4.7 Article

Phylogenomic conflict analyses of the plastid and mitochondrial genomes via deep genome skimming highlight their independent evolutionary histories: A case study in the cinquefoil genus Potentilla sensu lato (Potentilleae, Rosaceae)

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Biochemistry & Molecular Biology

Genome-scale angiosperm phylogenies based on nuclear, plastome, and mitochondrial datasets

Hongyin Hu et al.

Summary: In this study, the phylogenies of 366 angiosperm species belonging to 97 families and 43 orders were reconstructed based on orthologous genes from the nuclear, plastid, and mitochondrial genomes. The results were largely consistent with previous studies, but there were major discrepancies in the phylogenetic relationships of the five Mesangiospermae lineages when different genomes were examined. The findings provide a basic framework for further research and can be used to explore the evolutionary trajectories of the three genome types.

JOURNAL OF INTEGRATIVE PLANT BIOLOGY (2023)

Article Plant Sciences

Mitochondrial genes from 18 angiosperms fill sampling gaps for phylogenomic inferences of the early diversification of flowering plants

Jia-Yu Xue et al.

Summary: The early diversification of angiosperms was a rapid process, leading to conflicting hypotheses regarding overall angiosperm phylogeny. Studies of mitochondrial genomes filled taxon-sampling gaps in various angiosperm lineages and provided additional evidence for exploring the early evolution and diversification of angiosperms. Despite conflicting phylogenies, there was congruence regarding deep relationships of several major angiosperm lineages, with third codon positions of mitochondrial genes producing better resolved phylogenetic relationships.

JOURNAL OF SYSTEMATICS AND EVOLUTION (2022)

Article Evolutionary Biology

Gene Tree Discord, Simplex Plots, and Statistical Tests under the Coalescent

Elizabeth S. Allman et al.

Summary: A simple graphical device, the simplex plot of quartet concordance factors, is introduced to explore a collection of gene trees on a common set of taxa. A statistical procedure is described to quantify the deviation from expectation for each subset of four taxa, suggesting when the data are not in accord with the multispecies coalescent model.

SYSTEMATIC BIOLOGY (2022)

Article Plant Sciences

What is Potentilla? A phylogeny-based taxonomy for Potentillinae (Rosaceae)

Torsten Eriksson et al.

Summary: The classification of Potentilla has historically varied greatly, with some collapsing it into a single genus and others dividing it into multiple genera. A phylogenetic perspective is used to discuss and achieve a reasonable classification based on a monophyletic clade. Other criteria, such as history, stability, gene flow, information content, and identification ease, are also taken into account.
Article Biochemistry & Molecular Biology

Phylogenomic conflict analyses in the apple genus Malus s.l. reveal widespread hybridization and allopolyploidy driving diversification, with insights into the complex biogeographic history in the Northern Hemisphere

Bin-Bin Liu et al.

Summary: Phylogenomic evidence from an increasing number of studies has shown that different data sets and analytical approaches often produce conflicting relationships. In this study, the phylogenetic relationships and historical biogeography of the economically important apple genus Malus sensu lato were investigated using multiple gene data sets and analytical methods. The results revealed discordance between nuclear and plastid genomes, and suggested the influence of hybridization and allopolyploidy events on the nuclear gene tree.

JOURNAL OF INTEGRATIVE PLANT BIOLOGY (2022)

Article Biochemistry & Molecular Biology

Plastid phylogenomic analyses of the Selaginella sanguinolenta group (Selaginellaceae) reveal conflict signatures resulting from sequence types, outlier genes, and pervasive RNA editing

Meng-Hua Zhang et al.

Summary: This study provides a comprehensive analysis of the plastomes of Selaginellaceae, revealing conflicts and uncertainties in their phylogenetic relationships and exploring the underlying causes. The results demonstrate that the coalescent method is more effective in overcoming issues caused by outlier genes and extreme RNA editing events.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2022)

Article Plant Sciences

Fragaria mitogenomes evolve rapidly in structure but slowly in sequence and incur frequent multinucleotide mutations mediated by microinversions

Weishu Fan et al.

