Target sequence capture in the Brazil nut family (Lecythidaceae): Marker selection and in silico capture from genome skimming data

AbstractThe tree of life is the fundamental biological roadmap for navigating the evolution and properties of life on Earth, and yet remains largely unknown. Even angiosperms (flowering plants) are fraught with data gaps, despite their critical role in sustaining terrestrial life. Today, high-throughput sequencing promises to significantly deepen our understanding of evolutionary relationships. Here, we describe a comprehensive phylogenomic platform for exploring the angiosperm tree of life, comprising a set of open tools and data based on the 353 nuclear genes targeted by the universal Angiosperms353 sequence capture probes. This paper (i) documents our methods, (ii) describes our first data release and (iii) presents a novel open data portal, the Kew Tree of Life Explorer (https://treeoflife.kew.org). We aim to generate novel target sequence capture data for all genera of flowering plants, exploiting natural history collections such as herbarium specimens, and augment it with mined public data. Our first data release, described here, is the most extensive nuclear phylogenomic dataset for angiosperms to date, comprising 3,099 samples validated by DNA barcode and phylogenetic tests, representing all 64 orders, 404 families (96%) and 2,333 genera (17%). Using the multi-species coalescent, we inferred a “first pass” angiosperm tree of life from the data, which totalled 824,878 sequences, 489,086,049 base pairs, and 532,260 alignment columns. The tree is strongly supported and highly congruent with existing taxonomy, while challenging numerous hypothesized relationships among orders and placing many genera for the first time. The validated dataset, species tree and all intermediates are openly accessible via the Kew Tree of Life Explorer. This major milestone towards a complete tree of life for all flowering plant species opens doors to a highly integrated future for angiosperm phylogenomics through the systematic sequencing of standardised nuclear markers. Our approach has the potential to serve as a much-needed bridge between the growing movement to sequence the genomes of all life on Earth and the vast phylogenomic potential of the world’s natural history collections.

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A Guide to Carrying Out a Phylogenomic Target Sequence Capture Project

Frontiers in Genetics ◽

10.3389/fgene.2019.01407 ◽

2020 ◽

Vol 10 ◽

Cited By ~ 8

Author(s):

Tobias Andermann ◽

Maria Fernanda Torres Jiménez ◽

Pável Matos-Maraví ◽

Romina Batista ◽

José L. Blanco-Pastor ◽

...

Keyword(s):

Target Sequence ◽

Sequence Capture

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In Silico Prediction of Mutant HIV-1 Proteases Cleaving a Target Sequence

PLoS ONE ◽

10.1371/journal.pone.0095833 ◽

2014 ◽

Vol 9 (5) ◽

pp. e95833 ◽

Cited By ~ 12

Author(s):

Jan H. Jensen ◽

Martin Willemoës ◽

Jakob R. Winther ◽

Luca De Vico

Keyword(s):

In Silico ◽

Target Sequence ◽

In Silico Prediction ◽

Hiv 1

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Filtering of target sequence capture individuals facilitates species tree construction in the plant subtribe Iochrominae (Solanaceae)

Molecular Phylogenetics and Evolution ◽

10.1016/j.ympev.2018.02.002 ◽

2018 ◽

Vol 123 ◽

pp. 26-34 ◽

Cited By ~ 3

Author(s):

Daniel J. Gates ◽

Diana Pilson ◽

Stacey D. Smith

Keyword(s):

Species Tree ◽

Target Sequence ◽

Sequence Capture ◽

Tree Construction

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In silico identification of off-target pesticidal dsRNA binding in honey bees (Apis mellifera)

10.7287/peerj.preprints.3287 ◽

2017 ◽

Author(s):

Christina L Mogren ◽

Jonathan Gary Lundgren

Keyword(s):

Honey Bee ◽

Sequence Homology ◽

Honey Bees ◽

In Silico ◽

Target Gene ◽

Target Sequence ◽

Phenotypic Effect ◽

Dsrna Binding ◽

High Sequence Homology ◽

Genomic Regions

Background. Pesticidal RNAs silencing critical gene function have great potential in pest management, but the benefits of this technology must be weighed against non-target organism risks. Methods. Published studies that developed pesticidal dsRNAs were collated into a database. The target gene sequences for these pesticidal RNAs were determined, and the degree of sequence homology with the honey bee genome were evaluated statistically for each. Results. We identified 101 insecticidal dsRNAs sharing high sequence homology with genomic regions in honey bees. The likelihood of off-target sequence homology increased with the parent dsRNA length. Non-target gene binding was unaffected by taxonomic relatedness of the target insect to honey bees, contrary to previous assertions. Gene groups active during honey bee development had disproportionately high sequence homology with pesticidal RNAs relative to other areas of the genome. Discussion. Although sequence homology does not itself guarantee a significant phenotypic effect in honey bees, in silico screening may help to identify appropriate experimental endpoints within a risk assessment framework for pesticidal RNAi.

