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PhyloHerb: A high-throughput phylogenomic pipeline for processing genome skimming data
Liming Cai1,2,3, Hongrui Zhang1, Charles C Davis1
1Harvard University Herbaria 22 Divinity Avenue, Cambridge Massachusetts 02138 USA.
Applications in Plant Sciences
|July 1, 2022
Summary
PhyloHerb is a new bioinformatic pipeline that efficiently assembles phylogenomic data from genome skimming of herbarium specimens. This tool aids biodiversity research by enabling rapid analysis of plastid, mitochondrial, and nuclear DNA across many species.
Area of Science:
- Genomics
- Bioinformatics
- Biodiversity Research
Background:
- High-throughput sequencing of herbarium specimens accelerates biodiversity research.
- Genome skimming (low-coverage sequencing of total DNA) recovers multiple genomic regions (plastid, mitochondrial, nuclear ribosomal).
Purpose of the Study:
- Introduce PhyloHerb, a novel bioinformatic pipeline for efficient assembly of phylogenomic datasets from genome skimming.
- Facilitate large-scale biodiversity research using ancient DNA.
Main Methods:
- PhyloHerb utilizes BLAST searches with built-in or user-specified references to extract orthologous sequences from multiple genomes.
- The pipeline processes data from genome skimming, outputting FASTA files and providing tools for alignment, partitioning, concatenation, and phylogeny inference.
Main Results:
- PhyloHerb accurately identifies genes, demonstrated using a Clusiaceae dataset.
- Simulations confirm the pipeline's effectiveness with fragmented DNA from herbarium specimens.
- The approach is scalable to thousands of species.
Conclusions:
- PhyloHerb provides an efficient solution for assembling phylogenomic data from genome skimming.
- The pipeline supports large-scale biodiversity studies using herbarium specimens.
- PhyloHerb is freely available, promoting accessibility in research.
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