Project description:Here, de novo transcriptome assemblies for leaf and flower tissues of Forsythias were performed, resulting in 81913 unigenes of F. suspensa, 88491 unigenes of F. viridissima and 69458 unigenes of F. koreana (F. viridissima var. koreana). Classification of the annotated unigenes by gene ontology terms and KEGG pathways was used to explore transcriptomic differences among the Forsythias. Orthogroup was introduced to compare expression levels of unigenes in tissues from different species, which unveiled that three leaf tissues of Fosythias were closely correlated based on expression values of orthologous unigenes. Showing high expression mainly in leaves of F. viridissima and F. koreana, candidate homologs for genes involved in the biosynthetic pathway of lignans and phenylethanoid glycosides were determined in these transcriptome assemblies.
Project description:Here, de novo transcriptome assemblies for leaf and flower tissues of Forsythias were performed, resulting in 81913 unigenes of F. suspensa, 88491 unigenes of F. viridissima and 69458 unigenes of F. koreana (F. viridissima var. koreana). Classification of the annotated unigenes by gene ontology terms and KEGG pathways was used to explore transcriptomic differences among the Forsythias. Orthogroup was introduced to compare expression levels of unigenes in tissues from different species, which unveiled that three leaf tissues of Fosythias were closely correlated based on expression values of orthologous unigenes. Showing high expression mainly in leaves of F. viridissima and F. koreana, candidate homologs for genes involved in the biosynthetic pathway of lignans and phenylethanoid glycosides were determined in these transcriptome assemblies.
Project description:Here, de novo transcriptome assemblies for leaf and flower tissues of Forsythias were performed, resulting in 81913 unigenes of F. suspensa, 88491 unigenes of F. viridissima and 69458 unigenes of F. koreana (F. viridissima var. koreana). Classification of the annotated unigenes by gene ontology terms and KEGG pathways was used to explore transcriptomic differences among the Forsythias. Orthogroup was introduced to compare expression levels of unigenes in tissues from different species, which unveiled that three leaf tissues of Fosythias were closely correlated based on expression values of orthologous unigenes. Showing high expression mainly in leaves of F. viridissima and F. koreana, candidate homologs for genes involved in the biosynthetic pathway of lignans and phenylethanoid glycosides were determined in these transcriptome assemblies.
Project description:The Zika outbreak, spread by the Aedes aegypti mosquito, highlights the need to create high-quality assemblies of large genomes in a rapid and cost-effective fashion. Here, we combine Hi-C data with existing draft assemblies to generate chromosome-length scaffolds. We validate this method by assembling a human genome, de novo, from short reads alone (67X coverage, Sample GSM1551550). We then combine our method with draft sequences to create genome assemblies of the mosquito disease vectors Aedes aegypti and Culex quinquefasciatus, each consisting of three scaffolds corresponding to the three chromosomes in each species. These assemblies indicate that virtually all genomic rearrangements among these species occur within, rather than between, chromosome arms. The genome assembly procedure we describe is fast, inexpensive, accurate, and can be applied to many species.
2017-03-24 | GSE95797 | GEO
Project description:Development microsatellite loci for three closely related Ficus species
Project description:The aims of our study were: 1) to elucidate physiological responses in three Miscanthus species and newly bred triploid hybrid in three water stress treatment conditions 2) utilise the induced physiological conditions for an in-depth transcriptome study on the molecular basis of water stress in Miscanthus spp.
Project description:Genomic surveys of yeast hybrid species isolated from the wild and from human-related environment, aimed at the reconstruction of the natural evolution of Saccharomyces spp. evolution
Project description:Artemisia argyi Lev. et Vant., a common ancient compositae species, is widely utilized in traditional Chinese medicine. The underlying mechanism of terpenoid biosynthesis in leaf has been suggested to play an important role in this medicine. However, the transcriptome of A. argyi has not been established. Here, we performed RNA sequencing in leaf, root and stem tissues to identify all possibly transcribed genes. We assembled a total of 99,807 unigenes by analyzing the expression profiling that were generated from the three tissues. Of them, 67,446 unigenes (67.58%) were annotated from public databases including GO, KEGG, COG. We further performed differential gene expression analysis between leaf with stem and root tissue. Our findings revealed that a total of 7,725 unigenes were specified transcribed in leaf. In particular, we determined multiple genes, which encode significant enzymes including HMGR, MVD, DXS, DXR, HDS and HDR, and transcription factors related to terpenoid synthesis. This study established a valuable resource of transcriptome and identified many transcribed genes related to terpenoid biosynthesis, providing the genomic basis for further studies on the molecular mechanism of the medicine for this species.
Project description:Hymenolepis spp. (H. diminuta, H. nana and H. microstoma) are rodent-hosted tapeworms (Platyhelminthes: Cestoda) that have been used as laboratory and teaching models since the 1950s, and consequently much of our understanding of the basic physiology, biochemistry and anatomy of tapeworms in general stems from research using these species. As representatives of the order Cyclophyllidea, they are closely related to species with significant medical and economic importance such as Taenia and Echinococcus spp., but unlike these may be maintained in vivo using only laboratory mice and flour beetles (n.b. Echinoccous spp. are hosted by foxes and Taenia spp. are hosted by pigs or cows). This effort brings a classical laboratory model into the genomic age, allowing researchers in silico access to its genome and expressed gene transcripts and thereby greatly expediting research directed at understanding the genetic basis of tapeworm biology.
