PhyloHerb: A high‐throughput phylogenomic pipeline for processing genome skimming data
Sign Up to like & getrecommendations! Published in 2022 at "Applications in Plant Sciences"
DOI: 10.1002/aps3.11475
Abstract: Abstract Premise The application of high‐throughput sequencing, especially to herbarium specimens, is rapidly accelerating biodiversity research. Low‐coverage sequencing of total genomic DNA (genome skimming) is particularly promising and can simultaneously recover the plastid, mitochondrial, and… read more here.
Keywords: genome skimming; high throughput; phyloherb high; throughput phylogenomic ... See more keywords
A curated benchmark dataset for molecular identification based on genome skimming
Sign Up to like & getrecommendations! Published in 2025 at "Scientific Data"
DOI: 10.1038/s41597-025-05230-2
Abstract: Genome skimming is a promising sequencing strategy for DNA-based taxonomic identification. However, the lack of standardized datasets for benchmarking genome skimming tools presents a challenge in comparing new methods to existing ones. As part of… read more here.
Keywords: benchmark dataset; curated benchmark; genome skimming; identification ... See more keywords
A genome-skimming phylogeny of ctenostome bryozoans
Sign Up to like & getrecommendations! Published in 2025 at "Zoological Journal of the Linnean Society"
DOI: 10.1093/zoolinnean/zlaf060
Abstract: Ctenostome bryozoans pose ongoing challenges for taxonomists and systematists, owing to their lack of character-rich mineralized skeletons. We present the largest (super)family-level phylogeny of Ctenostomatida to date. We resolved the three major clades (A–C) that… read more here.
Keywords: phylogeny ctenostome; skimming phylogeny; ctenostome; genome skimming ... See more keywords
Genome skimming supports two new crayfish species from the genus Pacifastacus Bott, 1950 (Decapoda: Astacidae).
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DOI: 10.11646/zootaxa.5632.3.4
Abstract: Recent phylogenetic analyses have suggested that the Signal Crayfish, Pacifastacus leniusculus (Dana, 1852), contains two highly distinct lineages that merit recognition as species. We further investigate these lineages here using genome skimming to conduct phylogenetic… read more here.
Keywords: two new; skimming supports; pacifastacus; crayfish pacifastacus ... See more keywords
Identification of herbal medicine species of Lysimachia L. (Primulaceae) in Southern China using genome skimming
Sign Up to like & getrecommendations! Published in 2025 at "BMC Plant Biology"
DOI: 10.1186/s12870-025-06948-2
Abstract: The accurate identification of herbal medicine is a prerequisite for safe and effective use. DNA barcoding has been widely used for the identification of herbal medicine. However, choosing and refining a suitable barcode is complex… read more here.
Keywords: herbal medicine; identification herbal; medicine; genome skimming ... See more keywords
Reassessing Banana Phylogeny and Organelle Inheritance Modes Using Genome Skimming Data
Sign Up to like & getrecommendations! Published in 2021 at "Frontiers in Plant Science"
DOI: 10.3389/fpls.2021.713216
Abstract: Bananas (Musa spp.) are some of the most important fruit crops in the world, contributing up to US$10 billion in export values annually. In this study, we use high-throughput sequencing to obtain genomic resources of… read more here.
Keywords: reassessing banana; skimming data; banana phylogeny; genome skimming ... See more keywords
Genome Skimming Reveals Plastome Conservation, Phylogenetic Structure, and Novel Molecular Markers in Valuable Orchid Changnienia amoena
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DOI: 10.3390/genes16070723
Abstract: Background/Objectives: Changnienia amoena is a rare and endangered terrestrial orchid endemic to China, valued for its ornamental and medicinal properties. However, limited genomic resources hinder its effective conservation strategies and sustainable utilization. This study aimed… read more here.
Keywords: skimming reveals; conservation; structure; molecular markers ... See more keywords
Exploring Taxonomic and Genetic Relationships in the Pinus mugo Complex Using Genome Skimming Data
Sign Up to like & getrecommendations! Published in 2024 at "International Journal of Molecular Sciences"
DOI: 10.3390/ijms251810178
Abstract: Genome skimming is a novel approach that enables obtaining large-scale genomic information based on high-copy DNA fractions from shallow whole-genome sequencing. The simplicity of this method, low analysis costs, and large amounts of generated data… read more here.
Keywords: pinus mugo; closely related; mugo complex; genome skimming ... See more keywords
Skimming for barcodes: rapid production of mitochondrial genome and nuclear ribosomal repeat reference markers through shallow shotgun sequencing
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DOI: 10.7717/peerj.13790
Abstract: DNA barcoding is critical to conservation and biodiversity research, yet public reference databases are incomplete. Existing barcode databases are biased toward cytochrome oxidase subunit I (COI) and frequently lack associated voucher specimens or geospatial metadata,… read more here.
Keywords: ribosomal repeat; dna; nuclear ribosomal; reference ... See more keywords
A pipeline for assembling low copy nuclear markers from plant genome skimming data for phylogenetic use
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DOI: 10.7717/peerj.14525
Abstract: Background Genome skimming is a popular method in plant phylogenomics that do not include a biased enrichment step, relying on random shallow sequencing of total genomic DNA. From these data the plastome is usually readily… read more here.
Keywords: copy nuclear; genome skimming; low copy; pipeline ... See more keywords
Genome skimming is a low-cost and robust strategy to assemble complete mitochondrial genomes from ethanol preserved specimens in biodiversity studies
Sign Up to like & getrecommendations! Published in 2019 at "PeerJ"
DOI: 10.7717/peerj.7543
Abstract: Global loss of biodiversity is an ongoing process that concerns both local and global authorities. Studies of biodiversity mainly involve traditional methods using morphological characters and molecular protocols. However, conventional methods are a time consuming… read more here.
Keywords: complete mitochondrial; genome skimming; skimming low; low cost ... See more keywords