4.8 Article

Subgenomic Stability of Progenitor Genomes During Repeated Allotetraploid Origins of the Same Grass Brachypodium hybridum

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。
Review Plant Sciences

Patterns, mechanisms, and consequences of homoeologous exchange in allopolyploid angiosperms: a genomic and epigenomic perspective

Sontosh K. Deb et al.

Summary: Allopolyploids are formed by hybridization between different evolutionary lineages with genome doubling. Homoeologous chromosomes can undergo recombination immediately after allopolyploid formation and continue over successive generations. Homoeologous exchanges have both negative and positive effects, leading to unbalanced gametes, reduced fertility, novel phenotypic diversity, and the formation of neo-allopolyploids. The causes and consequences of homoeologous exchanges vary across lineages, generations, and genomes. Recent technological advances provide insights into the mechanistic basis of homoeologous exchanges in allopolyploid angiosperms, which have implications for understanding allopolyploid evolution and developing important traits in polyploid crops.

NEW PHYTOLOGIST (2023)

Article Genetics & Heredity

Multiple origins, one evolutionary trajectory: gradual evolution characterizes distinct lineages of allotetraploid Brachypodium

Virginia T. Scarlett et al.

Summary: This study compares and analyzes the chromosome-scale reference genome of the natural allotetraploid grass Brachypodium hybridum, revealing gradual gene loss and chromosome rearrangement during genome integration. However, no signs of homeologous recombination or pronounced transposable element activation were found, indicating a relatively mild genome dominance.

GENETICS (2023)

Article Multidisciplinary Sciences

The lack of negative association between TE load and subgenome dominance in synthesized Brassica allotetraploids

Kang Zhang et al.

Summary: Polyploidization plays a crucial role in plant evolution. Subgenome dominance, characterized by higher expression levels of genes on the dominant subgenome, is a common phenomenon in allopolyploids. The underlying mechanism of subgenome dominance remains unclear, but it is suggested that differences in transposon and DNA methylation density near genes may be involved. In this study, eight generations of allotetraploid progenies were generated from the fusion of parental genomes Brassica rapa and Brassica oleracea. Despite the differences in transposon/methylation density between the parental genomes being maintained in the neotetraploids (synthetic Brassica napus), no subgenome dominance was observed. These findings challenge the idea that differences in methylated transposon near genes alone are sufficient to initiate subgenome dominance.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2023)

Article Multidisciplinary Sciences

Scattered differentiation of unlinked loci across the genome underlines ecological divergence of the selfing grass Brachypodium stacei

Wenjie Mu et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2023)

Article Plant Sciences

Tracking the ancestry of known and 'ghost' homeologous subgenomes in model grass Brachypodium polyploids

Ruben Sancho et al.

Summary: We designed a subgenome detection pipeline (PhyloSD) that can identify the progenitor subgenomes of six grass Brachypodium allopolyploids and infer their hypothetical evolutionary scenarios for their origins.

PLANT JOURNAL (2022)

Review Plant Sciences

Brachypodium: 20 years as a grass biology model the forward?

Robert Hasterok et al.

Summary: It has been 20 years since Brachypodium distachyon was suggested as a model grass species, and the research has now expanded to the entire genus. Extensive genome sequencing and cytomolecular studies have provided important resources for understanding population diversity and various aspects of plant biology. Brachypodium is not only relevant to the biofuel industry, but also serves as an intriguing model plant for studying climate change and combinatorial stress.

TRENDS IN PLANT SCIENCE (2022)

Article Biochemistry & Molecular Biology

WGDI: A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes

Pengchuan Sun et al.

Summary: Evidence of whole-genome duplications (WGDs) has been found in most lineages on Earth. To study the complex patterns of gene collinearity in genome analysis, researchers developed a Python-based commandline tool called WGDI, which allows comprehensive analysis of polyploidy events and genome alignments. WGDI is able to improve the detection of WGDs and help reconstruct detailed karyotype evolution.

MOLECULAR PLANT (2022)

Article Plant Sciences

A major quantitative trait locus on chromosome A9, BnaPh1, controls homoeologous recombination in Brassica napus

Erin E. Higgins et al.

Summary: The study identified genetic factors that differentiate newly resynthesised B. napus from established B. napus in their ability to control homoeologous recombination. Three quantitative trait loci (QTL) were identified, with a major QTL on BnaA9 contributing between 32 and 58% of the observed variation in homoeologous recombination in B. napus. The study suggests candidate meiotic genes for manipulation to control this important trait and develop molecular markers for exploiting homoeologous recombination in crops.

NEW PHYTOLOGIST (2021)

Article Biochemistry & Molecular Biology

pixy: Unbiased estimation of nucleotide diversity and divergence in the presence of missing data

Katharine L. Korunes et al.