Summary: Plant mitochondrial DNA evolves rapidly in structure but slowly in sequence. The noncoding portions of plant mitogenomes are not homologous among species, which raises questions about the rate and spectrum of mutations in noncoding regions. The study shows that plant mitogenomes have low point mutations genome-wide but exceptionally high structural variations, supporting a gain-and-loss model for the rapid loss of homology among plant mitogenomes.

NEW PHYTOLOGIST (2022)

Article Biochemistry & Molecular Biology

Plastid phylogenomic analyses of Fagales reveal signatures of conflict and ancient chloroplast capture

Ying-Ying Yang et al.

Summary: Plastid phylogenomic analyses have shed light on challenging relationships within the angiosperm Tree of Life, revealing contentious relationships and conflicting phylogenetic signals across the plastome. The study highlights the sensitivity of plastid phylogenomics to genic composition and suggests extensive introgression and chloroplast capture in the early diversification of Quercus and Quercoideae. The research provides a critical plastome perspective on Fagales phylogeny, paving the way for future studies utilizing more extensive nuclear genome data.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2021)

Article Biology

Both Conifer II and Gnetales are characterized by a high frequency of ancient mitochondrial gene transfer to the nuclear genome

Sheng-Long Kan et al.

Summary: The study on mitochondrial gene transfer/loss in gymnosperms reveals significant variations in gene content among different families, with missing genes observed in some families such as Conifer II and Gnetales. Additionally, the research suggests a two-step transfer mechanism for mitochondrial gene transfer in Conifer II and Gnetales. These findings provide insights into the evolutionary scenario of mitochondrial gene transfer in gymnosperms and factors affecting gene content variation in land plants.

BMC BIOLOGY (2021)

Article Plant Sciences

Capturing single-copy nuclear genes, organellar genomes, and nuclear ribosomal DNA from deep genome skimming data for plant phylogenetics: A case study in Vitaceae

Bin-Bin Liu et al.

Summary: With the decreasing cost and availability of bioinformatics pipelines, next-generation sequencing has revolutionized plant systematics. Genome skimming can obtain high-copy fractions of genomes and the optimal minimum sequencing depth for high-quality SCNs assembly through genome skimming is about 10x coverage. Deep genome skimming is as effective as the widely used Hyb-Seq approach for capturing large SCNs datasets.

JOURNAL OF SYSTEMATICS AND EVOLUTION (2021)

Article Evolutionary Biology

Phylogenetic Conflicts, Combinability, and Deep Phylogenomics in Plants

Stephen A. Smith et al.

SYSTEMATIC BIOLOGY (2020)

Article Biotechnology & Applied Microbiology

GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes

Jian-Jun Jin et al.

GENOME BIOLOGY (2020)

Article Biochemistry & Molecular Biology

Incongruence between gene trees and species trees and phylogenetic signal variation in plastid genes

Deise J. P. Goncalves et al.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2019)

Article Biochemical Research Methods

PGA: a software package for rapid, accurate, and flexible batch annotation of plastomes

Xiao-Jian Qu et al.

PLANT METHODS (2019)

Article Multidisciplinary Sciences

Characterizing gene tree conflict in plastome-inferred phylogenies

Joseph F. Walker et al.

Article Multidisciplinary Sciences

One thousand plant transcriptomes and the phylogenomics of green plants

James H. Leebens-Mack et al.

NATURE (2019)

Article Biochemical Research Methods

fastp: an ultra-fast all-in-one FASTQ preprocessor

Shifu Chen et al.

BIOINFORMATICS (2018)

Article Biochemical Research Methods

ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees

Chao Zhang et al.

BMC BIOINFORMATICS (2018)

Article Evolutionary Biology

Analyzing Contentious Relationships and Outlier Genes in Phylogenomics

Joseph F. Walker et al.

SYSTEMATIC BIOLOGY (2018)

Article Ecology

Contentious relationships in phylogenomic studies can be driven by a handful of genes

Xing-Xing Shen et al.

NATURE ECOLOGY & EVOLUTION (2017)

Article Plant Sciences

Conflicting results from mitochondrial genomic data challenge current views of Rubiaceae phylogeny

Catarina Rydin et al.

