The Highest-Copy Repeats are Methylated in the Small Genome of the Early Divergent Vascular Plant Selaginella moellendorffii

Background The lycophyte Selaginella moellendorffii is a vascular plant that diverged from the fern/seed plant lineage at least 400 million years ago. Although genomic information for S. moellendorffii is starting to be produced, little is known about basic aspects of its molecular biology. In order to provide the first glimpse to the epigenetic landscape of this early divergent vascular plant, we used the methylation filtration technique. Methylation filtration genomic libraries select unmethylated DNA clones due to the presence of the methylation-dependent restriction endonuclease McrBC in the bacterial host. Results We conducted a characterization of the DNA methylation patterns of the S. moellendorffii genome by sequencing a set of S. moellendorffii shotgun genomic clones, along with a set of methylation filtered clones. Chloroplast DNA, which is typically unmethylated, was enriched in the filtered library relative to the shotgun library, showing that there is DNA methylation in the extremely small S. moellendorffii genome. The filtered library also showed enrichment in expressed and gene-like sequences, while the highest-copy repeats were largely under-represented in this library. These results show that genes and repeats are differentially methylated in the S.moellendorffii genome, as occurs in other plants studied. Conclusion Our results shed light on the genome methylation pattern in a member of a relatively unexplored plant lineage. The DNA methylation data reported here will help understanding the involvement of this epigenetic mark in fundamental biological processes, as well as the evolutionary aspects of epigenetics in land plants

Castor bean organelle genome sequencing and worldwide genetic diversity analysis

Castor bean is an important oil-producing plant in the Euphorbiaceae family. Its high-quality oil contains up to 90% of the unusual fatty acid ricinoleate, which has many industrial and medical applications. Castor bean seeds also contain ricin, a highly toxic Type 2 ribosome-inactivating protein, which has gained relevance in recent years due to biosafety concerns. In order to gain knowledge on global genetic diversity in castor bean and to ultimately help the development of breeding and forensic tools, we carried out an extensive chloroplast sequence diversity analysis. Taking advantage of the recently published genome sequence of castor bean, we assembled the chloroplast and mitochondrion genomes extracting selected reads from the available whole genome shotgun reads. Using the chloroplast reference genome we used the methylation filtration technique to readily obtain draft genome sequences of 7 geographically and genetically diverse castor bean accessions. These sequence data were used to identify single nucleotide polymorphism markers and phylogenetic analysis resulted in the identification of two major clades that were not apparent in previous population genetic studies using genetic markers derived from nuclear DNA. Two distinct sub-clades could be defined within each major clade and large-scale genotyping of castor bean populations worldwide confirmed previously observed low levels of genetic diversity and showed a broad geographic distribution of each sub-clade

Abiotic Stress‐Related Expressed Sequence Tags from the Diploid Strawberry Fragaria vesca

Strawberry ( spp.) is a eudicotyledonous plant that belongs to the Rosaceae family, which includes other agronomically important plants such as raspberry ( L.) and several tree-fruit species. Despite the vital role played by cultivated strawberry in agriculture, few stress-related gene expression characterizations of this crop are available. To increase the diversity of available transcriptome sequence, we produced 41,430 L. expressed sequence tags (ESTs) from plants growing under water-, temperature-, and osmotic-stress conditions as well as a combination of heat and osmotic stresses that is often found in irrigated fields. Clustering and assembling of the ESTs resulted in a total of 11,836 contigs and singletons that were annotated using Gene Ontology (GO) terms. Furthermore, over 1200 sequences with no match to available Rosaceae ESTs were found, including six that were assigned the “response to stress” GO category. Analysis of EST frequency provided an estimate of steady state transcript levels, with 91 sequences exhibiting at least a 20-fold difference between treatments. This EST collection represents a useful resource to advance our understanding of the abiotic stress-response mechanisms in strawberry. The sequence information may be translated to valuable tree crops in the Rosaceae family, where whole-plant treatments are not as simple or practical

