ArticlePloS one2015
RNA-Seq Uncovers SNPs and Alternative Splicing Events in Asian Lotus (Nelumbo nucifera).
Article in PloS one, 2015. 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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Who cites it
16 citing papers in PubMed.
- Studies on Lotus Genomics and the Contribution to Its Breeding.International journal of molecular sciences · 2022Review
- Transcription Analysis of RecombinantJournal of microbiology and biotechnology · 2020Article
- Integrated Omics Analyses Identify Key Pathways Involved in Petiole Rigidity Formation in Sacred Lotus.International journal of molecular sciences · 2020Article
- 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.DNA research : an international journal for rapid publication of reports on genes and genomes · 2019Article
- The Latest Studies on Lotus (International journal of molecular sciences · 2019Review
- Alternative splicing and translation play important roles in hypoxic germination in rice.Journal of experimental botany · 2019Article
- Integrated Analysis of LncRNA-mRNA Coexpression in the Extracellular Matrix of Developing Deciduous Teeth in Miniature Pigs.BioMed research international · 2019Article
- Transcriptomic analysis identifies the key genes involved in stamen petaloid in lotus (Nelumbo nucifera).BMC genomics · 2018Article
- Gene-based SNP identification and validation in soybean using next-generation transcriptome sequencing.Molecular genetics and genomics : MGG · 2018Article
- Comparative genomics and transcriptome analysis of Lactobacillus rhamnosus ATCC 11443 and the mutant strain SCT-10-10-60 with enhanced L-lactic acid production capacity.Molecular genetics and genomics : MGG · 2018Article
- ACE: an efficient and sensitive tool to detect insecticide resistance-associated mutations in insect acetylcholinesterase from RNA-Seq data.BMC bioinformatics · 2017Article
- Small RNA and degradome profiling reveals miRNA regulation in the seed germination of ancient eudicot Nelumbo nucifera.BMC genomics · 2016Article
- Metabolomic and Proteomic Profiles Reveal the Dynamics of Primary Metabolism during Seed Development of Lotus (Nelumbo nucifera).Frontiers in plant science · 2016Article
- Development and characterization of polymorphic microRNA-based microsatellite markers in Nelumbo nucifera (Nelumbonaceae).Applications in plant sciences · 2016Article
- Article
- Cracking the Code of Human Diseases Using Next-Generation Sequencing: Applications, Challenges, and Perspectives.BioMed research international · 2015Review
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
RNA-Seq is an efficient way to comprehensively identify single nucleotide polymorphisms (SNPs) and alternative splicing (AS) events from the expressed genes. In this study, we conducted transcriptome sequencing of four Asian lotus (Nelumbo nucifera) cultivars using Illumina HiSeq2000 platform to identify SNPs and AS events in lotus. A total of 505 million pair-end RNA-Seq reads were generated from four cultivars, of which 86% were mapped to the lotus reference genome. Using the four sets of data together, a total of 357,689 putative SNPs were identified with an average density of one SNP per 2.2 kb. These SNPs were located in 1,253 scaffolds and 15,016 expressed genes. A/G and C/T were the two major types of SNPs in the Asian lotus transcriptome. In parallel, a total of 177,540 AS events were detected in the four cultivars and were distributed in 64% of the expressed genes of lotus. The predominant type of AS events was alternative 5' first exon, which accounted for 41.2% of all the observed AS events, and exon skipping only accounted for 4.3% of all AS. Gene Ontology analysis was conducted to analyze the function of the genes containing SNPs and AS events. Validation of selected SNPs and AS events revealed that 74% of SNPs and 80% of AS events were reliable, which indicates that RNA-Seq is an efficient approach to uncover gene-associated SNPs and AS events. A large number of SNPs and AS events identified in our study will facilitate further genetic and functional genomics research in lotus.
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