scholarly journals CicerSpTEdb: A web-based database for high-resolution genome-wide identification of transposable elements in Cicer species

PLoS ONE ◽  
2021 ◽  
Vol 16 (11) ◽  
pp. e0259540
Author(s):  
Morad M. Mokhtar ◽  
Alsamman M. Alsamman ◽  
Haytham M. Abd-Elhalim ◽  
Achraf El Allali
Keyword(s):  
Transposable Elements ◽  
Crop Improvement ◽  
Draft Genome ◽  
Structural Variations ◽  
Web Based ◽  
Cicer Echinospermum ◽  
Genome Wide ◽  
Cicer Species ◽  
Trait Improvement ◽  
Made In

Recently, Cicer species have experienced increased research interest due to their economic importance, especially in genetics, genomics, and crop improvement. The Cicer arietinum, Cicer reticulatum, and Cicer echinospermum genomes have been sequenced and provide valuable resources for trait improvement. Since the publication of the chickpea draft genome, progress has been made in genome assembly, functional annotation, and identification of polymorphic markers. However, work is still needed to identify transposable elements (TEs) and make them available for researchers. In this paper, we present CicerSpTEdb, a comprehensive TE database for Cicer species that aims to improve our understanding of the organization and structural variations of the chickpea genome. Using structure and homology-based methods, 3942 C. echinospermum, 3579 C. reticulatum, and 2240 C. arietinum TEs were identified. Comparisons between Cicer species indicate that C. echinospermum has the highest number of LTR-RT and hAT TEs. C. reticulatum has more Mutator, PIF Harbinger, Tc1 Mariner, and CACTA TEs, while C. arietinum has the highest number of Helitron. CicerSpTEdb enables users to search and visualize TEs by location and download their results. The database will provide a powerful resource that can assist in developing TE target markers for molecular breeding and answer related biological questions. Database URL: http://cicersptedb.easyomics.org/index.php

scholarly journals Draft Genome of the Wheat Rust Pathogen (Puccinia triticina)Unravels Genome-Wide Structural Variations during Evolution

2016 ◽  
Vol 8 (9) ◽  
pp. 2702-2721 ◽  
Author(s):  
Kanti Kiran ◽  
Hukam C. Rawal ◽  
Himanshu Dubey ◽  
Rajdeep Jaswal ◽  
B.N Devanna ◽  
...  
Keyword(s):  
Draft Genome ◽  
Puccinia Triticina ◽  
Structural Variations ◽  
Genome Wide ◽  
Rust Pathogen ◽  
Wheat Rust

scholarly journals Elevated transcription of transposable elements is accompanied by het-siRNA-driven de novo DNA methylation in grapevine embryogenic callus

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Darrell Lizamore ◽  
Ross Bicknell ◽  
Chris Winefield
Keyword(s):  
Dna Methylation ◽  
Transposable Elements ◽  
Embryogenic Callus ◽  
De Novo ◽  
Crop Improvement ◽  
Leaf Tissue ◽  
Callus Cultures ◽  
Small Rna Sequencing ◽  
Somatic Variation ◽  
Genome Wide

Abstract Background Somatic variation is a valuable source of trait diversity in clonally propagated crops. In grapevine, which has been clonally propagated worldwide for centuries, important phenotypes such as white berry colour are the result of genetic changes caused by transposable elements. Additionally, epiallele formation may play a role in determining geo-specific (‘terroir’) differences in grapes and thus ultimately in wine. This genomic plasticity might be co-opted for crop improvement via somatic embryogenesis, but that depends on a species-specific understanding of the epigenetic regulation of transposable element (TE) expression and silencing in these cultures. For this reason, we used whole-genome bisulphite sequencing, mRNA sequencing and small RNA sequencing to study the epigenetic status and expression of TEs in embryogenic callus, in comparison with leaf tissue. Results We found that compared with leaf tissue, grapevine embryogenic callus cultures accumulate relatively high genome-wide CHH methylation, particularly across heterochromatic regions. This de novo methylation is associated with an abundance of transcripts from highly replicated TE families, as well as corresponding 24 nt heterochromatic siRNAs. Methylation in the TE-specific CHG context was relatively low over TEs located within genes, and the expression of TE loci within genes was highly correlated with the expression of those genes. Conclusions This multi-‘omics analysis of grapevine embryogenic callus in comparison with leaf tissues reveals a high level of genome-wide transcription of TEs accompanied by RNA-dependent DNA methylation of these sequences in trans. This provides insight into the genomic conditions underlying somaclonal variation and epiallele formation in plants regenerated from embryogenic cultures, which is an important consideration when using these tissues for plant propagation and genetic improvement.

