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...
2 Probabilistic model of gene expression and allele counts from transcriptome sequencing experiments. cm, number of maternal chromosome copies. cp, number of paternal chromosome copies. λi, observed gene expression magnitude of gene i. \(\lambda _i^ \ast\), reference gene expression magnitude of...
Inbred animals were historically chosen for genome analysis to circumvent assembly issues caused by haplotype variation but this resulted in a composite of the two genomes. Here we report a haplotype-aware scaffolding and polishing pipeline which was used to create haplotype-resolved, chromosome-level ...
Haplotype-aware de novo assembly. Collapsed assembly approaches identify sequence variants on a consensus assembly and subsequently phase these variants into haplotypes using chromosome-scale data (Hi-C). Semi-collapsed approaches follow a similar approach, but after phasing, variants in the initial asse...
only 54% were present in all four haplotypes with an average of 3.2 copies per gene. Taking the leaf transcriptome as an example, 11% of the genes were differently expressed in at least one haplotype, where 25% of them were likely regulated through allele-specific DNA methylation. Our work...
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 ...
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...
After repetitive sequence masking, we used the Augustus59ab initio gene finder to identify gene models. BLASTn and tBLASTx from BLAST v2.2.28+ 60were used to map the transcriptome assembly to the genome; BLASTx was used to map protein sequences to the genome (protein models from 5 specie...
constructing maximum likelihood tree based on transcriptome data and remapping whole genome sequence reads to the assembled genome50,51(Supplementary Fig.30, Supplementary Table14), there was no possible progenitor was found. As we do not know whether IPIPIIPIIPis extant, it is impossible for us ...
To reduce the economic and biodiversity losses caused by the RPW, there has been growing interest to identify RPW genes that can be used to guide strategies for pest management in this species. Previous gene discovery efforts for the RPW have mainly relied on transcriptome data, using different...