ArticleBMC genomics2013
A comparison across non-model animals suggests an optimal sequencing depth for de novo transcriptome assembly.
Article in BMC genomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers, 2 of them syntheses that pooled it.
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Who cites it
53 citing papers in PubMed, 2 syntheses or guidelines pooled it, 105 citations in OpenAlex.
- A metaanalysis of bat phylogenetics and positive selection based on genomes and transcriptomes from 18 species.Proceedings of the National Academy of Sciences of the United States of America · 2019Pooled it
- Here We Are, But Where Do We Go? A Systematic Review of Crustacean Transcriptomic Studies from 2014-2015.Integrative and comparative biology · 2016Pooled it
- De novo assembly of plasmodium interspersed repeat (pir) genes from Plasmodium vivax RNAseq data suggests geographic conservation of sub-family transcription.BMC genomics · 2025Article
- De novo transcriptome assembly and differential gene expression analysis in different developmental stages of Agriotes sputator (click beetle).Scientific reports · 2024Article
- Identification of shared gene expression programs activated in multiple modes of torpor across vertebrate clades.Scientific reports · 2024Article
- Comprehensive Analysis of the Influence of Technical and Biological Variations on De Novo Assembly of RNA-Seq Datasets.Bioinformatics and biology insights · 2024Article
- A Practical Guide to Design and Assess a Phylogenomic Study.Genome biology and evolution · 2022Article
- Hidden diversity of Ctenophora revealed by new mitochondrial COI primers and sequences.Molecular ecology resources · 2022Article
- Comparative genomic and transcriptomic analyses of transposable elements in polychaetous annelids highlight LTR retrotransposon diversity and evolution.Mobile DNA · 2021Article
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- Biological rhythms in the deep-sea hydrothermal mussel Bathymodiolus azoricus.Nature communications · 2020Article
- Comparative Analysis of Strategies forHigh-throughput · 2019Article
- Optimal sequencing depth design for whole genome re-sequencing in pigs.BMC bioinformatics · 2019Article
- De novo transcriptomic analysis of gonad of Strongylocentrotus nudus and gene discovery for biosynthesis of polyunsaturated fatty acids.Genes & genomics · 2019Article
- Article
- Whole body transcriptomes and new insights into the biology of the tick Ixodes ricinus.Parasites & vectors · 2018Article
- AmpuBase: a transcriptome database for eight species of apple snails (Gastropoda: Ampullariidae).BMC genomics · 2018Article
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- The transcriptome of theAmerican journal of physiology. Renal physiology · 2017Article
Corrections and comments
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Authors and funding
6 authors at 4 institutions in 2 countries.
Funding
Abstract
backgroundThe lack of genomic resources can present challenges for studies of non-model organisms. Transcriptome sequencing offers an attractive method to gather information about genes and gene expression without the need for a reference genome. However, it is unclear what sequencing depth is adequate to assemble the transcriptome de novo for these purposes.
resultsWe assembled transcriptomes of animals from six different phyla (Annelids, Arthropods, Chordates, Cnidarians, Ctenophores, and Molluscs) at regular increments of reads using Velvet/Oases and Trinity to determine how read count affects the assembly. This included an assembly of mouse heart reads because we could compare those against the reference genome that is available. We found qualitative differences in the assemblies of whole-animals versus tissues. With increasing reads, whole-animal assemblies show rapid increase of transcripts and discovery of conserved genes, while single-tissue assemblies show a slower discovery of conserved genes though the assembled transcripts were often longer. A deeper examination of the mouse assemblies shows that with more reads, assembly errors become more frequent but such errors can be mitigated with more stringent assembly parameters.
conclusionsThese assembly trends suggest that representative assemblies are generated with as few as 20 million reads for tissue samples and 30 million reads for whole-animals for RNA-level coverage. These depths provide a good balance between coverage and noise. Beyond 60 million reads, the discovery of new genes is low and sequencing errors of highly-expressed genes are likely to accumulate. Finally, siphonophores (polymorphic Cnidarians) are an exception and possibly require alternate assembly strategies.
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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.