Recent advances in fluorescence and afterglow of CDs in matrices.

Carbon dots (CDs) are novel nanomaterials with dimensions less than 10 nm that have attracted much attention due to their outstanding optical properties. However, the development of solid-state fluorescence and afterglow methods has been relatively slow, although the properties of these materials under liquid conditions have been extensively studied. In recent years, embedding CDs in a matrix has been shown to prevent aggregation quenching and inhibit nonradiative transitions, thus realizing solid-state fluorescence and afterglow, which has greatly broadened the research and application areas of CDs. In terms of hydrogen bonding, ionic bonding, covalent bonding and spatial confinement, the interactions between CDs and matrices can effectively realize and improve the solid-state fluorescence and afterglow effects of CDs. Recent applications of CDs in matrices in optoelectronics, information security, sensing, biotherapeutics and imaging are also summarized. Finally, we summarize the challenges and developments of CDs in matrices.

Whole-genome sequencing of Oryza brachyantha reveals mechanisms underlying Oryza genome evolution.

The wild species of the genus Oryza contain a largely untapped reservoir of agronomically important genes for rice improvement. Here we report the 261-Mb de novo assembled genome sequence of Oryza brachyantha. Low activity of long-terminal repeat retrotransposons and massive internal deletions of ancient long-terminal repeat elements lead to the compact genome of Oryza brachyantha. We model 32,038 protein-coding genes in the Oryza brachyantha genome, of which only 70% are located in collinear positions in comparison with the rice genome. Analysing breakpoints of non-collinear genes suggests that double-strand break repair through non-homologous end joining has an important role in gene movement and erosion of collinearity in the Oryza genomes. Transition of euchromatin to heterochromatin in the rice genome is accompanied by segmental and tandem duplications, further expanded by transposable element insertions. The high-quality reference genome sequence of Oryza brachyantha provides an important resource for functional and evolutionary studies in the genus Oryza.

Comparison analysis of transcripts from the halophyte Thellungiella halophila.

The Brassicaceae family halophyte Thellungiella halophila has a high salinity tolerance and serves as a valuable halophytic genetic model plant with experimental convenience similar to Arabidopsis thaliana. A cDNA library of Thellungiella was generated from salt-treated seedlings including rosettes and roots. More than 1 000 randomly selected clones were sequenced and 946 expressed sequence tags (ESTs) were generated. The accession numbers of our EST data are available online in the GenBank database from EC598928 to EC599965. In total 679 unique clusters were assembled, and 632 (93%) had BLASTX hits in the nr databases and 7% are Thellungiella unique. According to the Gene Ontology (GO) hierarchy, 385 of 679 unigenes were categorized. Compared with public Arabidopsis microarray data, our results provide more potential salt tolerance genes in Thellungiella. These results will provide a broader coverage into Thellungiella transcriptome and benefit the discovery of salt tolerance related genes.

Transcriptomic and genomic evolution under constant cold in Antarctic notothenioid fish.

The antifreeze glycoprotein-fortified Antarctic notothenioid fishes comprise the predominant fish suborder in the isolated frigid Southern Ocean. Their ecological success undoubtedly entailed evolutionary acquisition of a full suite of cold-stable functions besides antifreeze protection. Prior studies of adaptive changes in these teleost fishes generally examined a single genotype or phenotype. We report here the genome-wide investigations of transcriptional and genomic changes associated with Antarctic notothenioid cold adaptation. We sequenced and characterized 33,560 ESTs from four tissues of the Antarctic notothenioid Dissostichus mawsoni and derived 3,114 nonredundant protein gene families and their expression profiles. Through comparative analyses of same-tissue transcriptome profiles of D. mawsoni and temperate/tropical teleost fishes, we identified 177 notothenioid protein families that were expressed many fold over the latter, indicating cold-related up-regulation. These up-regulated gene families operate in protein biosynthesis, protein folding and degradation, lipid metabolism, antioxidation, antiapoptosis, innate immunity, choriongenesis, and others, all of recognizable functional importance in mitigating stresses in freezing temperatures during notothenioid life histories. We further examined the genomic and evolutionary bases for this expressional up-regulation by comparative genomic hybridization of DNA from four pairs of Antarctic and basal non-Antarctic notothenioids to 10,700 D. mawsoni cDNA probes and discovered significant to astounding (3- to >300-fold, P < 0.05) Antarctic-specific duplications of 118 protein-coding genes, many of which correspond to the up-regulated gene families. Results of our integrative tripartite study strongly suggest that evolution under constant cold has resulted in dramatic genomic expansions of specific protein gene families, augmenting gene expression and gene functions contributing to physiological fitness of Antarctic notothenioids in freezing polar conditions.

