ArticleApplications in plant sciences2020
A two-tier bioinformatic pipeline to develop probes for target capture of nuclear loci with applications in Melastomataceae.
Article in Applications in plant sciences, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 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
18 citing papers in PubMed.
- Integrative utilization of genomic resources for improved phylogenetic resolution in Sonerileae (Melastomataceae).American journal of botany · 2026Article
- Evidence of introgression amid phylogenetic conflict in Brachyotum, a plant radiation from the Tropical Andes.American journal of botany · 2026Article
- Urticaceae542 as a novel probe set combining universal and lineage-specific loci for phylogenomics of Urticaceae.Scientific reports · 2025Article
- Artificial intelligence models for validating and predicting the impact of chemical priming of hydrogen peroxide (HPlant molecular biology · 2024Article
- A target Capture Probe Set Useful for Deep- and Shallow-Level Phylogenetic Studies in Cactaceae.Genes · 2022Article
- A New Approach Using Targeted Sequence Capture for Phylogenomic Studies across Cactaceae.Genes · 2022Article
- A Comprehensive Phylogenomic Platform for Exploring the Angiosperm Tree of Life.Systematic biology · 2022Article
- A nuclear target sequence capture probe set for phylogeny reconstruction of the charismatic plant family Bignoniaceae.Frontiers in genetics · 2022Article
- Lineage-specific vs. universal: A comparison of the Compositae1061 and Angiosperms353 enrichment panels in the sunflower family.Applications in plant sciences · 2021Article
- Exploring Angiosperms353: Developing and applying a universal toolkit for flowering plant phylogenomics.Applications in plant sciences · 2021Article
- Reconstructing Dipsacales phylogeny using Angiosperms353: issues and insights.American journal of botany · 2021Article
- Relative performance of customized and universal probe sets in target enrichment: A case study in subtribe Malinae.Applications in plant sciences · 2021Article
- A target enrichment probe set for resolving the flagellate land plant tree of life.Applications in plant sciences · 2021Article
- Enabling evolutionary studies at multiple scales in Apocynaceae through Hyb-Seq.Applications in plant sciences · 2020Article
- A two-tier bioinformatic pipeline to develop probes for target capture of nuclear loci with applications in Melastomataceae.Applications in plant sciences · 2020Article
- An updated and extended version of the Melastomataceae probe set for target capture.Applications in plant sciencesArticle
- A target enrichment probe set for resolving phylogenetic relationships in the coffee family, Rubiaceae.Applications in plant sciencesArticle
- Target capture and genome skimming for plant diversity studies.Applications in plant sciencesArticle
Corrections and comments
- Commented on by
Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
premisePutatively single-copy nuclear (SCN) loci, which are identified using genomic resources of closely related species, are ideal for phylogenomic inference. However, suitable genomic resources are not available for many clades, including Melastomataceae. We introduce a versatile approach to identify SCN loci for clades with few genomic resources and use it to develop probes for target enrichment in the distantly related
methodsWe present a two-tiered pipeline. First, we identified putatively SCN loci using MarkerMiner and transcriptomes from distantly related species in Melastomataceae. Published loci and genes of functional significance were then added (384 total loci). Second, using HybPiper, we retrieved 689 homologous template sequences for these loci using genome-skimming data from within the focal clades.
resultsWe sequenced 193 loci common to DISCUSSION: Our pipeline successfully identified and targeted SCN loci in
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.