A target enrichment probe set for resolving the flagellate land plant tree of life

Breinholt, Jesse W.; Carey, Sarah B.; Tiley, George P.; Davis, Emily; Endara, Lorena; McDaniel, Stuart F.; Neves, Leandro G.; Sessa, Emily B.; Konrat, Matt Von; Chantanaorrapint, Sahut; Fawcett, Susan; Ickert‐Bond, Stefanie M.; Labiak, Paulo H.; Larraín, Juan; Lehnert, Marcus; Lewis, Lily R.; Nagalingum, Nathalie S.; Patel, Nikisha; Rensing, Stefan A.; Testo, Weston; Vasco, Alejandra; Villarreal, Juan Carlos; Williams, Evelyn W.; Burleigh, J. Gordon

doi:10.1002/aps3.11406

Cited by 66 publications

(86 citation statements)

References 30 publications

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“…However, development of universal probe sets for plants (e.g., ferns: (Wolf et al 2018); flagellate plants: (Breinholt et al 2021); and angiosperms: (Johnson et al 2019)) facilitates sequencing of hundreds of loci for any system, regardless of genomic resources available. This provides an opportunity to improve phylogenetic resolution in understudied systems, including Andean plant clades.…”

Section: Frost and Lagomarsinomentioning

confidence: 99%

“…Until recently, development of probesets for target sequence capture required genomic resources in close relatives of the focal system– resources that are often lacking in Neotropical lineages. However, development of universal probe sets for plants (e.g., ferns: (Wolf et al 2018); flagellate plants: (Breinholt et al 2021); and angiosperms:(Johnson et al 2019)) facilitates sequencing of hundreds of loci for any system, regardless of genomic resources available. This provides an opportunity to improve phylogenetic resolution in understudied systems, including Andean plant clades.…”

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confidence: 99%

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Strong phylogenetic signal despite high phylogenomic complexity in an Andean plant radiation (Freziera,Pentaphylacaceae)

Lagomarsino

2021

Preprint

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The Andes mountains in South America are a biodiversity hotspot within a hotspot, the New World Tropics, for seed plants. Much of this diversity is concentrated at middle-elevations in cloud forests, yet the evolutionary patterns underlying this extraordinary diversity remain poorly understood. This is partially due to a paucity of resolved phylogenies for cloud forest plant lineages: the young age of the Andes and generally high diversification rates among Andean systems precludes robust phylogenetic inference, and remote populations, few genomic resources, and generally understudied organisms make acquiring high-quality data difficult. We present the first phylogeny of Freziera (Pentaphylacaceae), an Andean-centered, cloud forest radiation with potential to provide insight into some of the abiotic and extrinsic factors that promote the highest diversity observed on the globe. Our dataset, representing data for 50 of the ca. 75 spp. obtained almost entirely from herbarium specimens via hybrid-enriched target sequence capture with the universal bait set Angiosperms353, included a proportion of poorly assembled loci likely representing multi-copy genes, but with insufficient data to be flagged by paralog filters: cryptic paralogs. These cryptic paralogs likely result from limitations in data collection that are common in herbariomics combined with a history of genome duplication and are likely common in other plant phylogenomic datasets. Standard empirical metrics for identifying poor-quality genes, which typically focus on filtering for genes with high phylogenetic informativeness, failed to identify problematic loci in our dataset where strong but inaccurate signal was a greater problem. Filtering by bipartition support was the most successful method for selecting genes and resulted in a species tree with lower discordance, higher support, and a more accurate topology relative to a consensus tree. Using known paralogs, we investigate the utility of multi-copy genes in phylogenetic inference and find a role for paralogs in resolving deep nodes and major clades, though at the expense of gene tree concordance and support. With the first phylogeny, we infer the biogeographic history of Freziera and identify the northern Andes as a source region. We also identify distinct modes of diversification in the northern and central Andes, highlighting the importance of fine-scale biogeographic study in Andean cloud forest systems.