Genome-Wide Comparative Analysis of pogo-Like Transposable Elements in Different Fusarium Species

2011 ◽  
Vol 73 (3-4) ◽  
pp. 230-243 ◽  
Author(s):  
Marie Dufresne ◽  
Olivier Lespinet ◽  
Marie-Josée Daboussi ◽  
Aurélie Hua-Van
Keyword(s):  
Comparative Analysis ◽  
Transposable Elements ◽  
Fusarium Species ◽  
Genome Wide

Genome analysis reveals that the correct name of type strain Adlercreutzia caecicola DSM 22242T is Parvibacter caecicola Clavel et al. 2013

2021 ◽  
Vol 71 (5) ◽  
Author(s):  
Dominic A. Stoll ◽  
Nicolas Danylec ◽  
Christina Grimmler ◽  
Sabine E. Kulling ◽  
Melanie Huch
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Draft Genome ◽  
Amino Acid Identity ◽  
Average Nucleotide Identity ◽  
Content Type ◽  
Link Type ◽  
Genome Wide ◽  
Average Amino Acid Identity ◽  
Biochemical Analyses

The strain Adlercreutzia caecicola DSM 22242T (=CCUG 57646T=NR06T) was taxonomically described in 2013 and named as Parvibacter caecicola Clavel et al. 2013. In 2018, the name of the strain DSM 22242T was changed to Adlercreutzia caecicola (Clavel et al. 2013) Nouioui et al. 2018 due to taxonomic investigations of the closely related genera Adlercreutzia, Asaccharobacter and Enterorhabdus within the phylum Actinobacteria . However, the first whole draft genome of strain DSM 22242T was published by our group in 2019. Therefore, the genome was not available within the study of Nouioui et al. (2018). The results of the polyphasic approach within this study, including phenotypic and biochemical analyses and genome-based taxonomic investigations [genome-wide average nucleotide identity (gANI), alignment fraction (AF), average amino acid identity (AAI), percentage of orthologous conserved proteins (POCP) and genome blast distance phylogeny (GBDP) tree], indicated that the proposed change of the name Parvibacter caecicola to Adlercreutzia caecicola was not correct. Therefore, it is proposed that the correct name of Adlercreutzia caecicola (Clavel et al. 2013) Nouioui et al. 2018 strain DSM 22242T is Parvibacter caecicola Clavel et al. 2013.

Annotating Distributed Scores for Mutual Engagement in Daisyphone and Beyond

2011 ◽  
Vol 21 ◽  
pp. 51-55 ◽  
Author(s):  
Nick Bryan-Kinns
Keyword(s):  
Music Composition ◽  
Web Based ◽  
Mutual Engagement ◽  
Music Making ◽  
Musical Scores ◽  
Composition Process ◽  
Core Part ◽  
The Web ◽  
Made In

Written and drawn annotations of musical scores form a core part of the music composition process for both individuals and groups. This article reflects on the annotations made in new forms of distributed music-making wherein the score and its annotations are shared across the web. Four kinds of annotation are identified from 8 years of studies of mutual engagement through distributed music-making systems. It is suggested that new forms of web-based music-making might benefit from shared and persistent graphical annotation mechanisms.

scholarly journals Social and Solidarity Economy Web Information Systems

2014 ◽  
Vol 12 (1) ◽  
pp. 35-52 ◽  
Author(s):  
Mariana Curado Malta ◽  
Ana Alice Baptista ◽  
Cristina Parente
Keyword(s):  
Information Systems ◽  
State Of The Art ◽  
Bibliographic Databases ◽  
Sources Of Information ◽  
Solidarity Economy ◽  
Web Based ◽  
Web Information ◽  
The Social ◽  
Application Profile ◽  
Made In

This paper presents the state of the art on interoperability developments for the social and solidarity economy (SSE) community web based information systems (WIS); it also presents a framework of interoperability for the SSE' WIS and the developments made in a research-in-progress PhD project in the last 3 years. A search on the bibliographic databases showed that so far there are no papers on interoperability initiatives on the SSE, so it was necessary to have other sources of information: a preliminary analysis of the WIS that support SSE activities; and interviews with the representatives of some of the world's most important SSE organisations. The study showed that the WIS are still not interoperable yet. In order to become interoperable a group of the SSE community has been developing a Dublin Corre Application Profile to be used by the SSE community as reference and binding to describe their resources. This paper also describes this on-going process.

