ArticleMolecular ecology resources2016
Optimization of next-generation sequencing transcriptome annotation for species lacking sequenced genomes.
Article in Molecular ecology resources, 2016. 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, 27 citations in OpenAlex.
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- Phosphorus availability and planting patterns regulate soil microbial effects on plant performance in a semiarid steppe.Annals of botany · 2023Article
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- De novo characterization of placental transcriptome in the Eurasian beaver (Castor fiber L.).Functional & integrative genomics · 2019Article
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- Neural Circuits Underlying Rodent Sociality: A Comparative Approach.Current topics in behavioral neurosciences · 2019Article
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- De novo transcriptome assembly, annotation and comparison of four ecological and evolutionary model salmonid fish species.BMC genomics · 2018Article
- Illumina-based de novo transcriptome sequencing and analysis of Chinese forest musk deer.Journal of genetics · 2017Article
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- Pre- and Post-Natal Stress Programming: Developmental Exposure to Glucocorticoids Causes Long-Term Brain-Region Specific Changes to Transcriptome in the Precocial Japanese Quail.Journal of neuroendocrinology · 2016Article
- Insights into the Sesquiterpenoid Pathway by Metabolic Profiling andFrontiers in plant science · 2016Article
Corrections and comments
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Authors and funding
9 authors at 4 institutions in 2 countries.
Funding
Abstract
Next-generation sequencing methods, such as RNA-seq, have permitted the exploration of gene expression in a range of organisms which have been studied in ecological contexts but lack a sequenced genome. However, the efficacy and accuracy of RNA-seq annotation methods using reference genomes from related species have yet to be robustly characterized. Here we conduct a comprehensive power analysis employing RNA-seq data from Drosophila melanogaster in conjunction with 11 additional genomes from related Drosophila species to compare annotation methods and quantify the impact of evolutionary divergence between transcriptome and the reference genome. Our analyses demonstrate that, regardless of the level of sequence divergence, direct genome mapping (DGM), where transcript short reads are aligned directly to the reference genome, significantly outperforms the widely used de novo and guided assembly-based methods in both the quantity and accuracy of gene detection. Our analysis also reveals that DGM recovers a more representative profile of Gene Ontology functional categories, which are often used to interpret emergent patterns in genomewide expression analyses. Lastly, analysis of available primate RNA-seq data demonstrates the applicability of our observations across diverse taxa. Our quantification of annotation accuracy and reduced gene detection associated with sequence divergence thus provides empirically derived guidelines for the design of future gene expression studies in species without sequenced genomes.
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Registered trials
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.