ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2019
The complexity of alternative splicing and landscape of tissue-specific expression in lotus (Nelumbo nucifera) unveiled by Illumina- and single-molecule real-time-based RNA-sequencing.
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed, 38 citations in OpenAlex.
- 6mA DNA Methylation on Genes in Plants Is Associated with Gene Complexity, Expression and Duplication.Plants (Basel, Switzerland) · 2023Article
- Expression inheritance and constraints on cis- and trans-regulatory mutations underlying lotus color variation.Plant physiology · 2023Article
- Evolution of isoform-level gene expression patterns across tissues during lotus species divergence.The Plant journal : for cell and molecular biology · 2022Article
- Genome-wide identification and functional analysis of circRNAs in Trichophyton rubrum conidial and mycelial stages.BMC genomics · 2022Article
- Full-length transcriptome analysis and identification of transcript structures in Eimeria necatrix from different developmental stages by single-molecule real-time sequencing.Parasites & vectors · 2021Article
- Long-read RNA sequencing reveals widespread sex-specific alternative splicing in threespine stickleback fish.Genome research · 2021Article
- Biased allelic expression in tissues of F1 hybrids between tropical and temperate lotus (Nelumbo nuicfera).Plant molecular biology · 2021Article
- Nelumbo genome database, an integrative resource for gene expression and variants of Nelumbo nucifera.Scientific data · 2021Article
- Genome-wide identification of MADS-box gene family in sacred lotus (Nelumbo nucifera) identifies a SEPALLATA homolog gene involved in floral development.BMC plant biology · 2020Article
- SMRT and Illumina RNA sequencing reveal novel insights into the heat stress response and crosstalk with leaf senescence in tall fescue.BMC plant biology · 2020Article
- Integrated Omics Analyses Identify Key Pathways Involved in Petiole Rigidity Formation in Sacred Lotus.International journal of molecular sciences · 2020Article
- PacBio single molecule long-read sequencing provides insight into the complexity and diversity of the Pinctada fucata martensii transcriptome.BMC genomics · 2020Article
- Integrative expression network analysis of microRNA and gene isoforms in sacred lotus.BMC genomics · 2020Article
- Characterization and Analysis of the Full-Length Transcriptomes of Multiple Organs inInternational journal of molecular sciences · 2020Article
- Alternative Splicing Enhances the Transcriptome Complexity ofFrontiers in plant science · 2020Article
- The Latest Studies on Lotus (International journal of molecular sciences · 2019Review
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Alternative splicing (AS) plays a critical role in regulating different physiological and developmental processes in eukaryotes, by dramatically increasing the diversity of the transcriptome and the proteome. However, the saturation and complexity of AS remain unclear in lotus due to its limitation of rare obtainment of full-length multiple-splice isoforms. In this study, we apply a hybrid assembly strategy by combining single-molecule real-time sequencing and Illumina RNA-seq to get a comprehensive insight into the lotus transcriptomic landscape. We identified 211,802 high-quality full-length non-chimeric reads, with 192,690 non-redundant isoforms, and updated the lotus reference gene model. Moreover, our analysis identified a total of 104,288 AS events from 16,543 genes, with alternative 3' splice-site being the predominant model, following by intron retention. By exploring tissue datasets, 370 tissue-specific AS events were identified among 12 tissues. Both the tissue-specific genes and isoforms might play important roles in tissue or organ development, and are suitable for 'ABCE' model partly in floral tissues. A large number of AS events and isoform variants identified in our study enhance the understanding of transcriptional diversity in lotus, and provide valuable resource for further functional genomic studies.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.