AMERICAN JOURNAL OF BOTANY (2017)

Article Biochemistry & Molecular Biology

Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies

Erfan Sayyari et al.

MOLECULAR BIOLOGY AND EVOLUTION (2016)

Article Multidisciplinary Sciences

AMAS: a fast tool for alignment manipulation and computing of summary statistics

Marek L. Borowiec

Article Plant Sciences

COMPARISON OF NUCLEAR, PLASTID, AND MITOCHONDRIAL PHYLOGENIES AND THE ORIGIN OF WILD OCTOPLOID STRAWBERRY SPECIES

Rajanikanth Govindarajulu et al.

AMERICAN JOURNAL OF BOTANY (2015)

Article Biochemical Research Methods

Bandage: interactive visualization ofde novogenome assemblies: Fig. 1.

Ryan R. Wick et al.

BIOINFORMATICS (2015)

Article Biochemistry & Molecular Biology

Deep phylogenetic incongruence in the angiosperm clade Rosidae

Miao Sun et al.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2015)

Article Biochemistry & Molecular Biology

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

Lam-Tung Nguyen et al.

MOLECULAR BIOLOGY AND EVOLUTION (2015)

Article Plant Sciences

Sibbaldia: a molecular phylogenetic study of a remarkably polyphyletic genus in Rosaceae

Torsten Eriksson et al.

PLANT SYSTEMATICS AND EVOLUTION (2015)

Article Biochemical Research Methods

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

Alexandros Stamatakis

BIOINFORMATICS (2014)

Article Biochemistry & Molecular Biology

Novel Information Theory-Based Measures for Quantifying Incongruence among Phylogenetic Trees

Leonidas Salichos et al.

MOLECULAR BIOLOGY AND EVOLUTION (2014)

Article Multidisciplinary Sciences

Phylotranscriptomic analysis of the origin and early diversification of land plants

Norman J. Wickett et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)

Article Multidisciplinary Sciences

Phylogenomics resolves the timing and pattern of insect evolution

Bernhard Misof et al.

SCIENCE (2014)

Article Biochemistry & Molecular Biology

Ultrafast Approximation for Phylogenetic Bootstrap

Bui Quang Minh et al.

MOLECULAR BIOLOGY AND EVOLUTION (2013)

Article Biochemistry & Molecular Biology

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

Kazutaka Katoh et al.

MOLECULAR BIOLOGY AND EVOLUTION (2013)

Article Biochemical Research Methods

The Newick utilities: high-throughput phylogenetic tree processing in the Unix shell

Thomas Junier et al.

BIOINFORMATICS (2010)

Article Multidisciplinary Sciences

Phylogenetic analysis of 83 plastid genes further resolves the early diversification of eudicots

Michael J. Moore et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)

Article Biochemical Research Methods

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

Salvador Capella-Gutierrez et al.

BIOINFORMATICS (2009)

Article Multidisciplinary Sciences

Fine-scale mergers of chloroplast and mitochondrial genes create functional, transcompartmentally chimeric mitochondrial genes

Weilong Hao et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)

Review Ecology

Gene tree discordance, phylogenetic inference and the multispecies coalescent

James H. Degnan et al.

TRENDS IN ECOLOGY & EVOLUTION (2009)

Article Multidisciplinary Sciences

Broad phylogenomic sampling improves resolution of the animal tree of life

Casey W. Dunn et al.

NATURE (2008)

Article Multidisciplinary Sciences

Genome-wide analyses of Geraniaceae plastid DNA reveal unprecedented patterns of increased nucleotide substitutions

Mary M. Guisinger et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)

Article Multidisciplinary Sciences

Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns

Robert K. Jansen et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)

Article Biochemistry & Molecular Biology

Probabilistic analysis indicates discordant gene trees in chloroplast evolution

C Vogl et al.

JOURNAL OF MOLECULAR EVOLUTION (2003)

Article Biology

Linkage disequilibrium and phylogenetic congruence between chloroplast and mitochondrial haplotypes in Silene vulgaris

MS Olson et al.

PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2000)