1,721,004 research outputs found
Grape color variation involves genetic and micro-environmental changes that alter berry phenolic and aromatic composition
No full textBlack- and white-berried grapevine cultivars are distinguished by their ability to accumulate anthocyanins in the berry skin. To assess possible side effects of color variation in berry development and composition in a near-isogenic background, we compared white-berried somatic variants (WV) to their black-berried ancestors in ‘Garnacha’ and ‘Tempranillo’ cultivars. Absence of anthocyanins correlated with lower berry temperature during daytime in WV. At the transcriptome level, besides genes related to anthocyanin accumulation, transcripts encoding enzymes involved in flavonoid backbone biosynthesis and modification were downregulated from veraison in WV skin. Genes mapping to hemizygous genome regions in WV were also downregulated irrespective of berry tissue or developmental stage. Light-responsive genes including flavonol and monoterpenoid biosynthesis genes were upregulated in WV from veraison. In agreement, flavonol partitioning was altered and trihydroxylated forms were practically absent in WV, whereas higher levels of specific volatile monoterpenoids and their soluble precursors were detected in WV pericarp. Amino acid precursors of phenolic compounds tended to be higher in WV pericarp. Collectively, greater differences were observed in ‘Tempranillo’ than in ‘Garnacha’, revealing effects of genetic background. These results indicate that the grape color locus directly controls the metabolism of colorless flavonoids, whereas additional alterations in grape quality compounds are established in a cultivar-dependent manner in response to alteration of the berry microclimate caused by the absence of anthocyanins
Recent progress on genome assemblies and annotation of six pistachio cultivars
No full textPlant breeding has been revolutionized by the advent of high-throughput genome sequencing, which provides valuable insights into the genetic basis of crops and enables the development of novel and improved cultivars. This is particularly important for long-lived crops such as pistachio since the breeding cycle is much longer than annual crops. To facilitate genome-enabled breeding efforts for improved pistachio cultivars, especially in the face of emerging environmental stresses, an international collaboration spanning five institutes and countries is working to create a pistachio pan-genome. We recently sequenced the genomes of six diverse pistachio genotypes with PacBio HiFi sequencing. Gene discovery (annotation) was facilitated by whole transcriptome data from multiple tissues with Iso-Seq in each genotype. These data provide an early glimpse into functional genomic diversity in pistachio and the basis to begin discovering targets for accelerated breeding. We discuss progress and promise to further develop and apply these new genomic resources
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
Genome assemblies and long-read sequencing to search for functional variation in grapevine
No full textDomesticated grapevines exhibit a high level of genome diversityamong cultivars. In addition, grapevine cultivars are usually highlyheterozygous, with great diversity between the two haploidcomplements comprising their diploid genome. Therefore, to increasethe possibilities of capturing the genome variants responsible for phenotype variation in traits of agronomic interest, we have developedcultivar-specific and diploid genome assemblies for relevant grapevinecultivars. To overcome the highly repetitive and heterozygous nature ofgrapevine genomes, we either combined noisy PacBio and Nanoporelong reads with trio binning of haplotypes or used accurate HiFi PacBiolong reads. The obtained genome assemblies, combined in specificcases with long read-based gene annotations and methylation analysis,were useful for detecting genome and epigenome variations associatedwith intra-cultivar variants displaying diversity in fruit colour ordecreased bunch compactness
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Genomic approaches to study somatic variation as a source of cultivar innovation
No full textSomatic variation is a natural source of diversity that has long been exploitedto improve traditional grapevine wine cultivars and adapt them to changingenvironmental conditions and market demands. Somatic variation is also asource of novel traits such as grape color variation enabling cultivar innovationand diversification of products. To understand the mutational mechanismsgenerating somatic variation in grape color, we compared the TempranilloBlanco white berry somatic variant with its black berry ancestor, TempranilloTinto. By whole-genome resequencing and structural variation analysis weidentified that complex genome rearrangements involving three chromosomesand hemizygous deletion of 1.7% of the genome resulted in the loss of thegrape color locus functional allele in Tempranillo Blanco. We showed that thiscomplex genome reshuffling has additional consequences affecting productionin Tempranillo Blanco. Similar structural variation analyses in Grenache grapecolor somatic variants identified more simple deletion events as the causalmutations. To assist future intra-varietal studies in Tempranillo, the third mostwidely grown wine cultivar in the world, we are now using long-readsequencing PacBio and Nanopore technologies to build a haplotype-resolvedgenome assembly and to annotate it. These genomic tools will be exploited tosearch for causal mutations in improved Tempranillo somatic variantsidentified in clonal selection programs
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
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