Summary: Population genetic analyses often use summary statistics such as pi and d(XY) to describe genetic variation patterns. However, biases can be introduced due to missing data, which can lead to underestimation of genetic diversity within and between populations. In this study, a user-friendly UNIX command line utility, pixy, is introduced to address this issue and provide unbiased estimates of pi and d(XY) regardless of the amount or form of missing data.

MOLECULAR ECOLOGY RESOURCES (2021)

Article Multidisciplinary Sciences

Ph2 encodes the mismatch repair protein MSH7-3D that inhibits wheat homoeologous recombination

Heidi Serra et al.

Summary: In wheat, meiotic recombination between homoeologues is suppressed through the action of multiple loci. The discovery of the Ph2 gene and validation of its function have provided insight into reducing homoeologous recombination. The role of the MSH7-3D protein in meiotic stabilization of allopolyploidy offers an opportunity to enhance genetic diversity in wheat through alien gene introgression.

NATURE COMMUNICATIONS (2021)

Article Chemistry, Multidisciplinary

Whole-Genome Sequence of Synthesized Allopolyploids in Cucumis Reveals Insights into the Genome Evolution of Allopolyploidization

Xiaqing Yu et al.

Summary: The study reports the first fully sequenced synthetic allopolyploid constructed from a cross between Cucumis sativus and C. hystrix, providing insights into genomic changes that occur during polyploidy and confirming that these changes emerge immediately after interspecific hybridization.

ADVANCED SCIENCE (2021)

Article Multidisciplinary Sciences

A separation-of-function ZIP4 wheat mutant allows crossover between related chromosomes and is meiotically stable

Azahara C. Martin et al.

Summary: The study reveals the critical role of TaZIP4-B2 in wheat, as well as the potential value of the 'separation-of-function' mutant line zip4-ph1d in wheat breeding.

SCIENTIFIC REPORTS (2021)

Article Plant Sciences

Comparative Genomics, Evolution, and Drought-Induced Expression of Dehydrin Genes in Model Brachypodium Grasses

Maria Angeles Decena et al.

Summary: The study conducted a comparative genomics and evolution analysis of DHN genes in Brachypodium grass species, showing that key Bdhn genes are regulated by drought induction in different ecotypes, which may be a crucial factor in acquiring water-stress tolerance in plants.

PLANTS-BASEL (2021)

Article Biochemistry & Molecular Biology

Extending approximate Bayesian computation with supervised machine learning to infer demographic history from genetic polymorphisms using DIYABC Random Forest

Francois-David Collin et al.

Summary: The DIYABC Random Forest v1.0 software package is introduced for analyzing large SNP data sets to make inferences about complex population genetic histories. This package integrates the functionality of simulating different types of molecular data under custom evolutionary scenarios and evaluating the accuracy of inferences.

MOLECULAR ECOLOGY RESOURCES (2021)

Article Ecology

Gradual evolution of allopolyploidy in Arabidopsis suecica

Robin Burns et al.

Summary: Arabidopsis suecica is a natural allotetraploid species formed through hybridization of Arabidopsis thaliana and Arabidopsis arenosa. Despite the lack of major genomic changes, changes in the meiotic machinery and cyto-nuclear processes suggest gradual adaptation to polyploidy. The absence of a genome shock and the presence of upregulation of certain genes in the A. thaliana and A. arenosa subgenomes indicate subsequent evolution in A. suecica.

NATURE ECOLOGY & EVOLUTION (2021)

Article Biodiversity Conservation

Plant genomes: Markers of evolutionary history and drivers of evolutionary change

Pamela S. Soltis et al.

Summary: The study of plant genomes helps understand the evolutionary history of plants, guiding crop improvement, medicine discovery, and species conservation. Plant genomes show diversity and carry evolutionary history, but our knowledge of them is limited.

PLANTS PEOPLE PLANET (2021)

Review Biochemistry & Molecular Biology

Polyploidy: an evolutionary and ecological force in stressful times

Yves Van de Peer et al.

Summary: Polyploidy is hypothesized to play a role in both evolutionary dead-ends and diversification. Research suggests that whole-genome duplications may be linked with extinction events or global changes, while polyploids thrive in harsh environments. Biotic interactions, particularly with pathogens or mutualists, have differing effects on polyploids compared to nonpolyploids. Stress response is identified as a key factor in the establishment and success of polyploidy.

PLANT CELL (2021)

Article Plant Sciences

Phenology and polyploidy in annual Brachypodium species (Poaceae) along the aridity gradient in Israel

Shira Penner et al.

