Qihui Zhu

PlantTFDB: a comprehensive plant transcription factor database

Transcription factors (TFs) play key roles in controlling gene expression. Systematic identification and annotation of TFs, followed by construction of TF databases may serve as useful resources for studying the function and evolution of transcription factors. We developed a comprehensive plant transcription factor database PlantTFDB (http://planttfdb.cbi.pku.edu.cn), which contains 26 402 TFs predicted from 22 species, including five model organisms with available whole genome sequence and 17 plants with available EST sequences. To provide comprehensive information for those putative TFs, we made extensive annotation at both family and gene levels. A brief introduction and key references were presented for each family. Functional domain information and cross-references to various well-known public databases were available for each identified TF. In addition, we predicted putative orthologs of those TFs among the 22 species. PlantTFDB has a simple interface to allow users to search the database by IDs or free texts, to make sequence similarity search against TFs of all or individual species, and to download TF sequences for local analysis.

DRTF: a database of rice transcription factors

SUMMARY DRTF contains 2025 putative transcription factors (TFs) in Oryza sativa L. ssp. indica and 2384 in ssp. japonica, distributed in 63 families, identified by computational prediction and manual curation. It includes detailed annotations of each TF including sequence features, functional domains, Gene Ontology assignment, chromosomal localization, EST and microarray expression information, as well as multiple sequence alignment of the DNA-binding domains for each TF family. The database can be browsed and searched with a user-friendly web interface. AVAILABILITY DRTF is available at http://drtf.cbi.pku.edu.cn

Genome-wide identification and evolutionary analysis of the plant specific SBP-box transcription factor family.

We made genome-wide analyses to explore the evolutionary process of the SBP-box gene family. We identified 120 SBP-box genes from nine species representing the main green plant lineages: green alga, moss, lycophyte, gymnosperm and angiosperm. A maximum-likelihood phylogenetic tree was constructed using the protein sequences of the DNA-binding domain of SBP-box genes (SBP-domain). Our results revealed that all SBP-box genes of green alga clustered into a single clade (CR group), while all genes from land-plants fell into two distinct groups. Group I had a single copy in each species except for poplar while group II had several members in each species and can be divided into several subgroups. The SBP-domain encoded by all SBP-box genes possesses two zinc fingers. The C-terminal zinc finger of both group I and group II had the same C2HC motif while their N-terminal zinc finger showed different signatures, C4 in group I and C3H in group II. The patterns of exon-intron structure in Arabidopsis and rice SBP-box genes were consistent with the phylogenetic results. A target site of microRNA miR156 was highly conserved among land-plant SBP-box genes. Our results suggested that the SBP-box gene family might have originated from a common ancestor of green plants, followed by duplication and divergence in each lineage including exon-intron loss processes.

Selection on grain shattering genes and rates of rice domestication.

Molecular cloning of major quantitative trait loci (QTLs) responsible for the reduction of rice grain shattering, a hallmark of cereal domestication, provided opportunities for in-depth investigation of domestication processes. Here, we studied nucleotide variation at the shattering loci, sh4 and qSH1, for cultivated rice, Oryza sativa ssp. indica and Oryza sativa ssp. japonica, and the wild progenitors, Oryza nivara andOryza rufipogon. The nonshattering sh4 allele was fixed in all rice cultivars, with levels of sequence polymorphism significantly reduced in both indica and japonica cultivars relative to the wild progenitors. The sh4 phylogeny together with the neutrality tests and coalescent simulations suggested that sh4 had a single origin and was fixed by artificial selection during the domestication of rice. Selection on qSH1 was not detected in indica and remained unclear in japonica. Selection on sh4 could be strong enough to have driven its fixation in a population of cultivated rice within a period of c. 100 yr. The slow fixation of the nonshattering phenotype observed at the archeological sites might be a result of relatively weak selection on mutations other than sh4 in early rice cultivation. The fixation of sh4 could have been achieved later through strong selection for the optimal phenotype.

DPTF: a database of poplar transcription factors

The database of poplar transcription factors (DPTF) is a plant transcription factor (TF) database containing 2576 putative poplar TFs distributed in 64 families. These TFs were identified from both computational prediction and manual curation. We have provided extensive annotations including sequence features, functional domains, GO assignment and expression evidence for all TFs. In addition, DPTF contains cross-links to the Arabidopsis and rice transcription factor databases making it a unique resource for genome-scale comparative studies of transcriptional regulation in model plants. Availiability: DPTF is available at http://dptf.cbi.pku.edu.cn.

Statistical inference of chromosomal homology based on gene colinearity and applications to Arabidopsis and rice

BackgroundThe identification of chromosomal homology will shed light on such mysteries of genome evolution as DNA duplication, rearrangement and loss. Several approaches have been developed to detect chromosomal homology based on gene synteny or colinearity. However, the previously reported implementations lack statistical inferences which are essential to reveal actual homologies.ResultsIn this study, we present a statistical approach to detect homologous chromosomal segments based on gene colinearity. We implement this approach in a software package ColinearScan to detect putative colinear regions using a dynamic programming algorithm. Statistical models are proposed to estimate proper parameter values and evaluate the significance of putative homologous regions. Statistical inference, high computational efficiency and flexibility of input data type are three key features of our approach.ConclusionWe apply ColinearScan to the Arabidopsis and rice genomes to detect duplicated regions within each species and homologous fragments between these two species. We find many more homologous chromosomal segments in the rice genome than previously reported. We also find many small colinear segments between rice and Arabidopsis genomes.

Computational identification of plant transcription factors and the construction of the PlantTFDB database.

Transcription factors (TFs) play an important role in gene regulation. Computational identification and annotation of TFs at genome scale are the first step toward understanding the mechanism of gene expression and regulation. We started to construct the database of Arabidopsis TFs in 2005 and developed a pipeline for systematic identification of plant TFs from genomic and transcript sequences. In the following years, we built a database of plant TFs (PlantTFDB, http://planttfdb.cbi.pku.edu.cn ) which contains putative TFs identified from 22 species including five model organisms and 17 economically important plants with available EST sequences. To provide comprehensive information for the putative TFs, we made extensive annotation at both the family and gene levels. A brief introduction and key references were presented for each family. Functional domain information and cross-references to various well-known public databases were available for each identified TF. In addition, we predicted putative orthologs of the TFs in other species. PlantTFDB has a simple interface to allow users to make text queries, or BLAST searches, and to download TF sequences for local analysis. We hope that PlantTFDB could provide the user community with a useful resource for studying the function and evolution of transcription factors.

Characterization of the genome expression trends in the heading-stage panicle of six rice lineages

To study how changes in gene regulation shape phenotypic variations in rice, we performed a comparative analysis of genome expression in the heading-stage panicle from six lineages of cultivated and wild rice, including Oryza sativa subsp. indica, japonica and javanica, O. nivara , O. rufipogon and O. glaberrima. While nearly three-quarters of the genes are expressed at a constant level in all six lineages, a large portion of the genome, ranging from 1767 to 4489 genes, exhibited differential expression between Asian domesticated and wild rice with repression or down-regulation of genome expression in Asian cultivated rice as the dominant trend. Importantly, we found this repression was achieved to a large extent by the differential expression of a single member of paralogous gene families. Functional analysis of the differentially expressed genes revealed that genes related to catabolism are repressed while genes related to anabolism up-regulated. Finally, we observed that distinct evolutionary forces may have acted on gene expression and the coding sequences in the examined rice lineages.