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Genomic expression dominance in the natural allopolyploid Coffea arabica is massively affected by growth temperature.

Evidence of transcription profile divergence between the allopolyploid and its parental species, greatly affected by environmental conditions, is revealed and clues to the plasticity phenomenon in allopoly Ploidy are provided.
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Characterization of the Active Bacterial Community Involved in Natural Attenuation Processes in Arsenic-Rich Creek Sediments

To investigate how this particular ecosystem functions, the bacterial community was characterized in water and sediments by 16S rRNA encoding gene library analysis and several GroEL orthologs expressed by the community were characterized, and the active members of the prokaryotic community inhabiting the creek sediments were identified.
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Transposons played a major role in the diversification between the closely related almond and peach genomes: results from the almond genome sequence

In sweet almond cultivars, highly methylated TE insertions surround a gene involved in the biosynthesis of amygdalin, whose reduced expression has been correlated with the sweet almond phenotype, suggesting a key role of TEs in the recent history and diversification of almond and its close relative peach.
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Evolutionary dynamics of retrotransposons following autopolyploidy in the Buckler Mustard species complex.

Low expression levels of transpositionally active LTR-RT families in autopolyploids further supported that genome shock and redundancy are non-mutually exclusive triggers of L TR-RT proliferation.
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The Greater Phenotypic Homeostasis of the Allopolyploid Coffea arabica Improved the Transcriptional Homeostasis Over that of Both Diploid Parents

It is found that the overall transcriptional response to TRs of the allopolyploid was more homeostatic compared with its parents, which afforded a greater phenotypic homeostasis when faced with environments that are unsuited to the diploid parental species.
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Transposons played a major role in the diversification between the closely related almond (Prunus dulcis) and peach (P. persica) genomes: Results from the almond genome sequence

Comparison between peach and almond genomes confirmed the high synteny between these close relatives, but also revealed high numbers of presence-absence variants, many attributable to the movement of transposable elements (TEs).
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The 'PUCE CAFE' Project: the First 15K Coffee Microarray, a New Tool for Discovering Candidate Genes correlated to Agronomic and Quality Traits

An oligo-based microarray using 15,721 unigenes derived from published coffee EST sequences mostly obtained from different stages of fruit development and leaves in Coffea Canephora is developed, drastically enlarging its impact for high-throughput gene expression in the community of coffee research.
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Gene expression divergences between the allopolyploid Coffea arabica and its diploids relatives appear environment-dependant

It is shown that numerous genes in C. arabica are non-additively expressed and that divergences in gene expression pattern between allo and diploid genomes are function of the environment conditions, which reinforce the hypothesis of a better functional plasticity of the allopolyploids in comparison to their related diploids species and consequently the evolutionary advantage of this genome architecture.

The replicative amplification of MITEs and their impact on rice trait variability

An analysis of 103,109 Transposon Insertion Polymorphisms (TIPs) in 1,059 O. sativa genomes representing the main rice population groups shows that an important fraction of MITE insertions has been fixed in rice concomitantly with rice domestication, suggesting a mechanism of amplification uncoupled from the typical cut-and-paste mechanism of class II transposons.
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Whole genome duplications and recruitment of ecologically relevant genes in alpine Mustards

WGDs thus recurrently fostered genome reorganization and adaptive recruitment of genes responding to environmental factors, indicating that similar proximate and ultimate factors of genome dynamics may consistently act through time.
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