Building a reference transcriptome for Juniperus squamata (Cupressaceae) based on single-molecule real-time sequencing

Objectives Cupressaceae is the second largest family of coniferous trees (Coniferopsida) with important economic and ecological values. However, like other conifers, the members of Cupressaceae have extremely large genome (> 8 gigabytes), which limited the researches of these taxa. A high-quality transcriptome is an important resource for gene discovery and annotation for non-model organisms. Data description Juniperus squamata, a tetraploid species which is widely distributed in Asian mountains, represents the largest genus, Juniperus, in Cupressaceae. Single-molecule real-time sequencing was used to obtain full-length transcriptome of Juniperus squamata. The full-length transcriptome was corrected with Illumina RNA-seq data from the same individual. A total of 47,860 non-redundant full-length transcripts, N50 of which was 2839, were obtained. A total of 57,393 simple sequence repeats were identified and 268,854 open reading frames were predicted for Juniperus squamata. A BLAST alignment against non-redundant protein database was conducted and 10,818 sequences were annotated in Gene Ontology database. InterPro analysis shows that 30,403 sequences have been functionally characterized against its member database. This data presents the first comprehensive transcriptome characterization of Juniperus species, and provides an important reference for researches on the genomics and evolutionary history of Cupressaceae plants and conifers in the future.

Euler diagrams drawn with ellipses area-proportionally (Edeap)

BackgroundArea-proportional Euler diagrams are frequently used to visualize data from Microarray experiments, but are also applied to a wide variety of other data from biosciences, social networks and other domains.ResultsThis paper details Edeap, a new simple, scalable method for drawing area-proportional Euler diagrams with ellipses. We use a search-based technique optimizing a multi-criteria objective function that includes measures for both area accuracy and usability, and which can be extended to further user-defined criteria. The Edeap software is available for use on the web, and the code is open source. In addition to describing our system, we present the first extensive evaluation of software for producing area-proportional Euler diagrams, comparing Edeap to the current state-of-the-art; circle-based method, venneuler, and an alternative ellipse-based method, eulerr.ConclusionsOur evaluation—using data from the Gene Ontology database via GoMiner, Twitter data from the SNAP database, and randomly generated data sets—shows an ordering for accuracy (from best to worst) of eulerr, followed by Edeap and then venneuler. In terms of runtime, the results are reversed with venneuler being the fastest, followed by Edeap and finally eulerr. Regarding scalability, eulerr cannot draw non-trivial diagrams beyond 11 sets, whereas no such limitation is present in Edeap or venneuler, both of which draw diagrams up to the tested limit of 20 sets.

Identification of potential biomarkers associated with pathogenesis of primary prostate cancer based on meta-analysis approaches

Worldwide prostate cancer (PCa) is recognized as the second most common diagnosed cancer and the fifth leading cause of cancer death among men globally. Rising incidence rates of PCa have been observed over the last few decades. It is necessary to improve prostate cancer detection, diagnosis, treatment and survival. However, there are few reliable biomarkers for early prostate cancer diagnosis and prognosis. In the current study, systems biology method was applied for transcriptomic data analysis to identify potential biomarkers for primary PCa. We firstly identified differentially expressed genes (DEGs) between primary PCa and normal samples. Then the DEGs were mapped in Wikipathways and gene ontology database to conduct functional categories enrichment analysis. 1575 unique DEGs with adjusted p-value < 0.05 were achieved from two sets of DEGs. 132 common DEGs between two sets of DEGs were retrieved. The final DEGs were selected from 60 common upregulated and 72 common downregulated genes between datasets. In conclusion, we demonstrated some potential biomarkers (FOXA1, AGR2, EPCAM, CLDN3, ERBB3, GDF15, FHL1, NPY, DPP4, and GADD45A) and HIST2H2BE as a candidate one which are tightly correlated with the pathogenesis of PCa.

Genome Sequencing and Analysis of Thraustochytriidae sp. SZU445 Provides Novel Insights into the Polyunsaturated Fatty Acid Biosynthesis Pathway

Thraustochytriidae sp. have broadly gained attention as a prospective resource for the production of omega-3 fatty acids production in significant quantities. In this study, the whole genome of Thraustochytriidae sp. SZU445, which produces high levels of docosapentaenoic acid (DPA) and docosahexaenoic acid (DHA), was sequenced and subjected to protein annotation. The obtained clean reads (63.55 Mb in total) were assembled into 54 contigs and 25 scaffolds, with maximum and minimum lengths of 400 and 0.0054 Mb, respectively. A total of 3513 genes (24.84%) were identified, which could be classified into six pathways and 44 pathway groups, of which 68 genes (1.93%) were involved in lipid metabolism. In the Gene Ontology database, 22,436 genes were annotated as cellular component (8579 genes, 38.24%), molecular function (5236 genes, 23.34%), and biological process (8621 genes, 38.42%). Four enzymes corresponding to the classic fatty acid synthase (FAS) pathway and three enzymes corresponding to the classic polyketide synthase (PKS) pathway were identified in Thraustochytriidae sp. SZU445. Although PKS pathway-associated dehydratase and isomerase enzymes were not detected in Thraustochytriidae sp. SZU445, a putative DHA- and DPA-specific fatty acid pathway was identified.

Transcriptome characterization and screening of molecular markers in ecologically important Himalayan species (Rhododendron arboreum)

Rhododendron arboreum is an ecologically prominent species, which also lends commercial and medicinal benefits in the form of palatable juices and useful herbal drugs. Local abundance and survival of the species under a highly fluctuating climate make it an ideal model for genetic structure and functional analysis. However, a lack of genomic data has hampered additional research. In the present study, cDNA libraries from floral and foliar tissues of the species were sequenced to provide a foundation for understanding the functional aspects of the genome and to construct an enriched repository that will promote genomics studies in the genera. Illumina’s platform facilitated the generation of ∼100 million high-quality paired-end reads. De novo assembly, clustering, and filtering out of shorter transcripts predicted 113 167 non-redundant transcripts with an average length of 1164.6 bases. Of these, 71 961 transcripts were categorized based on functional annotations in the Gene Ontology database, whereby 5710 were grouped into 141 pathways and 23 746 encoded for different transcription factors. Transcriptome screening further identified 35 419 microsatellite regions, of which, 43 polymorphic loci were characterized on 30 genotypes. Seven hundred and nineteen transcripts had 811 high-quality single-nucleotide polymorphic variants with a minimum coverage of 10, a total score of 20, and SNP% of 50.