4.8 Article

Transition to Self-compatibility Associated With Dominant S-allele in a Diploid Siberian Progenitor of Allotetraploid Arabidopsis kamchatica Revealed by Arabidopsis lyrata Genomes

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

Origin, loss, and regain of self-incompatibility in angiosperms

Hong Zhao et al.

Summary: Research shows that different species with the SI system can detoxify S-RNases from Petunia, which may have ancestral features and have evolved additional SLFs. Type-1 is likely maintained in many lineages through deletion of duplicate S-loci, while in other lineages SI may have been lost through deletion of S-loci or retention of duplications.

PLANT CELL (2022)

Article Genetics & Heredity

Male and female recombination landscapes of diploid Arabidopsis arenosa

Marinela Dukic et al.

Summary: The study discusses the impact of meiotic crossover events on chromosome segregation and inheritance patterns, emphasizing the influence of recombination landscape variations on evolutionary processes. Using Arabidopsis arenosa as a model, the research reveals the molecular basis of recombination rate evolution and uncovers differences in recombination rates between different populations.

GENETICS (2022)

Review Biology

The selfing syndrome and beyond: diverse evolutionary consequences of mating system transitions in plants

Takashi Tsuchimatsu et al.

Summary: The shift from outcrossing to self-fertilization is a common evolutionary transition in flowering plants. Selfing species share similar reproductive traits, known as the selfing syndrome. Recent studies have used population genomics and high-throughput sequencing to uncover the molecular and genetic basis for the evolution of the selfing syndrome in several plant genera. These studies have identified specific genes and mutations responsible for selfing syndrome traits, and have investigated the relationship between selfing and interspecific pollen transfer.

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2022)

Article Multidisciplinary Sciences

Recent speciation associated with range expansion and a shift to self-fertilization in North American Arabidopsis

Yvonne Willi et al.

Summary: Geographic separation, divergent selection, and chance genomic change are the main processes promoting reproductive isolation and speciation. This study suggests that climate change, range expansion, and a shift in mating behavior can also initiate the processes of parapatric speciation.

NATURE COMMUNICATIONS (2022)

Review Plant Sciences

Ancestral self-compatibility facilitates the establishment of allopolyploids in Brassicaceae

Polina Yu Novikova et al.

Summary: Self-incompatibility systems based on self-recognition play a role in maintaining genetic variation and reducing inbreeding in hermaphroditic plants. However, for polyploids that often have limited mating partners, self-incompatibility can hinder reproduction. In contrast, self-compatibility offers an advantage by allowing for immediate reproductive viability. Diploid selfing lineages may facilitate the formation of new allopolyploid species by transitioning to selfing. The establishment of allopolyploid species in Brassicaceae involves the loss of the self-incompatibility mechanism in one ancestor, which promotes selfing in allopolyploids.

PLANT REPRODUCTION (2022)

Article Biochemistry & Molecular Biology

Maintenance of Adaptive Dynamics and No Detectable Load in a Range-Edge Outcrossing Plant Population

Margarita Takou et al.

Summary: The study found that in the populations of the European subspecies Arabidopsis lyrata ssp. petraea, edge populations faced a decline in effective population size and an increase in derived nonsynonymous variants, indicating an increase in the genomic burden of deleterious mutations but a decrease in rare deleterious variants. While the demographic history predicted a slight decrease in per-individual fitness for the range-edge population, it performed well in terms of growth and survival, showing strong resilience to the effect of range expansion.

MOLECULAR BIOLOGY AND EVOLUTION (2021)

Article Biochemical Research Methods

Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm

Haoyu Cheng et al.

Summary: hifiasm is a novel assembler that utilizes long high-fidelity sequence reads to accurately represent haplotype information, outperforming existing tools in haplotype-resolved assembly on various datasets, including a hexaploid genome dataset.