JOURNAL OF SYSTEMATICS AND EVOLUTION (2020)

Editorial Material Genetics & Heredity

Revisiting the origin of octoploid strawberry

Aaron Liston et al.

NATURE GENETICS (2020)

Editorial Material Genetics & Heredity

Reply to: Revisiting the origin of octoploid strawberry

Patrick P. Edger et al.

NATURE GENETICS (2020)

Article Multidisciplinary Sciences

Exceptional subgenome stability and functional divergence in the allotetraploid Ethiopian cereal teff

Robert VanBuren et al.

NATURE COMMUNICATIONS (2020)

Review Plant Sciences

One subgenome to rule them all: underlying mechanisms of subgenome dominance

Elizabeth Alger et al.

CURRENT OPINION IN PLANT BIOLOGY (2020)

Review Genetics & Heredity

Genomics of Evolutionary Novelty in Hybrids and Polyploids

Gonzalo Nieto Feliner et al.

FRONTIERS IN GENETICS (2020)

Review Genetics & Heredity

Homoeologous Exchanges, Segmental Allopolyploidy, and Polyploid Genome Evolution

Annaliese S. Mason et al.

FRONTIERS IN GENETICS (2020)

Article Biotechnology & Applied Microbiology

Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies

Arang Rhie et al.

GENOME 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 Genetics & Heredity

Origin and evolution of the octoploid strawberry genome

Patrick P. Edger et al.

NATURE GENETICS (2019)

Article Biochemistry & Molecular Biology

Breaking Free: The Genomics of Allopolyploidy-Facilitated Niche Expansion in White Clover

Andrew G. Griffiths et al.

PLANT CELL (2019)

Article Biotechnology & Applied Microbiology

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

Daehwan Kim et al.

NATURE BIOTECHNOLOGY (2019)

Article Biotechnology & Applied Microbiology

SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies

Manish Goel et al.

GENOME BIOLOGY (2019)

Article Biochemical Research Methods

Minimap2: pairwise alignment for nucleotide sequences

Heng Li

BIOINFORMATICS (2018)

Article Biochemical Research Methods

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

Shifu Chen et al.

BIOINFORMATICS (2018)

Article Cell Biology

The long and short of doubling down: polyploidy, epigenetics, and the temporal dynamics of genome fractionation

Jonathan F. Wendel et al.

CURRENT OPINION IN GENETICS & DEVELOPMENT (2018)

Review Biochemistry & Molecular Biology

Brachypodium: A Monocot Grass Model Genus for Plant Biology

Karen-Beth G. Scholthof et al.

PLANT CELL (2018)

Article Evolutionary Biology

Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7

Andrew Rambaut et al.

SYSTEMATIC BIOLOGY (2018)

Article Multidisciplinary Sciences

GOATOOLS: A Python library for Gene Ontology analyses

D. V. Klopfenstein et al.

SCIENTIFIC REPORTS (2018)

Article Biochemical Research Methods

MUMmer4: A fast and versatile genome alignment system

Guillaume Marcais et al.

PLOS COMPUTATIONAL BIOLOGY (2018)

Article Biochemical Research Methods

findGSE: estimating genome size variation within human and Arabidopsis using k-mer frequencies

Hequan Sun et al.

BIOINFORMATICS (2018)

Review Genetics & Heredity

The evolutionary significance of polyploidy

Yves Van de Peer et al.

NATURE REVIEWS GENETICS (2017)

Article Biochemical Research Methods

KMC 3: counting and manipulating k-mer statistics

Marek Kokot et al.

BIOINFORMATICS (2017)

Review Plant Sciences

Impact of transposable elements on polyploid plant genomes

Carlos M. Vicient et al.

ANNALS OF BOTANY (2017)

Article Plant Sciences

Polyploidy: Pitfalls and paths to a paradigm

Douglas E. Soltis et al.

AMERICAN JOURNAL OF BOTANY (2016)

Review Plant Sciences

Genomic legacies of the progenitors and the evolutionary consequences of allopolyploidy

Kim A. Steige et al.

CURRENT OPINION IN PLANT BIOLOGY (2016)

Article Biochemistry & Molecular Biology

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

Neva C. Durand et al.

CELL SYSTEMS (2016)

Article Biochemical Research Methods

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

Felipe A. Simao et al.

BIOINFORMATICS (2015)

Article Biotechnology & Applied Microbiology

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

Mihaela Pertea et al.

NATURE BIOTECHNOLOGY (2015)

Article Multidisciplinary Sciences

Hybrid origins and the earliest stages of diploidization in the highly successful recent polyploid Capsella bursa-pastoris

Gavin M. Douglas et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (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 Biochemical Research Methods

InterProScan 5: genome-scale protein function classification

Philip Jones et al.

