In this work, we extend these methods into transcriptomics to analyze sequencing data using the pantranscriptome: a population-level transcriptomic reference. Our novel toolchain can construct spliced pangenome graphs, map RNA-seq data to these graphs, and perform haplotype-aware expression ...
Genome instability and aberrant alterations of transcriptional programs both play important roles in cancer. Single-cell RNA sequencing (scRNA-seq) has the potential to investigate both genetic and nongenetic sources of tumor heterogeneity in a single as
Transcriptome and co-expression network analyses revealed the involvement of aquaporins (AQPs) and Ca2+-related ion channel genes in leaf movement. Moreover, we also identified nodulation-related genes and analyzed the structure and evolution of the key gene NIN in the process of symbiotic nitrogen...
J.-Y.G. and J.-H.K. performed the transcriptome analysis. M.-J.J., Y.-S.P., H.J.C. and M.-S.K. performed the resequencing analysis. D.Y.K., H.J.C., M.-J.J., S.-J.K. and S.-H.K. performed PAV and ASE validation. H.J.C. and E.-K.B. performed protein ...
Our toolchain, which consists of additions to the VG toolkit and a standalone tool, RPVG, can construct spliced pangenome graphs, map RNA sequencing data to these graphs, and perform haplotype-aware expression quantification of transcripts in a pantranscriptome. We show that this workflow improves...
Here, we present a diploid-aware assembly of the wheat stripe rust fungusPuccinia striiformisf. sp.triticibased on long reads using the FALCON-Unzip assembler. Transcriptome sequencing data sets were used to infer high-quality gene models and identify virulence genes involved in plant infection ...
RNA-seq reads from six tissues (root, stem, flower, bud, young leaves and mature leaves) were generated using three biological replicates. RNA-seq reads were trimmed using the Trimmomatic56program and mapped against allele-aware annotated gene models using Bowtie57with only the best alignment ret...
Transcriptome analysis was performed to identify differentially expressed genes (DEGs) in ginger rhizomes at five developmental stages, as well as in the roots and stems. A total of 6690 genes were significantly downregulated in ginger rhizomes from Rh1 to Rh5, whereas 773 genes were upregulated ...
Building an octaploid genome and transcriptome of the medicinal plant Pogostemon cablin from Lamiales. Data 5, 180274 (2018). CAS Google Scholar He, Y. et al. Survey of the genome of Pogostemon cablin provides insights into its evolutionary history and sesquiterpenoid biosynthesis. Sci. Rep. ...
BLASTn and tBLASTx from BLAST v2.2.28+ 60 were used to map the transcriptome assembly to the genome; BLASTx was used to map protein sequences to the genome (protein models from 5 species: Musa acuminate61, Oryza sativa62, Elaeis guineensis63, Phalaenopsis equestris64, Ananas comosus65) ...