics. Here we discuss new genomic resources available to the scientific community, comprising cDNA libraries and Expressed Sequence Tag (EST) sequences for a suite of phylogenetically basal angiosperms specifically selected to bridge the evolutionary gaps between model plants and provide insights into gene content and genome structure in the earliest flowering plants. RESULTS: Random sequencing of cDNAs from representatives of phylogenetically important eudicot, non-grass monocot, and gymnosperm lineages has so far (as of 12/1/04) generated 70,514 ESTs and 48,170 assembled unigenes. Efficient sorting of EST sequences into putative gene families based on whole Arabidopsis/rice proteome comparison has permitted ready identification of cDNA clones for finished sequencing. Preliminarily, (i) proportions of functional categories among sequenced floral genes seem representative of the entire Arabidopsis transcriptome, (ii) many known floral gene homologues have been captured, and (iii) phylogenetic analyses of ESTs are providing new insights into the process of gene family evolution in relation to the origin and diversification of the angiosperms. CONCLUSION: Initial comparisons illustrate the utility of the EST data sets toward discovery of the basic floral transcriptome. These first findings also afford the opportunity to address a number of conspicuous evolutionary genomic questions, including reproductive organ transcriptome overlap between angiosperms and gymnosperms, genome-wide duplication history, lineage-specific gene duplication and functional divergence, and analyses of adaptive molecular evolution. Since not all genes in the floral transcriptome will be associated with flowering, these EST resources will also be of interest to plant scientists working on other functions, such as photosynthesis, signal transduction, and metabolic pathways

Preliminary Genomic Characterization of Ten Hardwood Tree Species from Multiplexed Low Coverage Whole Genome Sequencing

Forest health issues are on the rise in the United States, resulting from introduction of alien pests and diseases, coupled with abiotic stresses related to climate change. Increasingly, forest scientists are finding genetic/genomic resources valuable in addressing forest health issues. For a set of ten ecologically and economically important native hardwood tree species representing a broad phylogenetic spectrum, we used low coverage whole genome sequencing from multiplex Illumina paired ends to economically profile their genomic content. For six species, the genome content was further analyzed by flow cytometry in order to determine the nuclear genome size. Sequencing yielded a depth of 0.8X to 7.5X, from which in silico analysis yielded preliminary estimates of gene and repetitive sequence content in the genome for each species. Thousands of genomic SSRs were identified, with a clear predisposition toward dinucleotide repeats and AT-rich repeat motifs. Flanking primers were designed for SSR loci for all ten species, ranging from 891 loci in sugar maple to 18,167 in redbay. In summary, we have demonstrated that useful preliminary genome information including repeat content, gene content and useful SSR markers can be obtained at low cost and time input from a single lane of Illumina multiplex sequence.All raw sequence data are available through NCBI SRA under project number SRP021923. Sequences containing SSRs and designed primers are attached as supplementary material

Pollen gene flow and molecular identification of full-sib families in small and isolated population fragments of Gleditsia triacanthos L

© 2016, Canadian Science Publishing. All rights reserved. To analyze the utility of isolated remnant populations for full-sibling (full-sib) identification among openpollinated single-tree progeny in the outcrossing and insect-pollinated tree Gleditsia triacanthos L. (honey locust), we performed paternity analyses in forest fragments from two geographic regions using nuclear microsatellites. The first plot (Butternut Valley population) comprised only 7 trees, and 552 seedlings from a single seed parent were characterized at nuclear microsatellites. A large number of putative pollen donors (59) were identified in kinship analyses, but their individual contributions to the progeny were highly variable. Kinship and paternity analyses identified 149 putative full-sibs for genetic mapping sired by an external (unsampled) pollen parent. To better assess the frequency of long-distance pollen dispersal, a total of 180 seeds were collected from 6 seed parents in another fragmented population. In both plots, contemporary pollen dispersal occurred generally from outside the plots (99.38% and 87.50%–100% at the Butternut Valley and Ames Plantation sites, respectively) and thus over very long distances (\u3e 12 000min the Ames Plantation) suggesting that in highly fragmented landscapes, insect pollinators of honey locust are likely very effective long-distance dispersers