BIOINFORMATICS (2014)

Article Multidisciplinary Sciences

Origin, inheritance, and gene regulatory consequences of genome dominance in polyploids

Margaret R. Woodhouse et al.

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

Article Multidisciplinary Sciences

Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome

Boulos Chalhoub et al.

SCIENCE (2014)

Article Biochemical Research Methods

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

Remco Bouckaert et al.

PLOS COMPUTATIONAL BIOLOGY (2014)

Review Plant Sciences

The more the better? The role of polyploidy in facilitating plant invasions

Mariska te Beest et al.

ANNALS OF BOTANY (2012)

Article Plant Sciences

Evolution and taxonomic split of the model grass Brachypodium distachyon

Pilar Catalan et al.

ANNALS OF BOTANY (2012)

Article Multidisciplinary Sciences

Evolution Canyon, a potential microscale monitor of global warming across life

Eviatar Nevo

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)

Article Multidisciplinary Sciences

Extensive chromosomal variation in a recently formed natural allopolyploid species, Tragopogon miscellus (Asteraceae)

Michael Chester et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)

Article Multidisciplinary Sciences

Ancestral polyploidy in seed plants and angiosperms

Yuannian Jiao et al.

NATURE (2011)

Article Genetics & Heredity

A framework for variation discovery and genotyping using next-generation DNA sequencing data

Mark A. DePristo et al.

NATURE GENETICS (2011)

Article Biochemical Research Methods

BEDTools: a flexible suite of utilities for comparing genomic features

Aaron R. Quinlan et al.

BIOINFORMATICS (2010)

Review Plant Sciences

POLYPLOIDY AND ANGIOSPERM DIVERSIFICATION

Douglas E. Soltis et al.

AMERICAN JOURNAL OF BOTANY (2009)

Article Biochemical Research Methods

The Sequence Alignment/Map format and SAMtools

Heng Li et al.

BIOINFORMATICS (2009)

Article Biochemistry & Molecular Biology

Fast model-based estimation of ancestry in unrelated individuals

David H. Alexander et al.

GENOME RESEARCH (2009)

Review Genetics & Heredity

Evolutionary Genetics of Genome Merger and Doubling in Plants

Jeff J. Doyle et al.

ANNUAL REVIEW OF GENETICS (2008)

Review Biochemical Research Methods

Recent developments in the MAFFT multiple sequence alignment program

Kazutaka Katoh et al.

BRIEFINGS IN BIOINFORMATICS (2008)

Editorial Material Multidisciplinary Sciences

Perspective - Genomic plasticity and the diversity of polyploid plants

A. R. Leitch et al.

SCIENCE (2008)

Editorial Material Multidisciplinary Sciences

Perspective - Synteny and collinearity in plant genomes

Haibao Tang et al.

SCIENCE (2008)

Article Biochemistry & Molecular Biology

NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins

Kim D. Pruitt et al.

NUCLEIC ACIDS RESEARCH (2007)

Article Genetics & Heredity

Population structure and eigenanalysis

Nick Patterson et al.

PLOS GENETICS (2006)

Article Biochemistry & Molecular Biology

AUGUSTUS:: ab initio prediction of alternative transcripts

Mario Stanke et al.

NUCLEIC ACIDS RESEARCH (2006)

Article Biochemistry & Molecular Biology

Application of phylogenetic networks in evolutionary studies

DH Huson et al.

MOLECULAR BIOLOGY AND EVOLUTION (2006)

Review Genetics & Heredity

The advantages and disadvantages of being polyploid

L Comai

NATURE REVIEWS GENETICS (2005)

Article Biochemical Research Methods

De novo identification of repeat families in large genomes

AL Price et al.

BIOINFORMATICS (2005)

Article Cell Biology

Repbase update, a database of eukaryotic repetitive elements

J Jurka et al.

CYTOGENETIC AND GENOME RESEARCH (2005)

Article Multidisciplinary Sciences

Role of transposable elements in heterochromatin and epigenetic control

Z Lippman et al.

NATURE (2004)

Review Plant Sciences

From diploids to allopolyploids: The emergence of efficient pairing control genes in plants

E Jenczewski et al.

CRITICAL REVIEWS IN PLANT SCIENCES (2004)

Article Biochemistry & Molecular Biology

Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies

BJ Haas et al.

NUCLEIC ACIDS RESEARCH (2003)

Article Biochemistry & Molecular Biology

OrthoMCL: Identification of ortholog groups for eukaryotic genomes

L Li et al.

GENOME RESEARCH (2003)

Article Biochemistry & Molecular Biology

The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000

A Bairoch et al.

NUCLEIC ACIDS RESEARCH (2000)