scholarly journals Diversity, dynamics and effects of LTR retrotransposons in the model grass Brachypodium distachyon

2019 ◽  
Author(s):  
C Stritt ◽  
M Wyler ◽  
EL Gimmi ◽  
M Pippel ◽  
AC Roulin
Keyword(s):  
Brachypodium Distachyon ◽  
Gc Content ◽  
List Type ◽  
High Plasticity ◽  
Long Terminal Repeat Retrotransposon ◽  
Transpositional Activity ◽  
Genome Wide ◽  
Model Grass ◽  
Diversity Dynamics ◽  
Evolutionary Lineages

SummaryTransposable elements (TEs) are the main reason for the high plasticity of plant genomes, where they occur as communities of diverse evolutionary lineages. Because research has typically focused on single abundant families or summarized TEs at a coarse taxonomic level, our knowledge about how these lineages differ in their effects on genome evolution is still rudimentary.Here we investigate the community composition and dynamics of 32 long terminal repeat retrotransposon (LTR-RT) families in the 272 Mb genome of the Mediterranean grass Brachypodium distachyon.We find that much of the recent transpositional activity in the B. distachyon genome is due to centromeric Gypsy families and Copia elements belonging to the Angela lineage. With a half-life as low as 66 ky, the latter are the most dynamic part of the genome and an important source of within-species polymorphisms. Second, GC-rich Gypsy elements of the Retand lineage are the most abundant TEs in the genome. Their presence explains more than 20 percent of the genome-wide variation in GC content and is associated to higher methylation levels.Our study shows how individual TE lineages change the genetic and epigenetic constitution of the host beyond simple changes in genome size.

scholarly journals Diversity, dynamics and effects of long terminal repeat retrotransposons in the model grass Brachypodium distachyon

2019 ◽  
Vol 227 (6) ◽  
pp. 1736-1748 ◽  
Author(s):  
Christoph Stritt ◽  
Michele Wyler ◽  
Elena L. Gimmi ◽  
Martin Pippel ◽  
Anne C. Roulin
Keyword(s):  
Long Terminal Repeat ◽  
Brachypodium Distachyon ◽  
Long Terminal Repeat Retrotransposons ◽  
Terminal Repeat ◽  
Model Grass ◽  
Diversity Dynamics

Genome-wide Characterization of Major Intrinsic Protein (MIP) Gene Family in Brachypodium distachyon

2018 ◽  
Vol 13 (5) ◽  
pp. 536-552 ◽  
Author(s):  
Ankush Ashok Saddhe ◽  
Shweta ◽  
Kareem A. Mosa ◽  
Kundan Kumar ◽  
Manoj Prasad ◽  
...  
Keyword(s):  
Gene Family ◽  
Brachypodium Distachyon ◽  
Major Intrinsic Protein ◽  
Intrinsic Protein ◽  
Genome Wide

Genome-Wide Search for Local DNA Segments with Anomalous GC-Content

2009 ◽  
Vol 16 (4) ◽  
pp. 555-564 ◽  
Author(s):  
Andrey Ilatovskiy ◽  
Michael Petukhov
Keyword(s):  
Gc Content ◽  
Genome Wide ◽  
Genome Wide Search

scholarly journals F-Box Genes in the Wheat Genome and Expression Profiling in Wheat at Different Developmental Stages

Genes ◽  
2020 ◽  
Vol 11 (10) ◽  
pp. 1154
Author(s):  
Min Jeong Hong ◽  
Jin-Baek Kim ◽  
Yong Weon Seo ◽  
Dae Yeon Kim
Keyword(s):  
Developmental Stages ◽  
Brachypodium Distachyon ◽  
Triticum Aestivum L ◽  
Wheat Genome ◽  
Post Translational Modification ◽  
Genome Wide ◽  
A Genome ◽  
High Sequence Homology ◽  
Wide Scale