A snapshot of the Chinese SOL Project.

In 2003, the International Solanaceae Project (SOL) was initiated by an international consortium of ten countries including Korea, China, the United Kingdom, India, the Netherlands, France, Japan, Spain, Italy and the United States. The first major effort of the SOL aimed to produce a DNA sequence map for euchromatin regions of 12 chromosomes of tomato (Solanum lycopersicum) before 2010. Here we present an update on Chinese effort for sequencing the euchromatin region of chromosome 3.

Transcription factors in rice: a genome-wide comparative analysis between monocots and eudicots.

It is not known how representative the Arabidopsis thaliana complement of transcription factors (TFs) is of other plants. The availability of rice (Oryza sativa) genome sequences makes possible a comparative analysis of TFs between monocots and eudicots, the two major monophyletic groups of angiosperms. Here, we identified 1611 TF genes that belong to 37 gene families in rice, comparable to the 1510 in Arabidopsis. Several gene subfamilies, but no families, were found to be lineage-specific. Phylogenetic analyses indicated that nearly half of the TF genes form clear orthologous pairs or groups, which were derived from 383 ancestral genes in the common ancestor of rice and Arabidopsis. Investigating gene duplication mechanisms revealed twelve pairs of large intragenomic duplicated blocks, which account for more than 40% of the rice genome. About 60% of the duplicated TF genes have been retained on duplicated segments. Functional conservation and diversification of TFs across monocot and eudicot lineages are discussed.

Evidence for an ancient whole-genome duplication event in rice and other cereals.

Gene duplication has been proposed as an accelerator of evolution. Ancient genome duplication events have been identified in diverse organisms, such as yeast, vertebrates, and Arabidopsis. Here, we have identified a whole genome duplication event (WGD) in the rice genome, which took place prior to the divergence of grasses about 70 million years ago (mya). A total of 117 duplicated blocks were detected, which are distributed on all 12 chromosomes and cover about 60% of the rice genome. About 20% genes on these duplicated segments are retained as duplicate pairs. In contrast, 60% of the transcription factor genes are retained as duplicates. The identification of a WGD in the ancestral grass genome will impact the study of grass genome evolution, and suggest that polyploidization and subsequent gene losses and chromosomal rearrangements have played an important role in the diversification of grasses.

Genome-wide analysis of the GRAS gene family in rice and Arabidopsis.

Members of the GRAS gene family encode transcriptional regulators that have diverse functions in plant growth and development such as gibberellin signal transduction, root radial patterning, axillary meristem formation, phytochrome A signal transduction, and gametogenesis. Bioinformatic analysis identified 57 and 32 GRAS genes in rice and Arabidopsis, respectively. Here, we provide a complete overview of this gene family, describing the gene structure, gene expression, chromosome localization, protein motif organization, phylogenetic analysis, and comparative analysis between rice and Arabidopsis. Phylogenetic analysis divides the GRAS gene family into eight subfamilies, which have distinct conserved domains and functions. Both genome/segmental duplication and tandem duplication contributed to the expansion of the GRAS gene family in the rice and Arabidopsis genomes. The existence of GRAS-like genes in bryophytes suggests that GRAS is an ancient family of transcription factors, which arose before the appearance of land plants over 400 million years ago.

An integrated physical and genetic map of the rice genome.

Rice was chosen as a model organism for genome sequencing because of its economic importance, small genome size, and syntenic relationship with other cereal species. We have constructed a bacterial artificial chromosome fingerprint-based physical map of the rice genome to facilitate the whole-genome sequencing of rice. Most of the rice genome ( approximately 90.6%) was anchored genetically by overgo hybridization, DNA gel blot hybridization, and in silico anchoring. Genome sequencing data also were integrated into the rice physical map. Comparison of the genetic and physical maps reveals that recombination is suppressed severely in centromeric regions as well as on the short arms of chromosomes 4 and 10. This integrated high-resolution physical map of the rice genome will greatly facilitate whole-genome sequencing by helping to identify a minimum tiling path of clones to sequence. Furthermore, the physical map will aid map-based cloning of agronomically important genes and will provide an important tool for the comparative analysis of grass genomes.