ArticlePloS one2013
Evaluation of assembly strategies using RNA-seq data associated with grain development of wheat (Triticum aestivum L.).
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers, 1 of them a synthesis that pooled it.
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Who cites it
19 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Pooled it
- Moving beyond species: fungal function in house dust provides novel targets for potential indicators of mold growth in homes.Microbiome · 2024Article
- A bird's-eye view: exploration of the flavin-containing monooxygenase superfamily in common wheat.Frontiers in plant science · 2024Article
- QTL cluster analysis and marker development for kernel traits based on DArT markers in spring bread wheat (Frontiers in plant science · 2023Article
- Meta-analysis reveals consensus genomic regions associated with multiple disease resistance in wheat (Molecular breeding : new strategies in plant improvement · 2022Article
- Dynamic transcriptome analysis suggests the key genes regulating seed development and filling in Tartary buckwheat (Frontiers in genetics · 2022Article
- De Novo Transcriptome Assembly, Functional Annotation, and Transcriptome Dynamics Analyses Reveal Stress Tolerance Genes in Mangrove Tree (International journal of molecular sciences · 2021Article
- Combining independent de novo assemblies to optimize leaf transcriptome of Persian walnut.PloS one · 2020Article
- Transcriptome Analysis Reveals Key Seed-Development Genes in Common Buckwheat (International journal of molecular sciences · 2019Article
- Serpins: Genome-Wide Characterisation and Expression Analysis of the Serine Protease Inhibitor Family inG3 (Bethesda, Md.) · 2019Article
- Article
- De novo assembly of wheat root transcriptomes and transcriptional signature of longitudinal differentiation.PloS one · 2018Article
- Transcriptomic Analysis Reveal the Molecular Mechanisms of Wheat Higher-Temperature Seedling-Plant Resistance toFrontiers in plant science · 2018Article
- De novo assembly, functional annotation, and analysis of the giant reed (Biotechnology for biofuels · 2017Article
- Pattern of Protein Expression in Developing Wheat Grains Identified through Proteomic Analysis.Frontiers in plant science · 2017Article
- expVIP: a Customizable RNA-seq Data Analysis and Visualization Platform.Plant physiology · 2016Article
- Selecting Superior De Novo Transcriptome Assemblies: Lessons Learned by Leveraging the Best Plant Genome.PloS one · 2016Article
- Single-molecule real-time transcript sequencing facilitates common wheat genome annotation and grain transcriptome research.BMC genomics · 2015Article
- Global Gene Expression of Kosteletzkya virginica Seedlings Responding to Salt Stress.PloS one · 2015Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Wheat (Triticum aestivum L.) is one of the most important crops cultivated worldwide. Identifying the complete transcriptome of wheat grain could serve as foundation for further study of wheat seed development. However, the relatively large size and the polyploid complexity of the genome have been substantial barriers to molecular genetics and transcriptome analysis of wheat. Alternatively, RNA sequencing has provided some useful information about wheat genes. However, because of the large number of short reads generated by RNA sequencing, factors that are crucial to transcriptome assembly, including software, candidate parameters and assembly strategies, need to be optimized and evaluated for wheat data. In the present study, four cDNA libraries associated with wheat grain development were constructed and sequenced. A total of 14.17 Gb of high-quality reads were obtained and used to assess different assembly strategies. The most successful approach was to filter the reads with Q30 prior to de novo assembly using Trinity, merge the assembled contigs with genes available in wheat cDNA reference data sets, and combine the resulting assembly with an assembly from a reference-based strategy. Using this approach, a relatively accurate and nearly complete transcriptome associated with wheat grain development was obtained, suggesting that this is an effective strategy for generation of a high-quality transcriptome from RNA sequencing data.
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