ipyrad: Interactive assembly and analysis of RADseq datasets

Bioinformatics, Journal Year: 2019, Volume and Issue: 36(8), P. 2592 - 2594

Published: Dec. 31, 2019

Abstract Summary ipyrad is a free and open source tool for assembling analyzing restriction site-associated DNA sequence datasets using de novo and/or reference-based approaches. It designed to be massively scalable hundreds of taxa thousands samples, can efficiently parallelized on high performance computing clusters. available both as command line interface Python package with an application programming interface, the latter which used interactively write complex, reproducible scripts implement suite downstream analysis tools. Availability implementation program written in Python. Source code from GitHub repository (https://github.com/dereneaton/ipyrad/), Linux MacOS installs are distributed through conda manager. Complete documentation, including numerous tutorials, Jupyter notebooks demonstrating example assemblies applications tools online: https://ipyrad.readthedocs.io/.

Language: Английский

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A Universal Probe Set for Targeted Sequencing of 353 Nuclear Genes from Any Flowering Plant Designed Using k-Medoids Clustering

Systematic Biology, Journal Year: 2018, Volume and Issue: 68(4), P. 594 - 606

Published: Dec. 7, 2018

Sequencing of target-enriched libraries is an efficient and cost-effective method for obtaining DNA sequence data from hundreds nuclear loci phylogeny reconstruction. Much the cost developing targeted sequencing approaches associated with generation preliminary needed identification orthologous probe design. In plants, identifying has proven difficult due to a large number whole-genome duplication events, especially in angiosperms (flowering plants). We used multiple alignments over 600 353 putatively single-copy protein-coding genes identified by One Thousand Plant Transcriptomes Initiative design set probes phylogenetic studies any angiosperm group. To maximize potential probes, while minimizing production, we introduce k-medoids clustering approach identify minimum sequences necessary represent each coding final set. Using this method, 5–15 representative were selected per locus, representing diversity more efficiently than if designed using available sequenced genomes alone. test our approximately 80,000 hybridized 42 species spanning all higher-order groups angiosperms, focus on taxa not present probes. Out possible sequences, recovered average 283 at least 100 species. Differences among recovery could be explained relatedness design, suggesting that there no bias Our set, which 260 kbp sequence, achieved median 137 taxon regions, maximum 250 kbp, additional 212 flanking non-coding regions across These results suggest Angiosperms353 described here effective group flowering plants would useful level groups, including entire clade itself.

Language: Английский

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PACVr: plastome assembly coverage visualization in R

BMC Bioinformatics, Journal Year: 2020, Volume and Issue: 21(1)

Published: May 24, 2020

Plastid genomes typically display a circular, quadripartite structure with two inverted repeat regions, which challenges automatic assembly procedures. The correct of plastid is prerequisite for the validity subsequent analyses on genome and evolution. average coverage depth often used as an indicator quality. Visualizing across draft critical step, allows users to inspect quality and, where applicable, identify regions reduced confidence. Despite interplay between quality, no contemporary, user-friendly software tool can visualize while taking its into account. A needed that fills this void.

Language: Английский

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Practical considerations for plant phylogenomics

Applications in Plant Sciences, Journal Year: 2018, Volume and Issue: 6(3)

Published: March 1, 2018

The past decade has seen a major breakthrough in our ability to easily and inexpensively sequence genome‐scale data from diverse lineages. development of high‐throughput sequencing long‐read technologies ushered the era phylogenomics, where hundreds thousands nuclear genes whole organellar genomes are routinely used reconstruct evolutionary relationships. As result, understanding which options best suited for particular set questions can be difficult, especially those just starting field. Here, we review most recent advances plant phylogenomic methods make recommendations project‐dependent practices considerations. We focus on costs benefits different approaches regard information they provide researchers address. also highlight unique challenges opportunities systems, such as polyploidy, reticulate evolution, use herbarium materials, identifying optimal methodologies each. Finally, draw attention lingering field reusability sets, look at some up‐and‐coming that may help propel even further.

Language: Английский

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Resolution of the ordinal phylogeny of mosses using targeted exons from organellar and nuclear genomes

Nature Communications, Journal Year: 2019, Volume and Issue: 10(1)

Published: April 2, 2019

Mosses are a highly diverse lineage of land plants, whose diversification, spanning at least 400 million years, remains phylogenetically ambiguous due to the lack fossils, massive early extinctions, late radiations, limited morphological variation, and conflicting signal among previously used markers. Here, we present phylogenetic reconstructions based on complete organellar exomes comparable set nuclear genes for this major plants. Our analysis 142 species representing 29 30 moss orders reveals that relative average rates non-synonymous substitutions in versus plastid much higher mosses than seed consistent with emerging concept evolutionary dynamism mosses. results highlight significance taxa reduced morphologies, shed light tempo mechanisms underlying cladogenic events, suggest hypotheses relationships delineation orders.

