ArticleBMC genomics2019
PacBio single-molecule long-read sequencing shed new light on the complexity of the Carex breviculmis transcriptome.
Article in BMC genomics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Review
- Full-Length Transcriptomes Reconstruction Reveals Intraspecific Diversity in Hairy Vetch (Plants (Basel, Switzerland) · 2024Article
- 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
- Single-molecule long-read sequencing analysis improves genome annotation and sheds new light on the transcripts and splice isoforms of Zoysia japonica.BMC plant biology · 2022Article
- Combination analysis of single-molecule long-read and Illumina sequencing provides insights into the anthocyanin accumulation mechanism in an ornamental grass, Pennisetum setaceum cv. Rubrum.Plant molecular biology · 2022Article
- Seed Germination Mechanism ofFrontiers in plant science · 2022Article
- Integrative Analysis of Long- and Short-Read Transcriptomes Identify the Regulation of Terpenoids Biosynthesis Under Shading Cultivation inFrontiers in genetics · 2022Article
- Full-length transcriptome sequencing analysis and characterization, development and validation of microsatellite markers inFrontiers in plant science · 2022Article
- Identification of long non-coding RNAs involved in floral scent ofFrontiers in plant science · 2022Article
- Alternative RNA splicing in stem cells and cancer stem cells: Importance of transcript-based expression analysis.World journal of stem cells · 2021Review
- The development of SSR markers based on RNA-sequencing and its validation between and within Carex L. species.BMC plant biology · 2021Article
- The landscape of lncRNAs in Cydia pomonella provides insights into their signatures and potential roles in transcriptional regulation.BMC genomics · 2021Article
- Organ-Specific Transcriptome Analysis Identifies Candidate Genes Involved in the Stem Specialization of Bermudagrass (Frontiers in genetics · 2021Article
- Research Progress on Plant Long Non-Coding RNA.Plants (Basel, Switzerland) · 2020Review
- Full Transcriptome Analysis of Callus Suspension Culture System ofFrontiers in genetics · 2020Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
backgroundCarex L., a grass genus commonly known as sedges, is distributed worldwide and contributes constructively to turf management, forage production, and ecological conservation. The development of next-generation sequencing (NGS) technologies has considerably improved our understanding of transcriptome complexity of Carex L. and provided a valuable genetic reference. However, the current transcriptome is not satisfactory mainly because of the enormous difficulty in obtaining full-length transcripts.
resultsIn this study, we employed PacBio single-molecule long-read sequencing (SMRT) technology for whole-transcriptome profiling in Carex breviculmis. We generated 60,353 high-confidence non-redundant transcripts with an average length of 2302-bp. A total of 3588 alternative splicing events, and 1273 long non-coding RNAs were identified. Furthermore, 40,347 complete coding sequences were predicted, providing an informative reference transcriptome. In addition, the transcriptional regulation mechanism of C. breviculmis in response to shade stress was further explored by mapping the NGS data to the reference transcriptome constructed by SMRT sequencing.
conclusionsThis study provided a full-length reference transcriptome of C. breviculmis using the SMRT sequencing method for the first time. The transcriptome atlas obtained will not only facilitate future functional genomics studies but also pave the way for further selective and genic engineering breeding projects for C. breviculmis.
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