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
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
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