Plastid Genome Assembly Using Long‐read data

Molecular Ecology Resources, Journal Year: 2023, Volume and Issue: 23(6), P. 1442 - 1457

Published: March 20, 2023

Although plastid genome (plastome) structure is highly conserved across most seed plants, investigations during the past two decades have revealed several disparately related lineages that experienced substantial rearrangements. Most plastomes contain a large inverted repeat and single-copy regions, few dispersed repeats; however, of some taxa harbour long sequences (>300 bp). These repeats make it challenging to assemble complete using short-read data, leading misassemblies consensus with spurious Single-molecule, long-read sequencing has potential overcome these challenges, yet there no on effective method for accurately assembling data. We generated pipeline, Genome Assembly Using Long-read data (ptGAUL), address problem plastome assembly from Oxford Nanopore Technologies (ONT) or Pacific Biosciences platforms. demonstrated efficacy ptGAUL pipeline 16 published sets. showed quickly produces accurate unbiased assemblies only ~50× coverage Additionally, we deployed four new Juncus (Juncaceae) ONT reads. Our results many rearrangements in compared basal Poales. The available GitHub: https://github.com/Bean061/ptgaul.

Language: Английский

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GeneMiner: A tool for extracting phylogenetic markers from next‐generation sequencing data

Molecular Ecology Resources, Journal Year: 2024, Volume and Issue: 24(3)

Published: Jan. 10, 2024

Abstract The advancement of next‐generation sequencing (NGS) technologies has been revolutionary for the field evolutionary biology. This technology led to an abundance available genomes and transcriptomes researchers mine. Specifically, can mine various types molecular markers that are vital phylogenetic, ecological studies. Numerous tools have developed extract these from NGS data. However, due insufficient number well‐annotated reference non‐model organisms, it remains challenging obtain accurately efficiently. Here, we present GeneMiner, improved expanded version our previous tool, Easy353. GeneMiner combines reference‐guided de Bruijn graph assembly with seed self‐discovery greedy extension. Additionally, includes a verification step using parameter‐bootstrap method reduce pitfalls associated relatively distant reference. Our results, both experimental simulation data, showed acquire phylogenetic plants transcriptomic, genomic other is designed be user‐friendly, fast memory‐efficient. Further, compatible Linux, Windows macOS. All source codes publicly on GitHub ( https://github.com/sculab/GeneMine r) Gitee https://gitee.com/sculab/GeneMiner ) easy accessibility transparency.

Language: Английский

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Comparative and phylogenetic analysis of Potentilla and Dasiphora (Rosaceae) based on plastid genome

BMC Plant Biology, Journal Year: 2025, Volume and Issue: 25(1)

Published: Feb. 10, 2025

Potentilla L. and Dasiphora are predominantly perennial herbs, occasionally manifesting as annuals or shrubs, primarily found in the northern temperate zone. However, taxonomic classification within this group remains contentious, particularly regarding genus boundaries species delineation. Therefore, study sequenced analyzed complete plastid genomes of 19 from Dasiphora, comparing them with five previously published sequences. Our objectives included reconstructing phylogenetic relationships investigating cytonuclear discordance among them. These were highly conserved structure, GC content, overall genome composition, comprising 84 protein-coding genes, 37 tRNA 8 rRNA genes. Notably, all lacked unique intron for rpl2. Comparative genomic analyses revealed that variations size due to differences lengths LSC, SSC, IR regions. The region was conserved, while non-coding regions exhibited higher variability than coding We screened SSR identified seven variable loci serve potential molecular markers, offering valuable insights into intergeneric between Dasiphora. Phylogenetic based on nuclear (ITS, ETS) cytoplasmic (plastid, mitochondrial) genes confirmed monophyly results largely consistent previous studies supported by robust reliability metrics. conflicts Potentilla, which frequently disrupt its monophyly. hypothesize these may result interspecific hybridization incomplete lineage sorting events during evolutionary history genus. This offers a theoretical foundation advancing identification research species. future work could benefit greater detail criteria selecting mitochondrial gene sequences nrDNA datasets.

