DNA Barcoding as a Plant Identification Method

Applied Sciences, Journal Year: 2024, Volume and Issue: 14(4), P. 1415 - 1415

Published: Feb. 8, 2024

In the last two decades, plant taxonomy has bloomed, following development of a novel technique, namely, DNA barcoding. barcodes are standardized sequences, ideally unique, coding or non-coding, either from genome organism its organelles, that used to identify/classify an organismal group; in short, method includes amplification barcode, sequencing and comparison with reference database containing relevant sequences different species. plants, use universal such as COI, which is animals, not been achieved so far. This review provides comprehensive overview progress made barcoding within field taxonomy. It highlights success various barcode loci, emergence super chloroplast genome, overall impact next-generation technologies on field. The discussion approaches reflects ongoing efforts refine optimize techniques for contributing advancement our understanding biodiversity.

Language: Английский

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Subfamily evolution analysis using nuclear and chloroplast data from the same reads

Scientific Reports, Journal Year: 2025, Volume and Issue: 15(1)

Published: Jan. 3, 2025

The chloroplast (cp) genome is a widely used tool for exploring plant evolutionary relationships, yet its effectiveness in fully resolving these relationships remains uncertain. Integrating cp data with nuclear DNA information offers more comprehensive view but often requires separate datasets. In response, we employed the same raw read sequencing to construct genome-based trees and phylogenetic using Read2Tree, cost-efficient method extracting conserved gene sequences from data, focusing on Aurantioideae subfamily, which includes Citrus relatives. resulting were consistent existing derived high-throughput sequencing, diverged trees. To elucidate underlying complex processes causing discordances, implemented an integrative workflow that utilized multiple alignments of each generated by conjunction other phylogenomic methods. Our analysis revealed incomplete lineage sorting predominantly drives while introgression ancient also contribute topological discrepancies within certain clades. This study underscores cost-effectiveness both analyses understanding relationships.

Language: Английский

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hybpiper‐nf and paragone‐nf: Containerization and additional options for target capture assembly and paralog resolution

Applications in Plant Sciences, Journal Year: 2023, Volume and Issue: 11(4)

Published: July 1, 2023

The HybPiper pipeline has become one of the most widely used tools for assembly target capture data phylogenomic analysis. After production locus sequences and before phylogenetic analysis, identification paralogs is a critical step ensuring accurate inference evolutionary relationships. Algorithmic approaches using gene tree topologies ortholog groups are computationally efficient broadly applicable to non-model organisms, especially in absence known species tree.

Language: Английский

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Target capture and genome skimming for plant diversity studies

Applications in Plant Sciences, Journal Year: 2023, Volume and Issue: 11(4)

Published: July 1, 2023

Recent technological advances in long-read high-throughput sequencing and assembly methods have facilitated the generation of annotated chromosome-scale whole-genome sequence data for evolutionary studies; however, generating such can still be difficult many plant species. For example, obtaining high-molecular-weight DNA is typically impossible samples historical herbarium collections, which often degraded DNA. The need to fast-freeze newly collected living conserve high-quality complicated when plants are only found remote areas. Therefore, short-read reduced-genome representations, as target capture genome skimming, remain important studies. Here, we review pros cons each technique non-model taxa. We provide guidance related logistics, budget, genomic resources previously available clade, nature study. Furthermore, assess bioinformatic analyses, detailing best practices pitfalls, suggest pathways combine generated with legacy data. Finally, explore possible downstream analyses allowed by type using technique. a practical guide help researchers make best-informed choice regarding reduced representation studies cases where remains impractical.

Language: Английский

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Genome and Metagenome Skimming: Future Sequencing Methods for Environmental DNA (eDNA) Studies

Molecular Ecology Resources, Journal Year: 2025, Volume and Issue: unknown

Published: March 7, 2025

Genome skimming (GS), also referred to as low-coverage shotgun sequencing, is an efficient and cost-effective sequencing method that targets high-copy regions in genomes. It most commonly used for species identification, phylogenetic analysis expansion of reference libraries. GS can be applied single or composite DNA samples representing multiple species; the latter termed metagenome (MGS). GS/MGS shows promise effective approach environmental (eDNA) studies, but it currently limited ancient sedimentary samples. There potential expand this methodology other eDNA sources, including water, soil airborne In paper, we introduce briefly review its current applications. We discuss benefits challenges using assay eDNA. a promising technology could broaden studies if some methodological addressed.

