Transcriptional Activity, Chromosomal Distribution and Expression Effects of Transposable Elements in Coffea Genomes

Lopes, Fabrício Ramon; Jjingo, Daudi; Silva, Carlos R. M. da; Andrade, Alan Carvalho; Marraccini, Pierre; Teixeira, J. B.; Carazzolle, Marcelo Falsarella; Pereira, Gonçalo Amarante Guimarães; Pereira, Luiz Filipe Protásio; Vanzela, André Luís Laforga; Wang, Lu; Jordan, King; Carareto, Claudia M. A.

doi:10.1371/journal.pone.0078931

Cited by 35 publications

(28 citation statements)

References 46 publications

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“…From the between-strains transcriptomic analysis, TEs again held a central role, with their expression showing strain-specificity as shown for fungi and plants [86][87][88]. The absence of specific TEs from the genomes of a couple of the strains (1189B3 and 1189A3), as well as the markedly different response to low, and for some genes, high, temperature of one of the three strains, B651, point to a high intraspecific variability.…”

Section: Discussionmentioning

confidence: 93%

Intraspecific Diversity in the Cold Stress Response of Transposable Elements in the Diatom Leptocylindrus aporus

Pargana

Musacchia

Sanges

et al. 2019

Genes

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Transposable elements (TEs), activated as a response to unfavorable conditions, have been proposed to contribute to the generation of genetic and phenotypic diversity in diatoms. Here we explore the transcriptome of three warm water strains of the diatom Leptocylindrus aporus, and the possible involvement of TEs in their response to changing temperature conditions. At low temperature (13 • C) several stress response proteins were overexpressed, confirming low temperature to be unfavorable for L. aporus, while TE-related transcripts of the LTR retrotransposon superfamily were the most enriched transcripts. Their expression levels, as well as most of the stress-related proteins, were found to vary significantly among strains, and even within the same strains analysed at different times. The lack of overexpression after many months of culturing suggests a possible role of physiological plasticity in response to growth under controlled laboratory conditions. While further investigation on the possible central role of TEs in the diatom stress response is warranted, the strain-specific responses and possible role of in-culture evolution draw attention to the interplay between the high intraspecific variability and the physiological plasticity of diatoms, which can both contribute to the adaptation of a species to a wide range of conditions in the marine environment.Genes 2020, 11, 9 2 of 25 (3) both of the above, as plasticity can be adaptive with respect to a function and may be altered by natural selection and ultimately become or facilitate adaptation.In addition to natural environmental variability, diatoms used in experimental research are also exposed to another source of variability; they are removed from their natural environment, isolated and transferred to laboratory conditions in which evolutionary processes do not cease to occur [8]. Many cases of novel genetic variation have been shown after years of maintenance in culture collection [9][10][11]. Considering the high adaptability of diatoms, it could be hard to interpret the intra-specific algal diversity observed in related studies as the result of (a) adaptation to the natural environment from which strains were isolated or (b) evolutionary changes while being in culture.Temperature is a very significant environmental variable that affects the physiological response of diatoms and ultimately determines their phenological patterns and geographic ranges [12][13][14], as well as one of the parameters that is usually kept constant in culture conditions. An increase in temperature leads to an increase in enzyme activity in metabolic processes, including photosynthesis and respiration, so the cells are expected to grow faster. Even algae obtained from cold habitats have shown at least short-term temperature optima for photosynthesis several degrees higher than the temperature at which they were growing. Low temperatures lead to the exact opposite direction so that, in order to survive, cells respond with an increase in enzyme synthesis [15,16]. A recent study ...

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Section: Discussionmentioning

confidence: 93%

Intraspecific Diversity in the Cold Stress Response of Transposable Elements in the Diatom Leptocylindrus aporus

Pargana

Musacchia

Sanges

et al. 2019

Genes

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“…In the study by Madlung et al [79] noted above, despite an increase in transcriptional activity after allopolyploidy, limited transpositional activation of the Sunfish transposon in allopolyploid Arabidopsis was detected through a methyl-insensitive Southern blot analysis [79]. In polyploid coffee (Coffea arabica), microarray analysis showed that the expression level of Tip100 in allopolyploid C. arabica is higher than the sum of the expression levels of Tip100 in its parents, C. eugenioides and C. canephora [89]. FISH results showed an increase in Tip100 copy number and a more prevalent interstitial chromosomal location in allotetraploid Coffea compared with the parental species, indicating an increase in transpositional activity in this species compared with the parental species [89].…”