NATURE METHODS (2021)

Article Biotechnology & Applied Microbiology

The molecular signatures of compatible and incompatible pollination in Arabidopsis

Chie Kodera et al.

Summary: This study utilized transcriptomic analysis based on genotypic differences in two Arabidopsis thaliana accessions to uncover the molecular signatures of compatible and incompatible pollinations at the male and female sides. Additionally, a tool was developed to predict gender-specific expression for genes without SNPs.

BMC GENOMICS (2021)

Article Ecology

On the origin of the widespread self-compatible allotetraploid Capsella bursa-pastoris (Brassicaceae)

Jorg A. Bachmann et al.

Summary: This study investigates the relationship between polyploidy and self-compatibility in crucifer plants, focusing on the mechanism of SI loss in the allopolyploid species Capsella bursa-pastoris. The results suggest that dominance modifiers in the S-haplotypes may have facilitated the loss of SI in this species. Additionally, spontaneous somatic tetraploidization after a wide cross between different Capsella species can lead to the production of self-compatible offspring.

HEREDITY (2021)

Article Biochemical Research Methods

fastsimcoal2: demographic inference under complex evolutionary scenarios

Laurent Excofffier et al.

Summary: fastsimcoal2 extends fastsimcoal by enabling estimation of demographic parameters under complex scenarios, with improvements such as multi-threading, handling of population inbreeding, extended input file syntax, and more efficient simulations.

BIOINFORMATICS (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 Biochemistry & Molecular Biology

Genotyping and De Novo Discovery of Allelic Variants at the Brassicaceae Self-Incompatibility Locus from Short-Read Sequencing Data

Mathieu Genete et al.

MOLECULAR BIOLOGY AND EVOLUTION (2020)

Article Biochemical Research Methods

Weighted minimizer sampling improves long read mapping

Chirag Jain et al.

BIOINFORMATICS (2020)

Article Biochemical Research Methods

ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R

Emmanuel Paradis et al.

BIOINFORMATICS (2019)

Article Multidisciplinary Sciences

Genome of Crucihimalaya himalaica, a close relative of Arabidopsis, shows ecological adaptation to high altitude

Ticao Zhang et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)

Article Plant Sciences

Genetic basis and timing of a major mating system shift in Capsella

Jorg A. Bachmann et al.

NEW PHYTOLOGIST (2019)

Article Biotechnology & Applied Microbiology

RaGOO: fast and accurate reference-guided scaffolding of draft genomes

Michael Alonge et al.

GENOME BIOLOGY (2019)

Article Biochemistry & Molecular Biology

Madeiran Arabidopsis thaliana Reveals Ancient Long-Range Colonization and Clarifies Demography in Eurasia

Andrea Fulgione et al.

MOLECULAR BIOLOGY AND EVOLUTION (2018)

Review Plant Sciences

Multilayered dominance hierarchy in plant self-incompatibility

Sota Fujii et al.

PLANT REPRODUCTION (2018)

Article Biochemical Research Methods

Minimap2: pairwise alignment for nucleotide sequences

Heng Li

BIOINFORMATICS (2018)

Article Biochemistry & Molecular Biology

Juicebox.js Provides a Cloud-Based Visualization System for Hi-C Data

James T. Robinson et al.

CELL SYSTEMS (2018)

Article Multidisciplinary Sciences

Patterns of polymorphism and selection in the subgenomes of the allopolyploid Arabidopsis kamchatica

Timothy Paape et al.

NATURE COMMUNICATIONS (2018)

Article Biochemistry & Molecular Biology

Two Methods for Mapping and Visualizing Associated Data on Phylogeny Using Ggtree

Guangchuang Yu et al.

MOLECULAR BIOLOGY AND EVOLUTION (2018)

Article Ecology

Adding Complexity to Complexity: Gene Family Evolution in Polyploids

Barbara K. Mable et al.

