Whole-genome sequence and annotation of <i>Penstemon davidsonii</i>

Ostevik, Kate L; Alabady, Magdy; Zhang, Mengrui; Rausher, Mark D

doi:10.1093/g3journal/jkad296

Cited by 2 publications

(1 citation statement)

References 53 publications

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“…Final sequence quality was verified with fastqc ( Andrews 2010 ) and multiqc ( Ewels et al 2016 ). Quality-filtered reads were mapped to the annotated P. davidsonii reference genome ( Ostevik et al 2023 ) with bwa-mem ( Li 2013 ), and reads with low mapping quality ( q < 20) were removed. Duplicated reads were marked and removed with SAMtools markdup ( Li et al 2009 ), and overlapping paired-end reads were clipped with bamutil clipOverlap ( Jun et al 2015 ).…”

Section: Methodsmentioning

confidence: 99%

Ecological Diversification in an Adaptive Radiation of Plants: The Role of De Novo Mutation and Introgression

Stone,

Wessinger

2024

Molecular Biology and Evolution

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Adaptive radiations are characterized by rapid ecological diversification and speciation events, leading to fuzzy species boundaries between ecologically differentiated species. Adaptive radiations are therefore key systems for understanding how species are formed and maintained, including the role of de novo mutations vs. pre-existing variation in ecological adaptation and the genome-wide consequences of hybridization events. For example, adaptive introgression, where beneficial alleles are transferred between lineages through hybridization, may fuel diversification in adaptive radiations and facilitate adaptation to new environments. In this study, we employed whole-genome resequencing data to investigate the evolutionary origin of hummingbird-pollinated flowers and to characterize genome-wide patterns of phylogenetic discordance and introgression in Penstemon subgenus Dasanthera, a small and diverse adaptive radiation of plants. We found that magenta hummingbird-adapted flowers have apparently evolved twice from ancestral blue-violet bee-pollinated flowers within this radiation. These shifts in flower color are accompanied by a variety of inactivating mutations to a key anthocyanin pathway enzyme, suggesting that independent de novo loss-of-function mutations underlie parallel evolution of this trait. Although patterns of introgression and phylogenetic discordance were heterogenous across the genome, a strong effect of gene density suggests that, in general, natural selection opposes introgression and maintains genetic differentiation in gene-rich genomic regions. Our results highlight the importance of both de novo mutation and introgression as sources of evolutionary change and indicate a role for de novo mutation in driving parallel evolution in adaptive radiations.

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Section: Methodsmentioning

confidence: 99%

Ecological Diversification in an Adaptive Radiation of Plants: The Role of De Novo Mutation and Introgression

Stone,

Wessinger

2024

Molecular Biology and Evolution

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Whole-genome assembly and annotation of the firecracker penstemon (Penstemon eatonii)

Jarvis,

Stevens,

Carter

et al. 2024

Journal of Heredity

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The penstemons are ornamental annual flowering plants native to the Intermountain West and Rocky Mountains and commonly used for urban landscaping. Elite commercial penstemons are generally susceptible to abiotic stresses, including drought, root rot, cold, and high salinity. Firecracker penstemon (Penstemon eatonii), however, is much more tolerant to these stresses than most elite cultivars. Importantly, firecracker penstemon has been reported to hybridize with many other penstemons and therefore provides the opportunity to develop more tolerant elite cultivars through strategic crossing. To facilitate the study and utilization of firecracker penstemon, we sequenced and annotated the genome of a P. eatonii accession collected from Utah, USA. We also performed low-coverage, whole-genome sequencing of 26 additional accessions from three different varieties of P. eatonii. This chromosome-scale genome assembly is the most contiguous and complete Penstemon genome sequenced to date.

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Whole-genome sequence and annotation of Penstemon davidsonii

Cited by 2 publications

References 53 publications

Ecological Diversification in an Adaptive Radiation of Plants: The Role of De Novo Mutation and Introgression

Ecological Diversification in an Adaptive Radiation of Plants: The Role of De Novo Mutation and Introgression

Whole-genome assembly and annotation of the firecracker penstemon (Penstemon eatonii)

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