Ambiente de trabajo cooperativo en internet para la educación en valores

TesisEl presente trabajo de investigación que lleva por título "AMBIENTE DE TRABAJO COOPERATIVO EN INTERNET PARA LA EDUCACION EN VALORES" responde a la necesidad de desarrollar nuevas formas de planificar y desarrollar la educación, de manera que se promueva la participación sincrónica y asincrónica entre tos sujetos que no se encuentran físicamente en el mismo lugar, ni en las mismas coordenadas temporales. El objetivo fue desarrollar un Ambiente de Trabajo Cooperativo en Internet para la educación en valores utilizando la Metodología Orientada a objetos y la Filosofía de Software Libre propiciando básicamente la reunión síncrona y. asíncrona para los miembros de la Federación de Familias para la Paz Mundial. Se ha utilizado Moodle, el cual es un . proyecto en desarrollo diseñado para dar soporte a un marco de educación social . constructivista. Esta herramienta se ha integrado al Ambiente de Trabajo Cooperativo principalmente para diseñar diferentes cursos en diferentes niveles y a diferentes usuarios. Tambíén se ha empleado los indicadores de calidad del Estándar IS0-9126, tales como funcionalidad, fiabilidad, usabilidad, eficiencia, mantenibilidad y portabilidad en una escala de 1 a 5 puntos. Se llega a la conclusión de que los ambientes de trabajo cooperativos para la educación en valores, permite mejorar el proceso de educación básicamente en la comunicación de los miembros de la Federación de Familias para la Paz Mundial cumpliendo con aprobar el estándar de calidad de software ISO 9126 en el que se observa que un 60% de los profesionales de cada país dicen que el Ambiente de Trabajo Cooperativo es bueno y un 10% afirma que es muy bueno. Palabras Claves: Ambiente de trabajo cooperativo, valores, internet, educació

Construction of a Framework Genetic Linkage Map in Gleditsia triacanthos L

© 2016, Springer Science+Business Media New York. Genomic resources are sparse in most ecologically and economically important North American hardwood species. As part of the Hardwood Genomics project (http://www.hardwoodgenomics.org/), we evaluated the utility of restriction site associated DNA sequencing (RAD-Seq) for framework genetic linkage map construction in honeylocust (Gleditsia triacanthos L.), a leguminous tree common in eastern North America. Starting with a large open-pollinated family of progeny from a single tree, a mapping pedigree of 92 putative full-sibs was identified by kin group assignment and paternity analyses with microsatellite markers. RAD-Seq using Illumina next-generation DNA sequencing (NGS) generated over 117 M reads among the 92 plants. De novo reference genome clustering and alignment of samples to the reference genome revealed 5849 candidate single nucleotide polymorphisms (SNPs), of which 1570 were retained after quality filtering. Of the 1570 SNPs, 236 were in pseudo-testcross mapping configuration in the maternal parent and segregated approximately in the expected 1:1 ratio. The final map generated has a total length of 815.57 cM and consists of 178 markers on 14 linkage groups, corresponding to the haploid chromosome number in honey locust. Synteny and collinearity between honey locust and model legumes Glycine max, Medicago truncatula, and Phaseolus vulgaris were found for six of the honey locust linkage groups. RAD-Seq proved to be useful for framework linkage map construction in honey locust, a species for which no genomic resources had previously been available. However, greater sequence coverage and larger full-sib mapping pedigrees are necessary for the development of high-density linkage maps with future applications in quantitative trait locus (QTL) mapping

Effects of Seedling Quality and Family on Performance of Northern Red Oak Seedlings on a Xeric Upland Site