Language: Английский

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Phylogenetic relationships and the repeated loss of traits associated with sicklebill pollination in Centropogon subgenus Centropogon (Campanulaceae)

American Journal of Botany, Journal Year: 2025, Volume and Issue: unknown

Published: March 10, 2025

Centropogon subgenus comprises 55 species found primarily in midelevation Andean forests featuring some of the most curved flowers among angiosperms. Floral curvature is linked to coevolution with sicklebill hummingbird, which pollinates species. Despite charismatic flowers, there limited knowledge about phylogenetic relationships and floral evolution. We conducted first densely sampled phylogenomic analysis clade using methods that account for incomplete lineage sorting on a sequence capture dataset generated lineage-specific probe set. Using comparative methods, we test correlated evolution two traits central pollination. improve understanding by more than doubling past taxon sampling. confirm monophyly sections, non-monophyly remaining sections. The characterized high gene tree discordance. Three widespread display contrasting dynamics, C. cornutus forming granulosus solanifolius non-monophyletic, biogeographically clustered lineages. Correlated inflorescence structure has led multiple putative losses adds growing body literature plant clades This phylogeny serves as foundational framework further macroevolutionary investigations into environmental biogeographic factors shaping pollination-related traits.

Language: Английский

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Target capture sequencing clarifies key relationships in the Eriostemon group (Rutaceae: Zanthoxyloideae) and supports a reclassification of Philotheca, including the recognition of two new genera

Taxon, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 6, 2025

Abstract The Eriostemon group (Rutaceae) is a clade of 16 genera and ~ 209 species endemic to Australia, New Zealand Caledonia. Recent efforts address taxonomic phylogenetic uncertainty in the using plastome nuclear ribosomal DNA sequences have made some progress but also highlighted problematic areas that require further research. In particular, current circumscription Philotheca known be non‐monophyletic, unclear relationships prevented reclassification group. We generated target capture data Angiosperms353 universal bait kit conducted analyses on with aims resolving uncertain backbone clarifying . Our results uncovered extensive cytonuclear discordance group, conflict between our phylogenies previous observed several key tree. Despite this, positions polyphyletic lineages were consistent enough across enable confident genus, which presented herein. Two sections , P. sect. Corynonema Erionema are raised generic rank under names Erioseira respectively. Cyanochlamys transferred into genus Muiriantha type section retained becomes entirety genus. Appropriate nomenclatural changes transfer all currently recognised subspecies their respective this new classification.

Language: Английский

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Being ghosted: determining the progenitor genomes and biogeographic origin of the invasive fern giant salvinia

Biological Invasions, Journal Year: 2025, Volume and Issue: 27(5)

Published: April 18, 2025

Language: Английский

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Leafing through genetic barcodes: An assessment of 14 years of plant DNA barcoding in South Africa

South African Journal of Botany, Journal Year: 2024, Volume and Issue: 172, P. 474 - 487

Published: Aug. 6, 2024

South Africa, a global biodiversity hotspot, faces escalating threats to its rich plant diversity, including habitat loss, climate change, invasive species, and illegal harvesting. These are further exacerbated by the country's taxonomic impediment, which hinders both conservation sustainable development efforts. This paper assesses efficiency of DNA barcoding as tool for species identification within African context. While offers promising applications in conservation, significant gaps challenges persist. We provide comprehensive overview initiatives Africa – querying public data portal records, 12,456 published specimen records encompassing 159 families ca. 3,449 were returned. numbers highlight historical progress, database contributions, technological advancements, coverage. Despite contributing third-highest number Magnoliophyta Barcode Life Data System (BOLD), endemic geographic regions urgent need targeted increased collaboration, only 16 % known flora has been barcoded. The underutilisation BOLD financial constraints pose barriers expanding records. However, advancements sequencing technologies offer cost-effective solutions. advocate concerted efforts enhance utilisation, harmonise databases, prioritise sampling underrepresented taxa effectively preserve Africa's diverse life.

Language: Английский

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PAV-spotter: using signal cross-correlations to identify Presence/Absence Variation in target capture data

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 29, 2024

Abstract High throughput sequencing technologies have become essential in the fields of evolutionary biology and genomics. When dealing with non-model organisms or genomic gigantism, whole genomes is still relatively costly therefore reduced-genome representations are frequently obtained, for instance by ‘target capture’ approaches. While computational tools exist that can handle target capture data identify small-scale variants such as single nucleotide polymorphisms micro-indels, options to large scale structural limited. To meet this need, we introduce PAV-spotter: a tool presence/absence variation (PAV) data. PAV-spotter conducts signal cross-correlation calculation, which distribution read counts per between samples different priori defined classes – e.g. male versus female, diseased healthy compared. We apply test our methodology studying Triturus newts: salamanders gigantic currently lack an annotated reference genome. newts suffer from hereditary disease kills half their offspring during embryogenesis. compare two types embryos, characterized unique deletions, those embryos. Our findings show helps expose variants, even face medium low coverage levels, sample sizes, background noise due mis-mapped reads. be used study underlying supergene systems absence genome assemblies. The code, including further explanation on how use customize it, available through GitHub repository: https://github.com/Wielstra-Lab/PAVspotter .

Language: Английский

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