Peeling back the layers: First phylogenomic insights into the Ledebouriinae (Scilloideae, Asparagaceae)

Howard, Cody Coyotee; Crowl, Andrew A.; Harvey, Timothy S.; Cellinese, Nico

doi:10.1016/j.ympev.2022.107430

Cited by 12 publications

(48 citation statements)

References 67 publications

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“…Ledebouriinae samples were obtained from the field, private collections, and herbarium vouchers (Howard et al, 2022). DNA extractions were performed using a modified CTAB protocol, followed by high throughput sequencing on an Illumina HiSeq using the Angiosperms353 universal probe set (Johnson et al, 2019).…”

Section: Phylogenetic Analysismentioning

confidence: 99%

“…Within a subclade of Ledebouria Clade A, phylogenetic relationships are poorly supported (Figure 2, node a) (Howard et al, 2022). However, given the potential rapid radiation along the backbone of this group, we wanted to explore the biogeography of this clade since it may contain an interesting history.…”

Section: Biogeographical Uncertaintymentioning

confidence: 99%

“…In sub-Saharan Africa, the Ledebouriinae are predominantly found within more seasonal landscapes, with highest diversity in the Limpopo, Mpumalanga, and KwaZulu-Natal regions of South Africa (Venter, 1993), yet some occurrences are documented from more wet, tropical regions (Figure 1). Much diversity within the Ledebouriinae, however, remains undescribed to science (Howard, 2014;Howard et al, 2022).…”

Section: Introductionmentioning

confidence: 99%

“…Additionally, an expanded phylogenomic analysis of the group suggests that a complex biogeographical history awaits to be thoroughly examined (Howard et al, 2022). Previous dating analyses have estimated the origin of the Ledebouriinae sometime within the last 25 myr in sub-Saharan Africa (Ali et al, 2012;Buerki et al, 2012).…”

Section: Introductionmentioning

confidence: 99%

“…Furthermore, the phylogenetic reconstructions of Pfosser et al (2012) suggested two independent dispersal events to Madagascar, but low phylogenetic resolution diminished confidence in this hypothesis. A recent phylogenomic analysis of the Ledebouriinae provided the framework to suggest (without testing) multiple dispersals to Madagascar, and a potential migration out of Africa via the Arabian Peninsula into India (Howard et al, 2022).…”

Section: Introductionmentioning

confidence: 99%

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Bioefficacy of hydroxytyrosol-rich food supplements on preventing lipid peroxidation in healthy men

Bender

Candi

Rogel

2022

Preprint

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In the present study we report the efficacy of food matrices derived from olives in preventing oxidation of low-density lipoprotein cholesterol (LDL) and lipid peroxidation. To this end, 12 healthy volunteers were divided into 3 groups and cross-received a single dose of olive phenolics, mainly hydroxytyrosol (HT), provided as a liquid dietary supplement (30.6 or 61.5 mg HT), or as fortified extra virgin olive oil (12.19 mg HT + tyrosol). Blood and urine samples were collected at baseline and up to 12 hours after ingestion. Plasma oxidized LDL levels were measured by ELISA using a monoclonal antibody, while F2-isoprostanes were quantified in urine by UHPLC-MS/MS. Despite the great variability between individuals, a tendency to reduce lipoxidation reactions has been observed after olive phenolics intake in both, blood and urine. In addition, the subgroup of individuals with the highest baseline lipoxidation level showed a decrease in F2-isoprostanes (p < 0.05) after taking the food supplements, as well as a marked decrease in oxidized LDL levels (p < 0.01) after intake of the food supplement with the lowest HT dose. These promising results suggest that HT supplementation could be a useful aid in preventing lipoxidation. Additionally, people with a redox imbalance could benefit even more from supplementing with bioavailable HT.

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Section: Phylogenetic Analysismentioning

confidence: 99%

Section: Biogeographical Uncertaintymentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Bioefficacy of hydroxytyrosol-rich food supplements on preventing lipid peroxidation in healthy men

Bender

Candi

Rogel

2022

Preprint

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Developing Asparagaceae1726: An Asparagaceae‐specific probe set targeting 1726 loci for Hyb‐Seq and phylogenomics in the family

Bentz,

Leebens‐Mack

2024

Appl Plant Sci

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PremiseTarget sequence capture (Hyb‐Seq) is a cost‐effective sequencing strategy that employs RNA probes to enrich for specific genomic sequences. By targeting conserved low‐copy orthologs, Hyb‐Seq enables efficient phylogenomic investigations. Here, we present Asparagaceae1726—a Hyb‐Seq probe set targeting 1726 low‐copy nuclear genes for phylogenomics in the angiosperm family Asparagaceae—which will aid the often‐challenging delineation and resolution of evolutionary relationships within Asparagaceae.MethodsHere we describe and validate the Asparagaceae1726 probe set (https://github.com/bentzpc/Asparagaceae1726) in six of the seven subfamilies of Asparagaceae. We perform phylogenomic analyses with these 1726 loci and evaluate how inclusion of paralogs and bycatch plastome sequences can enhance phylogenomic inference with target‐enriched data sets.ResultsWe recovered at least 82% of target orthologs from all sampled taxa, and phylogenomic analyses resulted in strong support for all subfamilial relationships. Additionally, topology and branch support were congruent between analyses with and without inclusion of target paralogs, suggesting that paralogs had limited effect on phylogenomic inference.DiscussionAsparagaceae1726 is effective across the family and enables the generation of robust data sets for phylogenomics of any Asparagaceae taxon. Asparagaceae1726 establishes a standardized set of loci for phylogenomic analysis in Asparagaceae, which we hope will be widely used for extensible and reproducible investigations of diversification in the family.

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Integrating genomic sequencing resources: an innovative perspective on recycling with universal Angiosperms353 probe sets

Wang,

Xiong,

Wang

et al. 2024

HORTIC. ADV.

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Sequencing strategies have continually advanced, with high-throughput sequencing (HTS) technologies emerging as pivotal tools in plant phylogenomics. As a standard form of target capture sequencing, hybridization target enrichment sequencing (Hyb-seq) is innovative and flexible, and then HTS strategy is widely adopted in phylogenomics. The universal Angiosperms353 probe sets (Angiosperms353) are instrumental in Hyb-seq and have been witnessed increased application in recent years. This review integrates numerous publications and empirical datasets to comprehensively assess the potential applications of Angiosperms353. Through evaluations using 18-taxa and 343-taxa genomic datasets, this review explores potential factors influencing Angiosperms353 gene capture. The RNA-seq strategy yielded the highest number of Angiosperms353 genes, followed by whole-genome sequencing and genome skimming. Increased sequencing depth enhanced gene capture yields, and no evident bias was observed across all tested angiosperm groups. In the genomics era with extensive HTS data, this review provides comprehensive guidelines for the practical application of Angiosperms353, promoting resource recycling and maximizing genomic data sharing and utilization.

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Peeling back the layers: First phylogenomic insights into the Ledebouriinae (Scilloideae, Asparagaceae)

Cited by 12 publications

References 67 publications

Bioefficacy of hydroxytyrosol-rich food supplements on preventing lipid peroxidation in healthy men

Bioefficacy of hydroxytyrosol-rich food supplements on preventing lipid peroxidation in healthy men

Developing Asparagaceae1726: An Asparagaceae‐specific probe set targeting 1726 loci for Hyb‐Seq and phylogenomics in the family

Integrating genomic sequencing resources: an innovative perspective on recycling with universal Angiosperms353 probe sets

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