1,720,968 research outputs found
NGS Analysis of Gene and Allelic Expression in Poplar Hybrids Subjected to Water Stress
No full textPoplar interspecific hybrids are largely cultivated because of their heterotic behaviour. To
contribute new data on molecular basis of heterosis, Illumina next generation sequencing
technology was used to compare gene and allelic expression in two Populus deltoides x P. nigra
hybrids, showing or not heterosis concerning stem circumference and height. Such an approach
allows the identification of genes and gene networks that contribute to poplar tolerance to waterlimiting environments, with a long-term aim of developing strategies to improve plant productivity
under drought.
Analyses were performed on RNAs isolated from leaves of plants grown in normal conditions
or exposed to moderate (85% leaf RWC) or severe (57% leaf RWC) drought. We generated
76,635,449 sequence reads, each 51 nt in length, encompassing 3.9 Gb of sequence data from 12
cDNA libraries obtained from leaves of plants of Populus deltoides x P. nigra subjected or not to
moderate or severe drought stress.
The expression of 45,033 poplar genes included in P. trichocarpa Phytozome database was
studied by mapping Illumina cDNA reads on poplar unigene models. Expressed genes were
characterized by gene ontology and by determining the metabolic pathway to which they belong.
Most genes resulted expressed in control and drought stressed plants, however a number of genes
were significantly induced or repressed by drought. Analysis of expression profiles revealed that
only genes involved in the biological process of stress response showed, in the majority, a
precocious induction at moderate drought stress. On the contrary, induction or repression of most of
other genes was more common after severe stress, even for genes that usually respond promptly to
changes in environmental conditions, as those encoding transcription factors.
On the whole, 1.80, 5.87, and 4.80% of genes resulted differentially expressed in the two
hybrids in control, moderate, and severe stress, respectively. Moreover, the number of genes
differentially expressed between the two hybrids increase in response to drought, suggesting that
genetic differences can have an important role in stress tolerance.
The occurrence of differential allelic expression in the same samples was also analysed in 200
randomly chosen genes. Fifty to sixty percent of these genes, depending on the hybrid and on the
treatment, showed equal allelic expression but in the other genes the proportion between two alleles
ranged from 60:40 to 90:10, i.e. they showed significant differential allelic expression. These resultsare comparable to those obtained in similar studies in the literature and point out the importance of
such phenomena in generating heterosis
NGS Analysis of LTR Retrotransposon Redundancy and Expression in Poplar Hybrids Subjected to Water Stress
No full textThough LTR-retrotransposons represent a major component in plant genomes, they are often
considered as silent, and their expression is rarely studied. The next generation sequencing methods
offer an unprecedented level and unexplored potentialities of analysis, allowing a comprehensive
study of the RNA expressed in different tissues and growth conditions. We evaluated the expression
of LTR-retrotransposons in a poplar interspecific hybrid, Populus deltoides x P. nigra, using
Illumina RNAseq and a LTR-retrotransposon database of P. trichocarpa. First, the occurrence and
redundancy of P. trichocarpa retrotransposons was studied in P. deltoides and P. nigra genomes.
Then, RNA was isolated from leaves of two hybrids obtained from the same parents, cultivated in
control conditions or subjected to moderate or severe drought stress.
Nearly all P. trichocarpa retrotransposons were found in P. deltoides and P. nigra, however
large differences in retrotransposon redundancy occur between the two species, arguably because of
retrotransposon activity occurred after Populus speciation. The majority of retrotransposons were
not expressed in the hybrids. Expressed retrotransposon show generally low transcription level,
however some of them resulted highly transcribed, i.e., with rates higher than those of genes
encoding housekeeping proteins as actin, with differences during drought stress. The two hybrids,
that are genetically different (being parents heterozygous), show different retrotransposon
expression and such difference increases at increasing stress levels. Gypsy retrotransposons are less
transcribed than Copia; the most expressed retrotransposons do not belong to any described
superfamily and can be defined as LARDs or TRIMs. Retroelements that do not belong to described
superfamilies and are reported as unknown show similar expression levels in control and stressed
plants, contrary to Gypsy and Copia elements, whose expression is increased by drought, suggesting
that these two superfamilies are more efficiently repressed in control conditions while, during
drought, the repression of expression is more relaxed. Drought-related cis-acting motifs are found in
higher number in LTRs of active retroelements than in those of inactive ones
Towards the construction of OLEAREP: a database of repeated sequences of Olea europaea L.
No full textTemporal dynamics in the sunflower genome evolution as revealed by sequencing and annotation of three BAC clones
No full text
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
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