Language: Английский

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An updated classification for the hyper‐diverse genusCorydalis(Papaveraceae: Fumarioideae) based on phylogenomic and morphological evidence

Journal of Integrative Plant Biology, Journal Year: 2023, Volume and Issue: 65(9), P. 2138 - 2156

Published: April 29, 2023

Abstract The genus Corydalis , with ca. 530 species, has long been considered taxonomically challenging because of its great variability. Previous molecular analyses, based on a few markers and incomplete taxonomic sampling, were clearly inadequate to delimit sections subgenera. We have performed phylogenetic analyses related taxa, using 65 shared protein‐coding plastid genes from 313 accessions (including 280 samples 226 species ) 152 universal low‐copy nuclear 296 271 covering all 42 previously recognized five independent “series”. Phylogenetic trees inferred Bayesian Inference Maximum Likelihood. Eight selected morphological characters estimated ancestral state reconstructions. Results include: (i) the three subgenera two are fully supported by both data; third, subg. Cremnocapnos is weakly DNA only, whereas in data included form successive outgroups rest genus; (ii) among “series”, 25 one “series” resolved as monophyletic sets; (iii) common ancestor likely be perennial plant taproot, yellow flowers short saccate spur, linear fruits recurved fruiting pedicels, seeds elaiosomes; (iv) we provide new classification four (of which Bipapillatae here newly described), 39 sections, 16 consistent previous classification, recircumscribed, section reinstated six established. Characters associated lifespan, underground structures, floral fruit elaiosomes important for recognition sections. These combined character reconstructions uncovered unrecognized relationships, greatly improved our understanding evolution genus.

Language: Английский

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Artifactual Orthologs and the Need for Diligent Data Exploration in Complex Phylogenomic Datasets: A Museomic Case Study from the Andean Flora

Systematic Biology, Journal Year: 2024, Volume and Issue: 73(2), P. 308 - 322

Published: Jan. 2, 2024

The Andes mountains of western South America are a globally important biodiversity hotspot, yet there is paucity resolved phylogenies for plant clades from this region. Filling an gap in our understanding the World's richest flora, we present first phylogeny Freziera (Pentaphylacaceae), Andean-centered, cloud forest radiation. Our dataset was obtained via hybrid-enriched target sequence capture Angiosperms353 universal loci 50 ca. 75 spp., almost entirely herbarium specimens. We identify high phylogenomic complexity Freziera, including presence data artifacts. Via by-eye observation gene trees, detailed examination warnings recently improved assembly pipelines, and tree filtering, identified that artifactual orthologs (i.e., only one copy multicopy due to differential assembly) were source heterogeneity had negative impact on phylogenetic inference support. These may be common datasets, where multiple instances genome duplication common. After accounting as error, significant, but nonspecific signal introgression using Patterson's D f4 statistics. Despite complexity, able resolve into 9 well-supported subclades whose evolution has been shaped by evolutionary processes, incomplete lineage sorting, historical flow, duplication. results highlight complexities phylogenomics, which heightened Andean radiations, show filtering processing artifacts standard approaches inference.

Language: Английский

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Nanopore Sequencing Technology as an Emerging Tool for Diversity Studies of Plant Organellar Genomes

Diversity, Journal Year: 2024, Volume and Issue: 16(3), P. 173 - 173

Published: March 7, 2024

In this comprehensive review, we explore the significant role that nanopore sequencing technology plays in study of plant organellar genomes, particularly mitochondrial and chloroplast DNA. To date, application has led to successful over 100 genomes around 80 genomes. These figures not only demonstrate technology’s robustness but also mark a substantial advancement field, highlighting its efficacy decoding complex dynamic nature these Nanopore sequencing, known for long-read capabilities, significantly surpasses traditional techniques, especially addressing challenges like structural complexity sequence repetitiveness This review delves into nuances elaborating on benefits compared conventional methods groundbreaking applications it fostered genomics. While transformative impact is clear, limitations, including error rates computational requirements, are discussed, alongside potential solutions prospects technological refinement.