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Gene count from target sequence capture places three whole genome duplication events in Hibiscus L. (Malvaceae)

10.21203/rs.3.rs-48002/v3 ◽

2021 ◽

Author(s):

Jonna Sofia Eriksson ◽

Christine D. Bacon ◽

Dominic J. Bennett ◽

Bernard E. Pfeil ◽

Bengt Oxelman ◽

...

Keyword(s):

Chromosome Number ◽

Chromosome Numbers ◽

Whole Genome Duplication ◽

Genome Duplication ◽

Single Copy ◽

Target Sequence ◽

Whole Genome ◽

Genome Doubling ◽

Sequence Capture ◽

Duplication Events

Abstract Background: The great diversity in plant genome size and chromosome number is partly due to polyploidization (i.e. genome doubling events). The differences in genome size and chromosome number among diploid plant species can be a window into the intriguing phenomenon of past genome doubling that may be obscured through time by the process of diploidization. The genus Hibiscus L. (Malvaceae) has a wide diversity of chromosome numbers and a complex genomic history. Hibiscus is ideal for exploring past genomic events because although two ancient genome duplication events have been identified, more are likely to be found due to its diversity of chromosome numbers. To reappraise the history of whole-genome duplication events in Hibiscus, we tested three alternative scenarios describing different polyploidization events. Results: Using target sequence capture, we designed a new probe set for Hibiscus and generated 87 orthologous genes from four diploid species. We detected paralogues in >54% putative single-copy genes. 34 of these genes were selected for testing three different genome duplication scenarios using gene counting. All species of Hibiscus sampled shared one genome duplication with H. syriacus, and one whole genome duplication occurred along the branch leading to H. syriacus. Conclusions: Here, we corroborated the independent genome doubling previously found in the lineage leading to H. syriacus and a shared genome doubling of this lineage and the remainder of Hibiscus. Additionally, we found a previously undiscovered genome duplication shared by the /Pavonia and /Malvaviscus clades (both nested within Hibiscus) with the occurrences of two copies in what were otherwise single-copy genes. Our results highlight the complexity of genomic diversity in some plant groups, which makes orthology assessment and accurate phylogenomic inference difficult.

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A guide to carrying out a phylogenomic target sequence capture project

10.7287/peerj.preprints.27968v1 ◽

2019 ◽

Cited By ~ 1

Author(s):

Tobias Andermann ◽

Maria Fernanda Torres Jimenez ◽

Pável Matos-Maraví ◽

Romina Batista ◽

José L Blanco-Pastor ◽

...

Keyword(s):

Sequence Data ◽

Phylogenetic Analyses ◽

Cost Effective ◽

Target Sequence ◽

Sequence Capture ◽

Large Sets ◽

Phylogenetic Studies ◽

Target Capture ◽

Whole Genomes ◽

High Throughput Dna Sequencing

High-throughput DNA sequencing techniques enable time- and cost-effective sequencing of large portions of the genome. Instead of sequencing and annotating whole genomes, many phylogenetic studies focus sequencing efforts on large sets of pre-selected loci, which further reduces costs and bioinformatic challenges while increasing sequencing depth. One common approach that enriches loci before sequencing is often referred to as target sequence capture. This technique has been shown to be applicable to phylogenetic studies of greatly varying evolutionary depth and has proven to produce powerful, large multi-locus DNA sequence datasets of selected loci, suitable for phylogenetic analyses. However, target capture requires careful theoretical and practical considerations, which will greatly affect the success of the experiment. Here we provide an easy-to-follow flowchart for adequately designing phylogenomic target capture experiments, and we discuss necessary considerations and decisions from the first steps in the lab to the final bioinformatic processing of the sequence data. We particularly discuss issues and challenges related to the taxonomic scope, sample quality, and available genomic resources of target capture projects and how these issues affect all steps from bait design to the bioinformatic processing of the data. Altogether this review outlines a roadmap for future target capture experiments and is intended to assist researchers with making informed decisions for designing and carrying out successful phylogenetic target capture studies

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ORTHOSKIM: in silico sequence capture from genomic and transcriptomic libraries for phylogenomic and barcoding applications

Molecular Ecology Resources ◽

10.1111/1755-0998.13584 ◽

2022 ◽

Author(s):

Charles Pouchon ◽

Frédéric Boyer ◽

Cristina Roquet ◽

France Denoeud ◽

Jérome Chave ◽

...

Keyword(s):

In Silico ◽

Sequence Capture

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