Genes of the F-box family play specific roles in protein degradation by post-translational modification in several biological processes, including flowering, the regulation of circadian rhythms, photomorphogenesis, seed development, leaf senescence, and hormone signaling. F-box genes have not been previously investigated on a genome-wide scale; however, the establishment of the wheat (Triticum aestivum L.) reference genome sequence enabled a genome-based examination of the F-box genes to be conducted in the present study. In total, 1796 F-box genes were detected in the wheat genome and classified into various subgroups based on their functional C-terminal domain. The F-box genes were distributed among 21 chromosomes and most showed high sequence homology with F-box genes located on the homoeologous chromosomes because of allohexaploidy in the wheat genome. Additionally, a synteny analysis of wheat F-box genes was conducted in rice and Brachypodium distachyon. Transcriptome analysis during various wheat developmental stages and expression analysis by quantitative real-time PCR revealed that some F-box genes were specifically expressed in the vegetative and/or seed developmental stages. A genome-based examination and classification of F-box genes provide an opportunity to elucidate the biological functions of F-box genes in wheat.

scholarly journals Genome-wide identification, phylogeny and expression analysis of AP2/ERF transcription factors family in Brachypodium distachyon

BMC Genomics ◽  
2016 ◽  
Vol 17 (1) ◽  
Author(s):  
Licao Cui ◽  
Kewei Feng ◽  
Mengxing Wang ◽  
Meng Wang ◽  
Pingchuan Deng ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Expression Analysis ◽  
Brachypodium Distachyon ◽  
Genome Wide ◽  
Erf Transcription Factors

scholarly journals Memory of the vernalized state in plants including the model grass Brachypodium distachyon

2014 ◽  
Vol 5 ◽  
Author(s):  
Daniel P. Woods ◽  
Thomas S. Ream ◽  
Richard M. Amasino
Keyword(s):  
Brachypodium Distachyon ◽  
Model Grass

scholarly journals Grain dormancy and light quality effects on germination in the model grass Brachypodium distachyon

2011 ◽  
Vol 193 (2) ◽  
pp. 376-386 ◽  
Author(s):  
José M. Barrero ◽  
John V. Jacobsen ◽  
Mark J. Talbot ◽  
Rosemary G. White ◽  
Stephen M. Swain ◽  
...  
Keyword(s):  
Light Quality ◽  
Brachypodium Distachyon ◽  
Grain Dormancy ◽  
Model Grass

scholarly journals Global Co-Existence of Two Evolutionary Lineages of Parvovirus B19 1a, Different in Genome-Wide Synonymous Positions

PLoS ONE ◽  
2012 ◽  
Vol 7 (8) ◽  
pp. e43206 ◽  
Author(s):  
Marijke W. A. Molenaar-de Backer ◽  
Vladimir V. Lukashov ◽  
Rob S. van Binnendijk ◽  
Hein J. Boot ◽  
Hans L. Zaaijer
Keyword(s):  
Parvovirus B19 ◽  
Genome Wide ◽  
Evolutionary Lineages

scholarly journals Interspecific introgression and natural selection in the evolution of Japanese apricot (Prunus mume)

2020 ◽  
Author(s):  
Koji Numaguchi ◽  
Takashi Akagi ◽  
Yuto Kitamura ◽  
Ryo Ishikawa ◽  
Takashige Ishii
Keyword(s):  
Adaptive Evolution ◽  
Artificial Selection ◽  
Population Differentiation ◽  
List Type ◽  
Nucleotide Polymorphisms ◽  
Prunus Mume ◽  
Japanese Apricot ◽  
Interspecific Introgression ◽  
Genome Wide ◽  
Evolutionary Paths

SummaryDomestication and population differentiation in crops involve considerable phenotypic changes. The logs of these evolutionary paths, including natural/artificial selection, can be found in the genomes of the current populations. However, these profiles have been little studied in tree crops, which have specific characters, such as long generation time and clonal propagation, maintaining high levels of heterozygosity.We conducted exon-targeted resequencing of 129 genomes in the genus Prunus, mainly Japanese apricot (Prunus mume), and apricot (P. armeniaca), plum (P. salicina), and peach (P. persica). Based on their genome-wide single nucleotide polymorphisms merged with published resequencing data of 79 Chinese P. mume cultivars, we inferred complete and ongoing population differentiation in P. mume.Sliding window characterization of the indexes for genetic differentiation identified interspecific fragment introgressions between P. mume and related species (plum and apricot). These regions often exhibited strong selective sweeps formed in the paths of establishment or formation of substructures of P. mume, suggesting that P. mume has frequently imported advantageous genes from other species in the subgenus Prunus as adaptive evolution.These findings shed light on the complicated nature of adaptive evolution in a tree crop that has undergone interspecific exchange of genome fragments with natural/artificial selection.

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