ArticleHeredity2015
Whole-genome re-sequencing of non-model organisms: lessons from unmapped reads.
Article in Heredity, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
23 citing papers in PubMed, 44 citations in OpenAlex.
- SwarmGenomics: A Unified Pipeline for Individual-Based Whole-Genome Analyses.Molecular ecology resources · 2026Article
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- Resequencing of 410 Sesame Accessions Identifies SINST1 as the Major Underlying Gene for Lignans Variation.International journal of molecular sciences · 2023Article
- Whole-Genome Sequencing Reveals Age-Specific Changes in the Human Blood Microbiota.Journal of personalized medicine · 2022Article
- Genome-wide SNP identification inEcology and evolution · 2021Article
- Adaptive markers distinguish North and South Pacific Albacore amid low population differentiation.Evolutionary applications · 2021Article
- Humic-acid-driven escape from eye parasites revealed by RNA-seq and target-specific metabarcoding.Parasites & vectors · 2020Article
- CAFU: a Galaxy framework for exploring unmapped RNA-Seq data.Briefings in bioinformatics · 2020Article
- Article
- Article
- Contemporary Demographic Reconstruction Methods Are Robust to Genome Assembly Quality: A Case Study in Tasmanian Devils.Molecular biology and evolution · 2019Article
- Exploring the unmapped DNA and RNA reads in a songbird genome.BMC genomics · 2019Article
- Multi-scale characterization of symbiont diversity in the pea aphid complex through metagenomic approaches.Microbiome · 2018Article
- Restriction associated DNA-genotyping at multiple spatial scales in Arabidopsis lyrata reveals signatures of pathogen-mediated selection.BMC genomics · 2018Article
- MetaMap: an atlas of metatranscriptomic reads in human disease-related RNA-seq data.GigaScience · 2018Article
- Disentangling the Causes for Faster-X Evolution in Aphids.Genome biology and evolution · 2018Article
- Bacterial Genetic Architecture of Ecological Interactions in Co-culture by GWAS-TakingFrontiers in microbiology · 2017Article
- Lessons for livestock genomics from genome and transcriptome sequencing in cattle and other mammals.Genetics, selection, evolution : GSE · 2016Article
- New Insights into the Genetic Diversity of Clostridium botulinum Group III through Extensive Genome Exploration.Frontiers in microbiology · 2016Article
- What's in your next-generation sequence data? An exploration of unmapped DNA and RNA sequence reads from the bovine reference individual.BMC genomics · 2015Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Unmapped reads are often discarded from the analysis of whole-genome re-sequencing, but new biological information and insights can be uncovered through their analysis. In this paper, we investigate unmapped reads from the re-sequencing data of 33 pea aphid genomes from individuals specialized on different host plants. The unmapped reads for each individual were retrieved following mapping to the Acyrthosiphon pisum reference genome and its mitochondrial and symbiont genomes. These sets of unmapped reads were then cross-compared, revealing that a significant number of these unmapped sequences were conserved across individuals. Interestingly, sequences were most commonly shared between individuals adapted to the same host plant, suggesting that these sequences may contribute to the divergence between host plant specialized biotypes. Analysis of the contigs obtained from assembling the unmapped reads pooled by biotype allowed us to recover some divergent genomic regions previously excluded from analysis and to discover putative novel sequences of A. pisum and its symbionts. In conclusion, this study emphasizes the interest of the unmapped component of re-sequencing data sets and the potential loss of important information. We here propose strategies to aid the capture and interpretation of this information.
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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.