Rice, one of the world's most important food plants, has important syntenic relationships with the other cereal species and is a model plant for the grasses. Here we present a map-based, finished quality sequence that covers 95% of the 389 Mb genome, including virtually all of the euchromatin and two complete centromeres. A total of 37,544 non-transposable-element-related protein-coding genes were identified, of which 71% had a putative homologue in Arabidopsis. In a reciprocal analysis, 90% of the Arabidopsis proteins had a putative homologue in the predicted rice proteome. Twenty-nine per cent of the 37,544 predicted genes appear in clustered gene families. The number and classes of transposable elements found in the rice genome are consistent with the expansion of syntenic regions in the maize and sorghum genomes. We find evidence for widespread and recurrent gene transfer from the organelles to the nuclear chromosomes. The map-based sequence has proven useful for the identification of genes underlying agronomic traits. The additional single-nucleotide polymorphisms and simple sequence repeats identified in our study should accelerate improvements in rice production.

/pdf/the-map-based-sequence-of-the-rice-genome-2y5gce5ixc.pdf

The map-based sequence of the rice genome

microRNA-Directed Phasing during Trans-Acting siRNA Biogenesis in Plants

Jasmonates are essential phytohormones for plant development and survival. However, the molecular details of their signalling pathway remain largely unknown. The identification more than a decade ago of COI1 as an F-box protein suggested the existence of a repressor of jasmonate responses that is targeted by the SCF(COI1) complex for proteasome degradation in response to jasmonate. Here we report the identification of JASMONATE-INSENSITIVE 3 (JAI3) and a family of related proteins named JAZ (jasmonate ZIM-domain), in Arabidopsis thaliana. Our results demonstrate that JAI3 and other JAZs are direct targets of the SCF(COI1) E3 ubiquitin ligase and jasmonate treatment induces their proteasome degradation. Moreover, JAI3 negatively regulates the key transcriptional activator of jasmonate responses, MYC2. The JAZ family therefore represents the molecular link between the two previously known steps in the jasmonate pathway. Furthermore, we demonstrate the existence of a regulatory feed-back loop involving MYC2 and JAZ proteins, which provides a mechanistic explanation for the pulsed response to jasmonate and the subsequent desensitization of the cell.

The JAZ family of repressors is the missing link in jasmonate signalling

Genes in the ERF family encode transcriptional regulators with a variety of functions involved in the developmental and physiological processes in plants. In this study, a comprehensive computational analysis identified 122 and 139 ERF family genes in Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa L. subsp. japonica), respectively. A complete overview of this gene family in Arabidopsis is presented, including the gene structures, phylogeny, chromosome locations, and conserved motifs. In addition, a comparative analysis between these genes in Arabidopsis and rice was performed. As a result of these analyses, the ERF families in Arabidopsis and rice were divided into 12 and 15 groups, respectively, and several of these groups were further divided into subgroups. Based on the observation that 11 of these groups were present in both Arabidopsis and rice, it was concluded that the major functional diversification within the ERF family predated the monocot/dicot divergence. In contrast, some groups/subgroups are species specific. We discuss the relationship between the structure and function of the ERF family proteins based on these results and published information. It was further concluded that the expansion of the ERF family in plants might have been due to chromosomal/segmental duplication and tandem duplication, as well as more ancient transposition and homing. These results will be useful for future functional analyses of the ERF family genes.

/pdf/genome-wide-analysis-of-the-erf-gene-family-in-arabidopsis-33fkj4btth.pdf

Genome-Wide Analysis of the ERF Gene Family in Arabidopsis and Rice

Perception of the bacterial PAMP EF-Tu by the receptor EFR restricts Agrobacterium-mediated transformation.

Over 225,000 independent Agrobacterium transferred DNA (T-DNA) insertion events in the genome of the reference plant Arabidopsis thaliana have been created that represent near saturation of the gene space. The precise locations were determined for more than 88,000 T-DNA insertions, which resulted in the identification of mutations in more than 21,700 of the approximately 29,454 predicted Arabidopsis genes. Genome-wide analysis of the distribution of integration events revealed the existence of a large integration site bias at both the chromosome and gene levels. Insertion mutations were identified in genes that are regulated in response to the plant hormone ethylene.

https://science.sciencemag.org/content/sci/301/5633/653.full.pdf

Genome-Wide Insertional Mutagenesis of Arabidopsis thaliana

OF THE THESIS Use of Ultra-High Resolution Imagery in the Estimation of Wildfire Fuel Load Across Chaparral Vegetation by Ian Thomas Schmidt Master of Science in Geography San Diego State University, 2014 Development of improved methods to more accurately estimate spatial distributions of fuel loads in shrublands will allow for improved understanding of ecological processes such as wildfire behavior and postburn recovery. The goal of this study is to develop and test remote sensing methods to scale-up from field plot estimates of shrubland fuel over landscapes or to pixels of coarser spatial resolution data sets using ultra high spatial resolution imagery captured by a light-sport aircraft. The study is conducted on chaparral shrublands located in eastern San Diego County, California. We measured fuel load in the field using an allometric approach and estimated ground coverage of individual shrub species by using ultra-high spatial resolution imagery and image processing routines. Study results show a strong relationship between shrub coverage and fuel loads in all three stands (7, 28, and 68 years since last wildfire). Ordinary least squares analysis using ground coverage as the independent variable regressed against biomass was conducted. The analysis yielded R values ranging from 0.78 to 0.96 in the older stands for the live shrub species, while R values for species in the younger stands ranged from 0.03 to 0.8. Pooling species-based data into larger sample sizes consisting of functional and all-shrub classes while obtaining suitable linear regression models supports the potential for these methods to be used for scaling-up fuel estimates to broader areal extents, without having to classify and map shrubland vegetation at the species level.

Ian Thomas Schmidt

Papers

Genome-Wide Insertional Mutagenesis of Arabidopsis thaliana

Use of ultra-high resolution imagery in the estimation of wildfire fuel load across chaparral vegetation