Cultural practices to develop larger, more robust oak seedlings have been developed, however, the potential improvement conferred by these larger seedlings has received limited testing in the Northeast. We evaluated the effect of seedling size and pedigree on the survival, growth, and competitive ability of northern red oak (Quercus rubra L.) seedlings planted on a xeric site in northeastern Pennsylvania. We planted seedlings from a state tree nursery that represented locally available seedling stock, as well as high-quality seedlings from seven half-sibling families grown following improved nursery protocol. Half-sibling families were split into three size classes based on their root collar diameter and height; large, average, and poor. Eleven years after planting, survival across seedling treatments ranged from 45 percent for locally available seedlings, to 96 percent for one half-sibling family. Two families showed superior growth, survival, and competitive ability compared with the others. Seedling size class conferred moderate height and diameter advantage in four and three of the families, respectively. Initial seedling size was an important variable in models predicting survival, diameter, and dominance (competitive ability). Over time, the relationship between initial diameter and height diminished

Geographically extensive hybridization between the forest trees American butternut and Japanese walnut

We investigate the question of naturally occurring interspecific hybrids between two forest trees: the native North American butternut (Juglans cinerea L.) and the introduced Japanese walnut (Juglans ailantifolia Carrière). Using nuclear and chloroplast DNA markers, we provide evidence for 29 F1 and 22 advanced generation hybrids in seven locations across the eastern and southern range of the native species. Two locations show extensive admixture (95% J. ailantifolia and hybrids) while other locations show limited admixture. Hybridization appears to be asymmetrical with 90.9 per cent of hybrids having J. ailantifolia as the maternal parent. This is, to our knowledge, the first genetic data supporting natural hybridization between these species. The long-term outcome of introgression could include loss of native diversity, but could also include transfer of useful traits from the introduced species

Comparisons of interspecies field performance of Fagaceae (Castanea and Quercus) planted in the southeastern United States with attention to soil fungal impacts on plant performance

The loss of Fagaceae species is an increasing concern globally, including in North American where American chestnut (Castanea dentata) has been virtually eliminated by non-native pathogens, and oaks (Quercus) are experiencing widespread regeneration failures and declines. Tree improvement and breeding programs are producing trees for disease resistance or improved performance traits but require field testing to refine efforts. We established a study in 2015 on a xeric pitch pine (Pinus rigida) site in the Blue Ridge Mountains of North Carolina to regenerate American chestnut and interspecies hybrids (BC3F3) and the co-occurring species of white oak (Q. alba) through planting bare-root, quality-graded seedlings. Chinese chestnut (C. mollissima) was also tested as a control species. We used pedigreed seed sources from open-pollinated genetic families that were nursery grown (1–0 bareroot seedlings for chestnut, 2–0 bareroot seedlings for white oak) to maximize overall size and competitive ability. Though there was variability within and among plant families in performance, American chestnut and BC3F3 hybrids generally outperformed Chinese chestnut (at least 13 % taller) and white oak (at least 29 % taller) for the first three years, but intraspecies differences among genetic families were significant for nearly all traits tested. Initial seedling root morphology poorly explained field performance (R2 \u3c 0.17), but this relationship was significant for both white oak families and the only northern BC3F3 seed source. American chestnuts and BC3F3 hybrids had higher stem height to ground diameter ratios compared to white oak (at least 11 % greater), indicating that white oak likely concentrates more resources to root development while chestnut concentrates more resources to maintaining above-ground competitive advantages. Additionally, we investigated soil fungal communities, both pre- and post-tree establishment and tested if these fungal communities can be used to predict plant performance or health. Soil fungi did a poor job predicting plant performance. Our results indicate that co-occurring Fagaceae species can be established in restoration plantings using well developed quality seedlings on relatively xeric sites. Managers should use diverse seed sources to avoid planting poor performing families and expect that chestnuts bred for blight resistance will outcompete planted white oak, at least in the short-term

Hoban_EvolApps_microsat_Data_For_Dryad

The genotypes for trees used in this study for all analyses, after clones, etc. have been removed. The data are referred to in the publication as "1515 unique genotypes for analysis: 79 J. ailantifolia reference, 7 hybrid 231 reference, 66 J. cinerea reference, and 1363 naturally occurring trees." The names of the populations are as in table one, or similar abbreviation. File format is Convert, tab delimited. All 12 microsatellite loci. Missing data with a '?'. Details about collections are in the manuscript