ArticleBiotechnology for biofuels2018
Revealing the transcriptomic complexity of switchgrass by PacBio long-read sequencing.
Article in Biotechnology for biofuels, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Lactococcus lactis NZ3900/pNZ8149-ChIL-4-ChIL-2 alleviates compound stress in chicks via reshaping immune homeostasis, gut microbiota and intestinal health.Poultry science · 2026Article
- PotatoRTD and TomatoRTD: Comprehensive Reference Transcript Datasets for Accurate Transcriptome Analysis and Isoform Discovery.Scientific data · 2026Article
- Characterization and analysis of the full-length transcriptome of Frankliniella occidentalis (Thysanoptera: Thripidae).BMC genomics · 2026Article
- New insights into the cold tolerance of upland switchgrass by integrating a haplotype-resolved genome and multi-omics analysis.Genome biology · 2025Article
- A species-level identification pipeline for human gut microbiota based on the V3-V4 regions of 16S rRNA.Frontiers in microbiology · 2025Article
- PacBio single-molecule long-read sequencing provides new insights into the complexity of full-length transcripts in oriental river prawn, macrobrachium nipponense.BMC genomics · 2023Article
- Full-length transcriptome profiling ofHeliyon · 2023Article
- Article
- Full-Length RNA Sequencing Provides Insights into Goldfish Evolution under Artificial Selection.International journal of molecular sciences · 2023Article
- A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis.Genome biology · 2022Article
- Unveiling the Complexity of Red Clover (International journal of molecular sciences · 2021Article
- Unveiling the transcriptomic complexity of Miscanthus sinensis using a combination of PacBio long read- and Illumina short read sequencing platforms.BMC genomics · 2021Article
- Comparative Analysis of PacBio and Oxford Nanopore Sequencing Technologies for Transcriptomic Landscape Identification ofLife (Basel, Switzerland) · 2021Article
- Transcriptomic resources for prairie grass (Bromus catharticus): expressed transcripts, tissue-specific genes, and identification and validation of EST-SSR markers.BMC plant biology · 2021Article
- Single-Molecule Long-Read Sequencing of Purslane (Plants (Basel, Switzerland) · 2021Article
- Article
- PacBio Single-Molecule Long-Read Sequencing Provides New Light on the Complexity of Full-Length Transcripts in Cattle.Frontiers in genetics · 2021Article
- PacBio Single-Molecule Long-Read Sequencing Reveals Genes Tolerating Manganese Stress inFrontiers in genetics · 2021Article
- SMRT- and Illumina-based RNA-seq analyses unveil the ginsinoside biosynthesis and transcriptomic complexity in Panax notoginseng.Scientific reports · 2020Article
- PacBio single molecule long-read sequencing provides insight into the complexity and diversity of the Pinctada fucata martensii transcriptome.BMC genomics · 2020Article
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Authors and funding
14 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundSwitchgrass (
resultsWe present an analysis of transcriptomes of six switchgrass tissue types pooled together, sequenced using Pacific Biosciences (PacBio) single-molecular long-read technology. Our analysis identified 105,419 unique transcripts covering 43,570 known genes and 8795 previously unknown genes. 45,168 are novel transcripts of known genes. A total of 60,096 AS transcripts are identified, 45,628 being novel. We have also predicted 1549 transcripts of genes involved in cell wall construction and remodeling, 639 being novel transcripts of known cell wall genes. Most of the predicted transcripts are validated against Illumina-based short reads. Specifically, 96% of the splice junction sites in all the unique transcripts are validated by at least five Illumina reads. Comparisons between genes derived from our identified transcripts and the current genome annotation revealed that among the gene set predicted by both analyses, 16,640 have different exon-intron structures.
conclusionsOverall, substantial amount of new information is derived from the PacBio RNA data regarding both the transcriptome and the genome of switchgrass.
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