scholarly journals Comparative genomic and transcriptomic analyses of transposable elements in polychaetous annelids highlight LTR retrotransposon diversity and evolution

Mobile DNA ◽  
2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Jonathan Filée ◽  
Sarah Farhat ◽  
Dominique Higuet ◽  
Laure Teysset ◽  
Dominique Marie ◽  
...  
Keyword(s):  
Transposable Elements ◽  
High Throughput Sequencing ◽  
Comparative Genomic ◽  
Ltr Retrotransposon ◽  
Genomic Evolution ◽  
Genome Wide ◽  
Genomic Analyses ◽  
Different Types ◽  
Evolutionary Success ◽  
Low Coverage

Abstract Background With the expansion of high throughput sequencing, we now have access to a larger number of genome-wide studies analyzing the Transposable elements (TEs) composition in a wide variety of organisms. However, genomic analyses often remain too limited in number and diversity of species investigated to study in depth the dynamics and evolutionary success of the different types of TEs among metazoans. Therefore, we chose to investigate the use of transcriptomes to describe the diversity of TEs in phylogenetically related species by conducting the first comparative analysis of TEs in two groups of polychaetes and evaluate the diversity of TEs that might impact genomic evolution as a result of their mobility. Results We present a detailed analysis of TEs distribution in transcriptomes extracted from 15 polychaetes depending on the number of reads used during assembly, and also compare these results with additional TE scans on associated low-coverage genomes. We then characterized the clades defined by 1021 LTR-retrotransposon families identified in 26 species. Clade richness was highly dependent on the considered superfamily. Copia elements appear rare and are equally distributed in only three clades, GalEa, Hydra and CoMol. Among the eight BEL/Pao clades identified in annelids, two small clades within the Sailor lineage are new for science. We characterized 17 Gypsy clades of which only 4 are new; the C-clade largely dominates with a quarter of the families. Finally, all species also expressed for the majority two distinct transcripts encoding PIWI proteins, known to be involved in control of TEs mobilities. Conclusions This study shows that the use of transcriptomes assembled from 40 million reads was sufficient to access to the diversity and proportion of the transposable elements compared to those obtained by low coverage sequencing. Among LTR-retrotransposons Gypsy elements were unequivocally dominant but results suggest that the number of Gypsy clades, although high, may be more limited than previously thought in metazoans. For BEL/Pao elements, the organization of clades within the Sailor lineage appears more difficult to establish clearly. The Copia elements remain rare and result from the evolutionary consistent success of the same three clades.

scholarly journals Moderated Online Social Therapy: Viewpoint on the Ethics and Design Principles of a Web-Based Therapy System (Preprint)

2019 ◽  
Author(s):  
Simon D'Alfonso ◽  
Jessica Phillips ◽  
Lee Valentine ◽  
John Gleeson ◽  
Mario Alvarez-Jimenez
Keyword(s):  
Social Networking Sites ◽  
Well Being ◽  
Web Based ◽  
Strategic Design ◽  
Holistic Concept ◽  
Ethical Design ◽  
Research Questions ◽  
The Impact ◽  
Health And Well Being ◽  
Made In

UNSTRUCTURED The modern omnipresence of social media and social networking sites (SNSs) brings with it a range of important research questions. One of these concerns the impact of SNS use on mental health and well-being, a question that has been pursued in depth by scholars in the psychological sciences and the field of human-computer interaction. Despite this attention, the design choices made in the development of SNSs and the notion of well-being employed to evaluate such systems require further scrutiny. In this viewpoint paper, we examine the strategic design choices made in our development of an enclosed SNS for young people experiencing mental ill-health in terms of ethical and persuasive design and in terms of how it fosters well-being. In doing so, we critique the understanding of well-being that is used in much of the existing literature to make claims about the impact of a given technology on well-being. We also demonstrate how the holistic concept of eudaimonic well-being and ethical design of SNSs can complement one another.

scholarly journals Pangenomics in crop improvement—from coding structural variations to finding regulatory variants with pangenome graphs

2021 ◽  
Author(s):  
Silvia F. Zanini ◽  
Philipp E. Bayer ◽  
Rachel Wells ◽  
Rod J. Snowdon ◽  
Jacqueline Batley ◽  
...  
Keyword(s):  
Crop Improvement ◽  
Structural Variations ◽  
Regulatory Variants
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