Targeted enrichment strategies for next‐generation plant biology

Cronn, Richard; Knaus, Brian J.; Liston, Aaron; Maughan, Peter J.; Parks, Matthew; Syring, John; Udall, Joshua A.

doi:10.3732/ajb.1100356

Cited by 198 publications

(217 citation statements)

References 138 publications

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“…A targeted approach can be particularly useful for focusing sequencing efforts on regions of particular interest, and is beneficial for lineages exhibiting marginal sequence divergence in which the whole genome sequencing approach may be superfluous. Several targeted enrichment approaches have been developed in recent years (Cronn et al, 2012), but they are often costly and can be time-consuming. An amplicon sequencing approach may be a simple and cheaper alternative, and multiplex PCR reduces the amount of DNA and destructive sampling required from valuable herbarium samples (Krause et al, 2006).…”

Section: Sequencing Chloroplast Genomes From Extinct and Ancient Planmentioning

confidence: 99%

The quest to resolve recent radiations: Plastid phylogenomics of extinct and endangered Hawaiian endemic mints (Lamiaceae)

Welch

Collins

Drautz–Moses

et al. 2016

Molecular Phylogenetics and Evolution

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(2016) 'The quest to resolve recent radiations : plastid phylogenomics of extinct and endangered Hawaiian endemic mints (Lamiaceae).', Molecular phylogenetics and evolution., 99 . pp. 16-33. Further information on publisher's website: Use policyThe full-text may be used and/or reproduced, and given to third parties in any format or medium, without prior permission or charge, for personal research or study, educational, or not-for-pro t purposes provided that:• a full bibliographic reference is made to the original source • a link is made to the metadata record in DRO • the full-text is not changed in any way The full-text must not be sold in any format or medium without the formal permission of the copyright holders.Please consult the full DRO policy for further details. AbstractThe Hawaiian mints (Lamiaceae), one of the largest endemic plant lineages in the archipelago, provide an excellent system to study rapid diversification of a lineage with a remote, likely paleohybrid origin. Since their divergence from New World mints 4-5 million years ago the members of this lineage have diversified greatly and represent a remarkable array of vegetative and reproductive phenotypes. Today many members of this group are endangered or already extinct, and molecular phylogenetic work relies largely on herbarium samples collected during the last century. So far a gene-by-gene approach has been utilized, but the recent radiation of the Hawaiian mints has resulted in minimal sequence divergence and hence poor phylogenetic resolution. In our quest to trace the reticulate evolutionary history of the lineage, a resolved maternal phylogeny is necessary. We applied a high-throughput approach to sequence 12 complete or nearly complete plastid genomes from multiple Hawaiian mint species and relatives, including extinct and rare taxa. We also targeted 108 hypervariable regions from throughout the chloroplast genomes in nearly all of the remaining Hawaiian species, and relatives, using a nextgeneration amplicon sequencing approach. This procedure generated ~20Kb of sequence data for each taxon and considerably increased the total number of variable sites over previous analyses. Our results demonstrate the potential of high-throughput sequencing of historic material for evolutionary studies in rapidly evolving lineages. Our study, however, also highlights the challenges of resolving relationships within recent radiations even at the genomic level.

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Section: Sequencing Chloroplast Genomes From Extinct and Ancient Planmentioning

confidence: 99%

The quest to resolve recent radiations: Plastid phylogenomics of extinct and endangered Hawaiian endemic mints (Lamiaceae)

Welch

Collins

Drautz–Moses

et al. 2016

Molecular Phylogenetics and Evolution

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“…High-throughput sequencing technologies greatly facilitate the creation of large marker sets, and numerous approaches exist for their generation ( Davey et al, 2011 ;Good, 2011 ;Cronn et al, 2012 ). Among these is low-coverage whole-genome shotgun sequencing (WGS), or genome skimming, which sequences a small fraction of the genome for characterization and 1 Manuscript received 30 May 2014; revision accepted 7 November 2014.…”

mentioning

confidence: 99%

The Parasitic Plant Genome Project: New Tools for Understanding the Biology ofOrobancheandStriga

et al. 2012

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The Parasitic Plant Genome Project has sequenced transcripts from three parasitic species and a nonparasitic relative in the Orobanchaceae with the goal of understanding genetic changes associated with parasitism. The species studied span the trophic spectrum from free-living nonparasite to obligate holoparasite. Parasitic species used wereTriphysaria versicolor, a photosynthetically competent species that opportunistically parasitizes roots of neighboring plants;Striga hermonthica, a hemiparasite that has an obligate need for a host; andOrobanche aegyptiaca, a holoparasite with absolute nutritional dependence on a host.Lindenbergia philippensisrepresents the closest nonparasite sister group to the parasitic Orobanchaceae and was included for comparative purposes. Tissues for transcriptome sequencing from each plant were gathered to identify expressed genes for key life stages from seed conditioning through anthesis. Two of the species studied,S. hermonthicaandO. aegyptiaca, are economically important weeds and the data generated by this project are expected to aid in research and control of these species and their relatives. The sequences generated through this project will provide an abundant resource of molecular markers for understanding population dynamics, as well as provide insight into the biology of parasitism and advance progress toward understanding parasite virulence and host resistance mechanisms. In addition, the sequences provide important information on target sites for herbicide action or other novel control strategies such as trans-specific gene silencing.

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“…This was achieved using a sequence capture approach (Cronn et al. 2012; Mandel et al. 2014) for the purpose of target enrichment prior to sequencing the reduced‐representation libraries.…”

Section: Methodsmentioning

confidence: 99%

Embracing discordance: Phylogenomic analyses provide evidence for allopolyploidy leading to cryptic diversity in a MediterraneanCampanula(Campanulaceae) clade

2017

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The Mediterranean Basin harbors a remarkable amount of biodiversity, a high proportion of which is endemic to this region. Here, we present an in‐depth study of an angiosperm species complex, in which cryptic taxonomic diversity has been hypothesized. Specifically, we focus on four currently recognized species in the Roucela complex, a well‐supported clade in the Campanulaceae/Campanuloideae: Campanula creutzburgii, C. drabifolia, C. erinus, and C. simulans. This study takes a phylogenomic approach, utilizing near‐complete plastomes and 130 nuclear loci, to uncover cryptic diversity and test hypotheses regarding hybridization and polyploidy within this clade. Genome size estimates recovered tetraploid and octoploid lineages within the currently recognized, widespread species C. erinus, showing an east‐west geographic pattern. Though genomic data clearly differentiate these two cytotypes, we failed to discern morphological differences. The formation of a cryptic octoploid lineage, distributed across the eastern Mediterranean, is hypothesized to be the result of an allopolyploid event in which one parental morphology is retained. The tetraploid C. erinus and C. creutzburgii (also a tetraploid) are implicated as parental lineages. Our results highlight the utility of target‐enrichment approaches for obtaining genomic datasets for thorough assessments of species diversity and the importance of carefully considering gene‐tree discordance within such datasets.

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Targeted enrichment strategies for next‐generation plant biology

Cited by 198 publications

References 138 publications

The quest to resolve recent radiations: Plastid phylogenomics of extinct and endangered Hawaiian endemic mints (Lamiaceae)

The quest to resolve recent radiations: Plastid phylogenomics of extinct and endangered Hawaiian endemic mints (Lamiaceae)

The Parasitic Plant Genome Project: New Tools for Understanding the Biology ofOrobancheandStriga

Embracing discordance: Phylogenomic analyses provide evidence for allopolyploidy leading to cryptic diversity in a MediterraneanCampanula(Campanulaceae) clade

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