Section: (E) Transposons and Noveltymentioning

confidence: 99%

“…In polyploid coffee (Coffea arabica), microarray analysis showed that the expression level of Tip100 in allopolyploid C. arabica is higher than the sum of the expression levels of Tip100 in its parents, C. eugenioides and C. canephora [89]. FISH results showed an increase in Tip100 copy number and a more prevalent interstitial chromosomal location in allotetraploid Coffea compared with the parental species, indicating an increase in transpositional activity in this species compared with the parental species [89]. Thus, although novel TE activity is noted in allopolyploids in both Arabidopsis and Coffea relative to their parents, in Arabidopsis, transcriptional and transpositional activities of TEs are negatively correlated, while in Coffea they are positively correlated.…”

Section: (E) Transposons and Noveltymentioning

confidence: 99%

Polyploidy and novelty: Gottlieb's legacy

Soltis

Liu

Marchant

et al. 2014

Phil. Trans. R. Soc. B

157

140

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Nearly four decades ago, Roose & Gottlieb (Roose & Gottlieb 1976 Evolution 30 , 818–830. ( doi:10.2307/2407821 )) showed that the recently derived allotetraploids Tragopogon mirus and T. miscellus combined the allozyme profiles of their diploid parents ( T. dubius and T. porrifolius , and T. dubius and T. pratensis , respectively). This classic paper addressed the link between genotype and biochemical phenotype and documented enzyme additivity in allopolyploids. Perhaps more important than their model of additivity, however, was their demonstration of novelty at the biochemical level. Enzyme multiplicity—the production of novel enzyme forms in the allopolyploids—can provide an extensive array of polymorphism for a polyploid individual and may explain, for example, the expanded ranges of polyploids relative to their diploid progenitors. In this paper, we extend the concept of evolutionary novelty in allopolyploids to a range of genetic and ecological features. We observe that the dynamic nature of polyploid genomes—with alterations in gene content, gene number, gene arrangement, gene expression and transposon activity—may generate sufficient novelty that every individual in a polyploid population or species may be unique. Whereas certain combinations of these features will undoubtedly be maladaptive, some unique combinations of newly generated variation may provide tremendous evolutionary potential and adaptive capabilities.

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“…In addition, transposable elements (TE), which are major components of plant genomes, might also shape the architecture, function and expression of plant genes and genomes throughout evolution [12]. In coffee plants, albeit previous studies have shown low TE expression, they can be detected in transcriptome analyses [13–14]. …”

Section: Introductionmentioning

confidence: 99%

Transcriptome Analysis of Leaves, Flowers and Fruits Perisperm of Coffea arabica L. Reveals the Differential Expression of Genes Involved in Raffinose Biosynthesis

et al. 2017

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Coffea arabica L. is an important crop in several developing countries. Despite its economic importance, minimal transcriptome data are available for fruit tissues, especially during fruit development where several compounds related to coffee quality are produced. To understand the molecular aspects related to coffee fruit and grain development, we report a large-scale transcriptome analysis of leaf, flower and perisperm fruit tissue development. Illumina sequencing yielded 41,881,572 high-quality filtered reads. De novo assembly generated 65,364 unigenes with an average length of 1,264 bp. A total of 24,548 unigenes were annotated as protein coding genes, including 12,560 full-length sequences. In the annotation process, we identified nine candidate genes related to the biosynthesis of raffinose family oligossacarides (RFOs). These sugars confer osmoprotection and are accumulated during initial fruit development. Four genes from this pathway had their transcriptional pattern validated by quantitative reverse transcription polymerase chain reaction (qRT-PCR). Furthermore, we identified ~24,000 putative target sites for microRNAs (miRNAs) and 134 putative transcriptionally active transposable elements (TE) sequences in our dataset. This C. arabica transcriptomic atlas provides an important step for identifying candidate genes related to several coffee metabolic pathways, especially those related to fruit chemical composition and therefore beverage quality. Our results are the starting point for enhancing our knowledge about the coffee genes that are transcribed during the flowering and initial fruit development stages.

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Transcriptional Activity, Chromosomal Distribution and Expression Effects of Transposable Elements in Coffea Genomes

Cited by 35 publications

References 46 publications

Intraspecific Diversity in the Cold Stress Response of Transposable Elements in the Diatom Leptocylindrus aporus

Intraspecific Diversity in the Cold Stress Response of Transposable Elements in the Diatom Leptocylindrus aporus

Polyploidy and novelty: Gottlieb's legacy

Transcriptome Analysis of Leaves, Flowers and Fruits Perisperm of Coffea arabica L. Reveals the Differential Expression of Genes Involved in Raffinose Biosynthesis

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