FRONTIERS IN ECOLOGY AND EVOLUTION (2018)

Article Biochemistry & Molecular Biology

VCFR: a package to manipulate and visualize variant call format data in R

Brian J. Knaus et al.

MOLECULAR ECOLOGY RESOURCES (2017)

Article Biochemistry & Molecular Biology

Genome assembly and annotation of Arabidopsis halleri, a model for heavy metal hyperaccumulation and evolutionary ecology

Roman V. Briskine et al.

MOLECULAR ECOLOGY RESOURCES (2017)

Article Biochemistry & Molecular Biology

Patterns of Polymorphism at the Self-Incompatibility Locus in 1,083 Arabidopsis thaliana Genomes

Takashi Tsuchimatsu et al.

MOLECULAR BIOLOGY AND EVOLUTION (2017)

Article Multidisciplinary Sciences

African genomes illuminate the early history and transition to selfing in Arabidopsis thaliana

Arun Durvasula et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2017)

Article Biochemical Research Methods

SynMap2 and SynMap3D: web-based whole-genome synteny browsers

Asher Haug-Baltzell et al.

BIOINFORMATICS (2017)

Article Biochemistry & Molecular Biology

1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana

Carlos Alonso-Blanco et al.

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)

Review Ecology

Evolution of Selfing: Recurrent Patterns in Molecular Adaptation

Kentaro K. Shimizu et al.

ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS, VOL 46 (2015)

Article Multidisciplinary Sciences

Improving the Annotation of Arabidopsis lyrata Using RNA-Seq Data

Vimal Rawat et al.

PLOS ONE (2015)

Article Biochemical Research Methods

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

Alexandros Stamatakis

BIOINFORMATICS (2014)

Article Multidisciplinary Sciences

Dominance hierarchy arising from the evolution of a complex small RNA regulatory network

Eleonore Durand et al.

SCIENCE (2014)

Article Biochemistry & Molecular Biology

Recent and Ancient Signature of Balancing Selection around the S-Locus in Arabidopsis halleri and A. lyrata

Camille Roux 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 Biochemistry & Molecular Biology

StAMPP: an R package for calculation of genetic differentiation and structure of mixed-ploidy level populations

Luke W. Pembleton et al.

MOLECULAR ECOLOGY RESOURCES (2013)

Article Genetics & Heredity

Robust Demographic Inference from Genomic and SNP Data

Laurent Excoffier et al.

PLOS GENETICS (2013)

Review Plant Sciences

Mating system shifts on the trailing edge

Donald A. Levin

ANNALS OF BOTANY (2012)

Article Biology

Genomic impacts of chromosomal inversions in parapatric Drosophila species

Suzanne E. McGaugh et al.

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2012)

Article Evolutionary Biology

Effects of Inversions on Within- and Between-Species Recombination and Divergence

Laurie S. Stevison et al.

GENOME BIOLOGY AND EVOLUTION (2011)

Article Biochemistry & Molecular Biology

Demographic Signatures Accompanying the Evolution of Selfing in Leavenworthia alabamica

Jeremiah W. Busch et al.

MOLECULAR BIOLOGY AND EVOLUTION (2011)

Article Genetics & Heredity

The Arabidopsis lyrata genome sequence and the basis of rapid genome size change

Tina T. Hu et al.

NATURE GENETICS (2011)

Article Plant Sciences

Evolution of the S-Locus Region in Arabidopsis Relatives

Ya-Long Guo et al.

PLANT PHYSIOLOGY (2011)

Article Biochemical Research Methods

genoPlotR: comparative gene and genome visualization in R

Lionel Guy et al.

BIOINFORMATICS (2010)

Article Biochemistry & Molecular Biology

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

Aaron McKenna et al.