INFLUENCE OF PLANTING DATE AND SEED TREATMENT ON EMERGENCE AND PREHARVEST SEED INFECTION IN SORGHUM

Low seed germination, early seedling death and infection of seeds by fungi before harvest are major problems in sorghum. Seeds of four sorghum cultivars treated with three fungicides were planted at different dates to determine if seed treatment and planting dates influenced seed germination, post emergence seedling death and preharvest seed infection. Germination was significantly lower when seeds were planted at soil temperature less than 20(DEGREES)C. Seed treatment with fungicides increased germination of the four sorghum cultivars when seeds were planted at low temperatures, but not at high soil temperature. The effect of seed treatment on germination at higher soil temperature was inconsistent. Post emergence seedling blight was higher when seeds were planted at higher temperature. Seed treatment with fungicide did not consistently reduce post emergence seedling death for all cultivars. Planting date influenced preharvest seed infection by various fungi and subsequent seed germination. Seeds obtained from May planting had significantly lower germination than those from June planting dates. Of the fungi isolated; Alternaria spp. and Fusarium spp. especially F. moniliforme, were the most prevalent. The incidence of Fusarium spp., was significantly higher on seeds from May than from June planting. Correlation analysis indicated that incidence of Alternaria spp. and seed germination were positively correlated, whereas the incidence of Fusarium spp. and germination of seeds from May plantings were negatively correlated. Greenhouse study of seedlings grown from Fusarium or Alternaria infected seeds showed that seedlings derived from Fusarium infected seeds were stunted, with reduced root and shoot growth; symptoms similar to post-emergence seedling blight in the field. Histopathological and scanning electron microscope studies showed that seed infection in the field by F. moniliforme is more damaging to sorghum than infection by other fungi. Of the sorghum cultivars, IS4225 was resistant to Fusarium seed infection. The results show that planting sorghum at soil temperature above 20C improves germination. At lower soil temperature, seed treatment with fungicides increased emergence. Seedborne Fusarium spp. reduces seed viability and might be involved in post emergence seedling blight

Abiotic Stress-Related Expressed Sequence Tags from the Diploid Strawberry Fragaria vesca f. semperflorens

Strawberry (Fragaria spp.) is a eudicotyledonous plant that belongs to the Rosaceae family, which includes other agronomically important plants such as raspberry (Rubus idaeus L.) and several tree-fruit species. Despite the vital role played by cultivated strawberry in agriculture, few stress- related gene expression characterizations of this crop are available. To increase the diversity of available Fragaria transcriptome sequence, we produced 41,430 Fragaria vesca L. expressed sequence tags (ESTs) from plants growing under water-, temperature-, and osmotic-stress conditions as well as a combination of heat and osmotic stresses that is often found in irrigated fi elds. Clustering and assembling of the ESTs resulted in a total of 11,836 contigs and singletons that were annotated using Gene Ontology (GO) terms. Furthermore, over 1200 sequences with no match to available Rosaceae ESTs were found, including six that were assigned the ?response to stress? GO category. Analysis of EST frequency provided an estimate of steady state transcript levels, with 91 sequences sequences exhibiting at least a 20-fold difference between treatments. This EST collection represents a useful resource to advance our understanding of the abiotic stress-response mechanisms in strawberry. The sequence information may be translated to valuable tree crops in the Rosaceae family, where whole-plant treatments are not as simple or practical.Fil: Rivarola, Maximo Lisandro. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Chan, Agnes P.. No especifíca;Fil: Liebke, David E.. University of Maryland; Estados UnidosFil: Melake Berhan, Admasu. No especifíca;Fil: Quan, Hui. No especifíca;Fil: Cheung, Foo. No especifíca;Fil: Ouyang, Shu. No especifíca;Fil: Folta, Kevin M.. University of Florida; Estados UnidosFil: Slovin, Janet P.. No especifíca;Fil: Rabinowicz, Pablo D.. University of Maryland; Estados Unido