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Section: Frost and Lagomarsinomentioning

confidence: 99%

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confidence: 99%

Strong phylogenetic signal despite high phylogenomic complexity in an Andean plant radiation (Freziera,Pentaphylacaceae)

Lagomarsino

2021

Preprint

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“…We need to fund more field work to identify new, potentially dioecious species and commongarden analyses to characterize development (e.g., [213]). We need better-supported, species-level phylogenies to infer the number of evolutions of dioecy, for example using Angiosperm353 [214] and GoFlag (Genealogy of Flagellate plants) [215] probe sets. We need more cytological analyses, to uncover how these chromosomes behave in the cell (e.g., [216,217]) or verifying in what tissues genes are expressed (e.g., [50]).…”

Section: The Future Of Plant Sex Chromosome Researchmentioning

confidence: 99%

The Diversity of Plant Sex Chromosomes Highlighted through Advances in Genome Sequencing

Carey

Harkess

2021

Genes

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For centuries, scientists have been intrigued by the origin of dioecy in plants, characterizing sex-specific development, uncovering cytological differences between the sexes, and developing theoretical models. Through the invention and continued improvements in genomic technologies, we have truly begun to unlock the genetic basis of dioecy in many species. Here we broadly review the advances in research on dioecy and sex chromosomes. We start by first discussing the early works that built the foundation for current studies and the advances in genome sequencing that have facilitated more-recent findings. We next discuss the analyses of sex chromosomes and sex-determination genes uncovered by genome sequencing. We synthesize these results to find some patterns are emerging, such as the role of duplications, the involvement of hormones in sex-determination, and support for the two-locus model for the origin of dioecy. Though across systems, there are also many novel insights into how sex chromosomes evolve, including different sex-determining genes and routes to suppressed recombination. We propose the future of research in plant sex chromosomes should involve interdisciplinary approaches, combining cutting-edge technologies with the classics to unravel the patterns that can be found across the hundreds of independent origins.

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“…We need to fund more field work to identify new, potentially dioecious species and common-garden analyses to characterize development (e.g., [184]). We need better-supported, species-level phylogenies to infer the number of evolutions of dioecy, for example using Angiosperm353 [185] and GoFlag (Genealogy of Flagellate plants) [186] probe sets. We need more cytological analyses, to uncover how these chromosomes behave in the cell (e.g., [187,188]) or verifying in what tissues genes are expressed (e.g., [48]).…”

Section: The Future Of Plant Sex Chromosome Researchmentioning

confidence: 99%

The diversity of plant sex chromosomes highlighted through advances in genome sequencing

Carey¹,

Yu²,

Harkess³

2021

Preprint

Self Cite

View full text Add to dashboard Cite

For centuries scientists have been intrigued by the origin of dioecy in plants, characterizing sex-specific development, uncovering cytological differences between the sexes, and developing theoretical models. However, through the invention and continued improvements in genomic technologies, we have truly begun to unlock the genetic basis of dioecy in many species. Here we broadly review the advances in research on dioecy and sex chromosomes. We start by first discussing the early works that built the foundation for current studies and the advances in genome sequencing that have facilitated more-recent findings. We next discuss the analyses of sex chromosomes and sex-determination genes uncovered by genome sequencing. We synthesize these results to find some patterns are emerging, such as the role of duplications, the involvement of hormones in sex-determination, and support for the two-locus model for the origin of dioecy. Though across systems, there also many novel insights into how sex chromosomes evolve, including different sex-determining genes and routes to suppressed recombination. We propose the future of research in plant sex chromosomes should involve interdisciplinary approaches, combining cutting-edge technologies with the classics to unravel the patterns that can be found across the hundreds of independent origins.

show abstract

A target enrichment probe set for resolving the flagellate land plant tree of life

Cited by 66 publications

References 30 publications

Strong phylogenetic signal despite high phylogenomic complexity in an Andean plant radiation (Freziera,Pentaphylacaceae)

Strong phylogenetic signal despite high phylogenomic complexity in an Andean plant radiation (Freziera,Pentaphylacaceae)

The Diversity of Plant Sex Chromosomes Highlighted through Advances in Genome Sequencing

The diversity of plant sex chromosomes highlighted through advances in genome sequencing

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