ArticlePloS one2015
Are differences in genomic data sets due to true biological variants or errors in genome assembly: an example from two chloroplast genomes.
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
33 citing papers in PubMed.
- Towards whole plastome phylogeography: resolving small genetic distances among European Arnica montana L. with the PlastidPipeline.Scientific reports · 2026Article
- Comparative and phylogenetic analysis of chloroplast genomes in the subtribe Leptoboeinae (Gesneriaceae).Frontiers in plant science · 2026Article
- Dissecting mitogenomic conflict to illuminate angiosperm deep phylogeny: Sequence and architectural evidence.Plant diversity · 2026Article
- The Complete Chloroplast Genome and the Phylogenetic Analysis ofInternational journal of molecular sciences · 2025Article
- Variation of and associations with the depth and evenness of sequencing coverage in archived plastid genomes.Scientific reports · 2025Article
- Variation of and associations with the depth and evenness of sequencing coverage in archived plastid genomes.Research square · 2025Article
- The Complete Chloroplast Genome and the Phylogenetic Analysis ofInternational journal of molecular sciences · 2025Article
- Comparative plastome genomics, taxonomic delimitation and evolutionary divergences of Tetraena hamiensis var. qatarensis and Tetraena simplex (Zygophyllaceae).Scientific reports · 2023Article
- Comparative Analysis of Whole Chloroplast Genomes of Three Common Species ofInternational journal of molecular sciences · 2022Article
- Software Choice and Sequencing Coverage Can Impact Plastid Genome Assembly-A Case Study in the Narrow EndemicFrontiers in plant science · 2022Article
- Chloroplast genomes in Populus (Salicaceae): comparisons from an intensively sampled genus reveal dynamic patterns of evolution.Scientific reports · 2021Article
- Comparative chloroplast genomes and phylogenetic analysis ofApplications in plant sciences · 2021Article
- Mangrove tree (Avicennia marina): insight into chloroplast genome evolutionary divergence and its comparison with related species from family Acanthaceae.Scientific reports · 2021Article
- Comparative Analyses of Five Complete Chloroplast Genomes from the GenusInternational journal of molecular sciences · 2020Article
- PACVr: plastome assembly coverage visualization in R.BMC bioinformatics · 2020Article
- Expanded inverted repeat region with large scale inversion in the first complete plastid genome sequence of Plantago ovata.Scientific reports · 2020Article
- Comparative Chloroplast Genomics of EndangeredPlants (Basel, Switzerland) · 2020Article
- Comparative analyses of chloroplast genomes from 22 Lythraceae species: inferences for phylogenetic relationships and genome evolution within Myrtales.BMC plant biology · 2019Article
- Article
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA sequencing has been revolutionized by the development of high-throughput sequencing technologies. Plummeting costs and the massive throughput capacities of second and third generation sequencing platforms have transformed many fields of biological research. Concurrently, new data processing pipelines made rapid de novo genome assemblies possible. However, high quality data are critically important for all investigations in the genomic era. We used chloroplast genomes of one Oryza species (O. australiensis) to compare differences in sequence quality: one genome (GU592209) was obtained through Illumina sequencing and reference-guided assembly and the other genome (KJ830774) was obtained via target enrichment libraries and shotgun sequencing. Based on the whole genome alignment, GU592209 was more similar to the reference genome (O. sativa: AY522330) with 99.2% sequence identity (SI value) compared with the 98.8% SI values in the KJ830774 genome; whereas the opposite result was obtained when the SI values in coding and noncoding regions of GU592209 and KJ830774 were compared. Additionally, the junctions of two single copies and repeat copies in the chloroplast genome exhibited differences. Phylogenetic analyses were conducted using these sequences, and the different data sets yielded dissimilar topologies: phylogenetic replacements of the two individuals were remarkably different based on whole genome sequencing or SNP data and insertions and deletions (indels) data. Thus, we concluded that the genomic composition of GU592209 was heterogeneous in coding and non-coding regions. These findings should impel biologists to carefully consider the quality of sequencing and assembly when working with next-generation data.
Indexed as
Identifiers
What OpenQuestion holds
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.