GENOME RESEARCH (2010)

Article Ecology

Evolutionary dynamics of mating system shifts in Arabidopsis lyrata

Y. Willi et al.

JOURNAL OF EVOLUTIONARY BIOLOGY (2010)

Article Biochemistry & Molecular Biology

Molecular Evolution within and between Self-Incompatibility Specificities

V. Castric et al.

MOLECULAR BIOLOGY AND EVOLUTION (2010)

Article Multidisciplinary Sciences

Trans-acting small RNA determines dominance relationships in Brassica self-incompatibility

Yoshiaki Tarutani et al.

NATURE (2010)

Article Multidisciplinary Sciences

Evolution of self-compatibility in Arabidopsis by a mutation in the male specificity gene

Takashi Tsuchimatsu et al.

NATURE (2010)

Article Biochemical Research Methods

The Sequence Alignment/Map format and SAMtools

Heng Li et al.

BIOINFORMATICS (2009)

Article Biochemical Research Methods

Fast and accurate short read alignment with Burrows-Wheeler transform

Heng Li et al.

BIOINFORMATICS (2009)

Article Biochemical Research Methods

Jalview Version 2-a multiple sequence alignment editor and analysis workbench

Andrew M. Waterhouse et al.

BIOINFORMATICS (2009)

Article Genetics & Heredity

Expression of Distinct Self-Incompatibility Specificities in Arabidopsis thaliana

Nathan A. Boggs et al.

GENETICS (2009)

Article Multidisciplinary Sciences

Recent speciation of Capsella rubella from Capsella grandiflora, associated with loss of self-incompatibility and an extreme bottleneck

Ya-Long Guo et al.

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

Article Genetics & Heredity

Independent S-Locus Mutations Caused Self-Fertility in Arabidopsis thaliana

Nathan A. Boggs et al.

PLOS GENETICS (2009)

Article Genetics & Heredity

Repeated Adaptive Introgression at a Gene under Multiallelic Balancing Selection

Vincent Castric et al.

PLOS GENETICS (2008)

Article Biochemistry & Molecular Biology

S locus genes and the evolution of self-fertility in Arabidopsis thaliana

Sue Sherman-Broyles et al.

PLANT CELL (2007)

Article Multidisciplinary Sciences

Mechanisms of chromosome number reduction in Arabidopsis thaliana and related Brassicaceae species

MA Lysak et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)

Article Biochemistry & Molecular Biology

Application of phylogenetic networks in evolutionary studies

DH Huson et al.

MOLECULAR BIOLOGY AND EVOLUTION (2006)

Review Plant Sciences

Poorly known relatives of Arabidopsis thaliana

Maria J. Clauss et al.

TRENDS IN PLANT SCIENCE (2006)

Review Plant Sciences

Plant self-incompatibility systems:: a molecular evolutionary perspective

D Charlesworth et al.

NEW PHYTOLOGIST (2005)

Review Plant Sciences

Self-incompatibility in plants

S Takayama et al.

ANNUAL REVIEW OF PLANT BIOLOGY (2005)

Article Biochemical Research Methods

APE: Analyses of Phylogenetics and Evolution in R language

E Paradis et al.

BIOINFORMATICS (2004)

Article Multidisciplinary Sciences

Natural variation in expression of self-incompatibility in Arabidopsis thaliana:: Implications for the evolution of selfing

ME Nasrallah et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2004)

Article Ecology

Uneven segregation of sporophytic self-incompatibility alleles in Arabidopsis lyrata

J Bechsgaard et al.

JOURNAL OF EVOLUTIONARY BIOLOGY (2004)

Article Biochemistry & Molecular Biology

Structure of the male determinant factor for Brassica self-incompatibility

M Mishima et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2003)

Article Multidisciplinary Sciences

Direct ligand-receptor complex interaction controls Brassica self-incompatibility

S Takayama et al.

NATURE (2001)

Review Ecology

Chromosomal rearrangements and speciation

LH Rieseberg

TRENDS IN ECOLOGY & EVOLUTION (2001)

Article Multidisciplinary Sciences

The pollen determinant of self-incompatibility in Brassica campestris

S Takayama et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2000)