ArticleG3 (Bethesda, Md.)2013
Allele identification for transcriptome-based population genomics in the invasive plant Centaurea solstitialis.
Article in G3 (Bethesda, Md.), 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 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
19 citing papers in PubMed, 52 citations in OpenAlex.
- Extremely Fine-Scale Soil Heterogeneity in a Rare Serpentine Endemic Plant Shape Patterns of Genetic Diversity.Ecology and evolution · 2026Article
- Transcriptome analysis identifies genes regulating self-compatibility, flowering time, and oil biosynthesis in Noug (Guizotia abyssinica).Scientific reports · 2025Article
- Genome size variation and evolution during invasive range expansion in an introduced plant.Evolutionary applications · 2024Article
- Can functional genomic diversity provide novel insights into mechanisms of community assembly? A pilot study from an invaded alpine streambed.Ecology and evolution · 2021Article
- Pilot RNA-seq data from 24 species of vascular plants at Harvard Forest.Applications in plant sciences · 2021Article
- TagSeq for gene expression in non-model plants: A pilot study at the Santa Rita Experimental Range NEON core site.Applications in plant sciences · 2020Article
- Multiple introductions and population structure during the rapid expansion of the invasive Sahara mustard (Ecology and evolution · 2019Article
- Expansion history and environmental suitability shape effective population size in a plant invasion.Molecular ecology · 2019Article
- Potential limits to the benefits of admixture during biological invasion.Molecular ecology · 2019Article
- Gall Wasp Transcriptomes Unravel Potential Effectors Involved in Molecular Dialogues With Oak and Rose.Frontiers in physiology · 2019Article
- A de novo transcriptome assembly of the zebra bullhead shark, Heterodontus zebra.Scientific data · 2018Article
- Comparative Transcriptomic Analysis of Two Actinorhizal Plants and the LegumeFrontiers in plant science · 2018Article
- Interacting amino acid replacements allow poison frogs to evolve epibatidine resistance.Science (New York, N.Y.) · 2017Article
- Population genomic analyses reveal a history of range expansion and trait evolution across the native and invaded range of yellow starthistle (Centaurea solstitialis).Molecular ecology · 2017Article
- Extensive analysis of native and non-nativePeerJ · 2017Article
- Early genome duplications in conifers and other seed plants.Science advances · 2015Article
- Transcriptome sequencing and De Novo analysis of Youngia japonica using the illumina platform.PloS one · 2014Article
- Dispersal pathways and genetic differentiation among worldwide populations of the invasive weed Centaurea solstitialis L. (Asteraceae).PloS one · 2014Article
- Invasive and non-invasive congeners show similar trait shifts between their same native and non-native ranges.PloS one · 2013Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transcriptome sequences are becoming more broadly available for multiple individuals of the same species, providing opportunities to derive population genomic information from these datasets. Using the 454 Life Science Genome Sequencer FLX and FLX-Titanium next-generation platforms, we generated 11-430 Mbp of sequence for normalized cDNA for 40 wild genotypes of the invasive plant Centaurea solstitialis, yellow starthistle, from across its worldwide distribution. We examined the impact of sequencing effort on transcriptome recovery and overlap among individuals. To do this, we developed two novel publicly available software pipelines: SnoWhite for read cleaning before assembly, and AllelePipe for clustering of loci and allele identification in assembled datasets with or without a reference genome. AllelePipe is designed specifically for cases in which read depth information is not appropriate or available to assist with disentangling closely related paralogs from allelic variation, as in transcriptome or previously assembled libraries. We find that modest applications of sequencing effort recover most of the novel sequences present in the transcriptome of this species, including single-copy loci and a representative distribution of functional groups. In contrast, the coverage of variable sites, observation of heterozygosity, and overlap among different libraries are all highly dependent on sequencing effort. Nevertheless, the information gained from overlapping regions was informative regarding coarse population structure and variation across our small number of population samples, providing the first genetic evidence in support of hypothesized invasion scenarios.
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.