Large-scale collection and annotation of gene models for date palm (Phoenix dactylifera, L.)

The date palm (Phoenix dactylifera L.), famed for its sugar-rich fruits (dates) and cultivated by humans since 4,000 B.C., is an economically important crop in the Middle East, Northern Africa, and increasingly other places where climates are suitable. Despite a long history of human cultivation, the understanding of P. dactylifera genetics and molecular biology are rather limited, hindered by lack of basic data in high quality from genomics and transcriptomics. Here we report a large-scale effort in generating gene models (assembled expressed sequence tags or ESTs and mapped to a genome assembly) for P. dactylifera, using the long-read pyrosequencing platform (Roche/454 GS FLX Titanium) in high coverage. We built fourteen cDNA libraries from different P. dactylifera tissues (cultivar Khalas) and acquired 15,778,993 raw sequencing reads—about one million sequencing reads per library—and the pooled sequences were assembled into 67,651 non-redundant contigs and 301,978 singletons. We annotated 52,725 contigs based on the plant databases and 45 contigs based on functional domains referencing to the Pfam database. From the annotated contigs, we assigned GO (Gene Ontology) terms to 36,086 contigs and KEGG pathways to 7,032 contigs. Our comparative analysis showed that 70.6 % (47,930), 69.4 % (47,089), 68.4 % (46,441), and 69.3 % (47,048) of the P. dactylifera gene models are shared with rice, sorghum, Arabidopsis, and grapevine, respectively. We also assigned our gene models into house-keeping and tissue-specific genes based on their tissue specificity. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11103-012-9924-z) contains supplementary material, which is available to authorized users

A New Urban Functional Zone-Based Climate Zoning System for Urban Temperature Study

The urban heat island (UHI) effect has been recognized as one of the most significant terrestrial surface climate-related consequences of urbanization. However, the traditional definition of the urban–rural (UR) division and the newly established local climate zone (LCZ) classification for UHI and urban climate studies do not adequately express the pattern and intensity of UHI. Moreover, these definitions of UHI find it hard to capture the human activity-induced anthropogenic heat that is highly correlated with urban functional zones (UFZ). Therefore, in this study, with a comparison (theory, technology, and application) of the previous definition (UR and LCZ) of UHI and integration of computer programming technology, social sensing, and remote sensing, we develop a new urban functional zone-based urban temperature zoning system (UFZC). The UFZC system is generally a social-based, planning-oriented, and data-driven classification system associated with the urban function and temperature; it can also be effectively used in city management (e.g., urban planning and energy saving). Moreover, in the Beijing case, we tested the UFZC system and preliminarily analyzed the land surface temperature (LST) difference patterns and causes of the 11 UFZC types. We found that, compared to other UFZCs, the PGZ (perseveration green zone)-UFZC has the lowest LST, while the CBZ (center business district zone)-UFZC and GCZ (general commercial zone)-UFZC contribute the most and stable heat sources. This implies that reducing the heat generated by the function of commercial (and industrial) activities is an effective measure to reduce the UHI effect. We also proposed that multi-source temperature datasets with a high spatiotemporal resolution are needed to obtain more accurate results; thus providing more accurate recommendations for mitigating UHI effects. In short, as a new and finer urban temperature zoning system, although UFZC is not intended to supplant the UR and LCZ classifications, it can facilitate more detailed and coupled urban climate studies

RNA binding profile analysis of N-acetyltransferase 10 in K562 cells

Objective To delineate RNA binding profile of NAT10(N-acetyltransferase 10) in human chronic myelogenous leukemia cell line K562. Methods Enhanced UV crosslinking and immunoprecipitation (eCLIP) were used to capture the transcript collection bound by NAT10 in K562 cells. Data were obtained through high throughput sequencing and then analyzed with bioinformatics. The type and regions of NAT10 binding genes were identified via peak-calling and annotation. The function of the binding RNA was further explored by gene function enrichment analysis. Results NAT10 binding transcripts which were enriched in 3′UTR region, were mainly protein coding genes. Further analysis showed that they were functionally associated with DNA damage and repair. Conclusions NAT10 may regulate gene expression by binding to the 3′UTR region of mRNA associated with DNA damage repair