ArticleApplications in plant sciences2015
MarkerMiner 1.0: A new application for phylogenetic marker development using angiosperm transcriptomes.
Article in Applications in plant sciences, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 62 papers.
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Who cites it
62 citing papers in PubMed.
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- Enrichment Probe Sets Combining Universal and Lineage-Specific Targets Help Resolve Recalcitrant Lineages.Molecular ecology resources · 2026Article
- Evolutionary history of Australian samphires (Salicornieae, Amaranthaceae).Annals of botany · 2026Article
- Urticaceae542 as a novel probe set combining universal and lineage-specific loci for phylogenomics of Urticaceae.Scientific reports · 2025Article
- Ortho2Web: a workflow for disentangling the roles of hybridization and allopolyploidization in reticulation within Campanulaceae.BMC biology · 2025Article
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- Specimen Identification Through Multilocus Species Tree Constructed From Single-Copy Orthologs (SCOs): A Case Study inEcology and evolution · 2025Article
- PhytoKeys · 2025Article
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- Phylogenomic insights into NeotropicalHeliyon · 2024Article
- Pseudomolecule-scale genome assemblies of Drepanocaryum sewerzowii and Marmoritis complanata.G3 (Bethesda, Md.) · 2024Article
- Shifts in evolutionary lability underlie independent gains and losses of root-nodule symbiosis in a single clade of plants.Nature communications · 2024Article
- Divergence and reticulation in the Mexican white oaks: ecological and phylogenomic evidence on species limits and phylogenetic networks in the Quercus laeta complex (Fagaceae).Annals of botany · 2024Article
- UPrimer: A Clade-Specific Primer Design Program Based on Nested-PCR Strategy and Its Applications in Amplicon Capture Phylogenomics.Molecular biology and evolution · 2023Article
- A New Approach Using Targeted Sequence Capture for Phylogenomic Studies across Cactaceae.Genes · 2022Article
- A nuclear target sequence capture probe set for phylogeny reconstruction of the charismatic plant family Bignoniaceae.Frontiers in genetics · 2022Article
- A pipeline for assembling low copy nuclear markers from plant genome skimming data for phylogenetic use.PeerJ · 2022Article
- A customised target capture sequencing tool for molecular identification of Aloe vera and relatives.Scientific reports · 2021Article
2 more citing papers are in PubMed but not listed here.
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9 authors.
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Abstract
premise of the studyTargeted sequencing using next-generation sequencing (NGS) platforms offers enormous potential for plant systematics by enabling economical acquisition of multilocus data sets that can resolve difficult phylogenetic problems. However, because discovery of single-copy nuclear (SCN) loci from NGS data requires both bioinformatics skills and access to high-performance computing resources, the application of NGS data has been limited. METHODS AND
resultsWe developed MarkerMiner 1.0, a fully automated, open-access bioinformatic workflow and application for discovery of SCN loci in angiosperms. Our new tool identified as many as 1993 SCN loci from transcriptomic data sampled as part of four independent test cases representing marker development projects at different phylogenetic scales.
conclusionsMarkerMiner is an easy-to-use and effective tool for discovery of putative SCN loci. It can be run locally or via the Web, and its tabular and alignment outputs facilitate efficient downstream assessments of phylogenetic utility, locus selection, intron-exon boundary prediction, and primer or probe development.
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