Language: Английский

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The Expanding Role of DNA Barcodes: Indispensable Tools for Ecology, Evolution, and Conservation

Diversity, Journal Year: 2022, Volume and Issue: 14(3), P. 213 - 213

Published: March 13, 2022

DNA barcoding has transformed the fields of ecology, evolution, and conservation by providing a rapid effective tool for species identification. The growth barcodes as resource biologists followed advances in computational sequencing technology that have enabled high-throughput applications. global barcode database is expanding to represent diversity on Earth thanks efforts international consortia biological collections. Today, instrumental advancing our understanding how evolve, they interact, we can slow down their extirpation extinction. This review focuses current applications sequences address fundamental lines research, well new which will play central role.

Language: Английский

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Phylogenomics and the flowering plant tree of life

Journal of Integrative Plant Biology, Journal Year: 2022, Volume and Issue: 65(2), P. 299 - 323

Published: Nov. 23, 2022

Abstract The advances accelerated by next‐generation sequencing and long‐read technologies continue to provide an impetus for plant phylogenetic study. In the past decade, a large number of studies adopting hundreds thousands genes across wealth clades have emerged ushered phylogenetics evolution into new era. meantime, roadmap researchers when making decisions different approaches their phylogenomic research design is imminent. This review focuses on utility genomic data (from organelle genomes, both reduced representation whole‐genome sequencing) in evolutionary investigations, describes baseline methodology experimental analytical procedures, summarizes recent progress flowering phylogenomics at ordinal, familial, tribal, lower levels. We also discuss challenges, such as adverse impact orthology inference reconstruction raised from systematic errors, underlying biological factors, duplication, hybridization/introgression, incomplete lineage sorting, together suggesting that bifurcating tree may not be best model life. Finally, we promising avenues future studies.

Language: Английский

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Plant pangenomes for crop improvement, biodiversity and evolution

Nature Reviews Genetics, Journal Year: 2024, Volume and Issue: 25(8), P. 563 - 577

Published: Feb. 20, 2024

Language: Английский

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Species delimitation 4.0: integrative taxonomy meets artificial intelligence

Trends in Ecology & Evolution, Journal Year: 2024, Volume and Issue: 39(8), P. 771 - 784

Published: June 6, 2024

Although species are central units for biological research, recent findings in genomics raising awareness that what we call can be ill-founded entities due to solely morphology-based, regional descriptions. This particularly applies groups characterized by intricate evolutionary processes such as hybridization, polyploidy, or asexuality. Here, challenges of current integrative taxonomy (genetics/genomics + morphology ecology, etc.) become apparent: different favored concepts, lack universal characters/markers, missing appropriate analytical tools processes, and highly subjective ranking fusion datasets. Now, combined with artificial intelligence under a unified concept enable automated feature learning data integration, thus reduce subjectivity delimitation. approach will likely accelerate revising unraveling eukaryotic biodiversity.

Language: Английский

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Factors Affecting Targeted Sequencing of 353 Nuclear Genes From Herbarium Specimens Spanning the Diversity of Angiosperms

Frontiers in Plant Science, Journal Year: 2019, Volume and Issue: 10

Published: Sept. 18, 2019

The world's herbaria collectively house millions of diverse plant specimens, including endangered or extinct species and type specimens. Unlocking genetic data from the typically highly degraded DNA obtained herbarium specimens was difficult until arrival high-throughput sequencing approaches, which can be applied to low quantities severely fragmented DNA. Target enrichment involves using short molecular probes that hybridise capture genomic regions interest for sequencing. In this study on herbariomics, we used targeted approach Angiosperms353 universal probe set recover up 351 nuclear genes 435 are 204 years old span breadth angiosperm diversity. We show average 207 were successfully retrieved although mean number target efficiency is significantly higher silica gel-dried Forty-seven recovered a specimen critically St Helena boxwood, Mellissia begoniifolia, collected in 1815. Herbarium yield less high-molecular-weight than quality declines with sample age, negatively correlated efficiency. Climate, taxon-specific traits, collection strategies additionally impact sequence recovery. also detected taxonomic bias outcomes 10 most numerous families investigated depth. recommend (1) distributed wet tropical climates, should preferentially; (2) seasonally dry similar results, either used; (3) traits explored established effective optimisation studies specimens; (4) all sheets should, future, annotated details preservation method (5) long-term storage stable, low-humidity, low-temperature environments; (6) probes, such as Angiosperms353, closely new barcoding will ensure better exploitation traditional Sanger approaches.

Language: Английский

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