ArticleBMC genomics2015
Optimal assembly strategies of transcriptome related to ploidies of eukaryotic organisms.
Article in BMC genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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24 citing papers in PubMed, 35 citations in OpenAlex.
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- Integrative Analysis of the Ethanol Tolerance ofInternational journal of molecular sciences · 2023Article
- Normalized Workflow to Optimize Hybrid De Novo Transcriptome Assembly for Non-Model Species: A Case Study inPlants (Basel, Switzerland) · 2022Article
- Phased small RNA-mediated systemic signaling in plants.Science advances · 2022Article
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- Computational screening of miRNAs and their targets in saffron (Crocus sativus L.) by transcriptome mining.Planta · 2021Article
- Comparing de novo transcriptome assembly tools in di- and autotetraploid non-model plant species.BMC bioinformatics · 2021Article
- Combining independent de novo assemblies to optimize leaf transcriptome of Persian walnut.PloS one · 2020Article
- Comparative Analysis of Strategies forHigh-throughput · 2019Article
- Transcriptome Landscape Variation in the GenusGenes · 2019Article
- Evaluating the Performance of De Novo Assembly Methods for Venom-Gland Transcriptomics.Toxins · 2018Article
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- A genome-wide transcriptome map of pistachio (Pistacia vera L.) provides novel insights into salinity-related genes and marker discovery.BMC genomics · 2017Article
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- A survey of the complex transcriptome from the highly polyploid sugarcane genome using full-length isoform sequencing and de novo assembly from short read sequencing.BMC genomics · 2017Article
- Comparative Transcriptome Analysis Reveals Critical Function of Sucrose Metabolism Related-Enzymes in Starch Accumulation in the Storage Root of Sweet Potato.Frontiers in plant science · 2017Article
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- De novo assembly, functional annotation, and analysis of the giant reed (Biotechnology for biofuels · 2017Article
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Corrections and comments
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Authors and funding
7 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundSeveral de novo transcriptome assemblers have been developed recently to assemble the short reads generated from the next-generation sequencing platforms and different strategies were employed for assembling transcriptomes of various eukaryotes without genome sequences. Though there are some comparisons among these de novo assembly tools for assembling transcriptomes of different eukaryotic organisms, there is no report about the relationship between assembly strategies and ploidies of the organisms.
resultsWhen we de novo assembled transcriptomes of sweet potato (hexaploid), Trametes gallica (a diploid fungus), Oryza meyeriana (a diploid wild rice), five assemblers, including Edena, Oases, Soaptrans, IDBA-tran and Trinity, were used in different strategies (Single-Assembler Single-Parameter, SASP; Single-Assembler Multiple-Parameters, SAMP; Combined De novo Transcriptome Assembly, CDTA, that is multiple assembler multiple parameter). It was found that CDTA strategy has the best performance compared with other two strategies for assembling transcriptome of the hexaploid sweet potato, whereas SAMP strategy with assembler Oases is better than other strategies for assembling transcriptomes of diploid fungus and the wild rice transcriptomes.
conclusionBased on the results from ours and others, it is suggested that CDTA strategy is better used for transcriptome assembly of polyploidy organisms and SAMP strategy of Oases is outperformed for those diploid organisms without genome sequences.
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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.