Language: Английский

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Phylogenomic insights into the historical biogeography, character-state evolution, and species diversification rates of Cypripedioideae (Orchidaceae)

Molecular Phylogenetics and Evolution, Journal Year: 2024, Volume and Issue: 199, P. 108138 - 108138

Published: July 6, 2024

Language: Английский

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Phylogenomics-driven host test list selection for weed biological control

Biological Control, Journal Year: 2024, Volume and Issue: 193, P. 105529 - 105529

Published: May 13, 2024

A concern in weed biological control research is the potential for candidate biocontrol agents to impact not only target but also native or economically important flora. The degree of evolutionary relatedness between species and a non-target key predictor susceptibility agent. To manage this risk, practitioners need understand phylogenetic position host relative plant species. However, comprehensively sampled trees are often unavailable, with incomplete information scattered across multiple publications. Further, older published phylogenies based on Sanger sequence data lack branch resolution support, which increases uncertainty decision making. Decreasing sequencing cost technological advances have led phylogenomic approaches being more widely used relationships For example, capture methods using bait kits such as Angiosperms353 enable cost-effective timely phylogenomic-level analysis flowering groups at different scales. Here, we introduce workflow embed comprehensive understanding into efficient development test lists control. We demonstrate effectiveness through case study major crop flaxleaf fleabane (Erigeron bonariensis). Phylogenomic was conducted 280 tribe Astereae (family Asteraceae) occurring Australia New Zealand, clarifying related clades non-native Astereae. consider tree context previously proposed list discuss taxonomic implications, highlighting avenues future molecular-based work uncover origin Australian fleabanes. This provides demonstrates practical application inference support risk making classical

Language: Английский

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Navigating phylogenetic conflict and evolutionary inference in plants with target capture data

Published: May 27, 2024

Target capture has quickly become a preferred approach for plant systematic and evolutionary research, marking step-change in the generation of data phylogenetic inference. While this advancement facilitated resolution many relationships, conflict continues to be reported, often attributed genome duplication, reticulation, deep coalescence or rapid speciation – processes that are particularly common evolution. The proliferation methods designed analyse target presence these can overwhelming researchers, especially students. In review, we guide researchers through bioinformatic workflow, with particular focus on robust inference conflict. Through highlight key considerations reducing artefactual conflict, synthesise strategies managing paralogs, explain causes measurement summarise current investigating biological underlying draw from examples Australian flora, review is broadly relevant any researcher working data. We conclude inherent inevitable but when properly managed, provide unprecedented insight into extraordinary complex histories plants.

Language: Английский

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Revisiting the backbone phylogeny and inferring the evolutionary trends in inflorescence of Elsholtzieae (Lamiaceae): new insights from orthologous nuclear genes

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

Published: Feb. 18, 2025

Abstract The angiosperm tribe of Elsholtzieae (Lamiaceae) is characterized by complex inflorescences and has notable medicinal economic significance. Relationships within Elsholtzieae, including the monophyly Elsholtzia Keiskea , relationships among Mosla Perilla remain uncertain, hindering insights into inflorescence evolution tribe. Using hybridization capture sequencing deep genome skimming data analysis, we reconstruct a phylogeny using 279 orthologous nuclear loci from 56 species. We evaluated uncertainty concatenation, coalescent network approaches. time‐calibrated phylogeny, reconstructed ancestral traits to elucidate patterns in their Our analyses consistently support paraphyly genus . Phylogenetic analyses, confirmed PhyloNetworks SplitsTree, showed reticulation events major lineages Elsholtzieae. unstable polyphyly observed ASTRAL (accurate species tree algorithm), ML (maximum likelihood) MP parsimony) may be related introgression Based on phylogenetic trees evolutionary trajectory demonstrates pattern diversification, with specialization as one aspect this process. hypothesis that compressed evolved larger more forms through successive compressions axis. Additionally, certain display trend towards simplified inflorescences, reduction number florets. This highlights both diversity structures

Language: Английский

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