Faculty Opinions recommendation of OrthoFiller: utilising data from multiple species to improve the completeness of genome annotations.

Author(s):  
Mario Stanke
2017 ◽  
Author(s):  
Michael P. Dunne ◽  
Steven Kelly

AbstractBackroundComplete and accurate annotation of sequenced genomes is of paramount importance to their utility and analysis. Differences in gene prediction pipelines mean that genome sequences for a species can differ considerably in the quality and quantity of their predicted genes. Furthermore, genes that are present in genome sequences sometimes fail to be detected by computational gene prediction methods. Erroneously unannotated genes can lead to oversights and inaccurate assertions in biological investigations, especially for smaller-scale genome projects which rely heavily on computational prediction.ResultsHere we present OrthoFiller, a tool designed to address the problem of finding and adding such missing genes to genome annotations. OrthoFiller leverages information from multiple related species to identify those genes whose existence can be verified through comparison with known gene families, but which have not been predicted. By simulating missing gene annotations in real sequence datasets from both plants and fungi we demonstrate the accuracy and utility of OrthoFiller for finding missing genes and improving genome annotation. Furthermore, we show that applying OrthoFiller to existing “complete” genome annotations can identify and correct substantial numbers of erroneously missing genes in these two sets of species.ConclusionsWe show that significant improvements in the completeness of genome annotations can be made by leveraging information from multiple species.


Author(s):  
Gary Genosko

While Deleuze explored the temporalities of alcoholism in American literature in The Logic of Sense, and Jean Clet Martin, among others, has extended this inquiry by further extracting the alcoholic’s lines of flight from the same literature, this chapter breaks the mould by understanding alcohol, distilled and in its pure form of ethanol, as well as its imbibition, as a question of a component that passes through anthropocentric, and across multiple non-anthropocentric assemblages. The exploitation of ethanol fermentation, for example, exists across species. Indeed, as we entertain more overtly human cultural examples, such as ‘wine’ for cats, a recent Japanese pet trend, the metabolic communion of interspecies companionship requires that the material expressivity of the substance is overcoded because the ‘wine’ is not only non-alcoholic but liquid catnip in a ‘wine’ bottle. Indeed, theorization of the pursuit of shared pleasures – using Guattari’s ethological terms, we might say deterritorializing from deterministic biological factors yet also modifying these in some measure as well (Machinic Unconscious) – and engaging multiple species is this chapter’s goal, achievable by plotting the passages of alcohol and its related components across assemblages and their material and socio-cultural expressive trajectories beyond strictly anthropocentric and Western prerogatives.


Author(s):  
Scott Jukes

Abstract This paper proposes some possibilities for thinking with a landscape as a pedagogical concept, inspired by posthuman theory. The idea of thinking with a landscape is enacted in the Australian Alps (AA), concentrating on the contentious environmental dilemma involving introduced horses and their management in this bio-geographical location. The topic of horses is of pedagogical relevance for place-responsive outdoor environmental educators as both a location-specific problem and an example of a troubling issue. The paper has two objectives for employing posthuman thinking. Firstly, it experiments with the alternative methodological possibilities that posthuman theory affords for outdoor environmental education, including new ways of conducting educational research. Secondly, it explores how thinking with a landscape as a pedagogical concept may help open ways of considering the dilemma that horses pose. The pedagogical concept is enacted through some empirical events which sketch human–horse encounters from the AA. These sketches depict some of the pedagogical conversations and discursive pathways that encounters can provoke. Such encounters and conversations are ways of constructing knowledge of the landscape, covering multiple species, perspectives and discursive opportunities. For these reasons, this paper may be of relevance for outdoor environmental educators, those interested in the AA or posthuman theorists.


2021 ◽  
Author(s):  
Cecilia Di Bernardi ◽  
Camilla Wikenros ◽  
Eva Hedmark ◽  
Luigi Boitani ◽  
Paolo Ciucci ◽  
...  

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Polina Drozdova ◽  
Alena Kizenko ◽  
Alexandra Saranchina ◽  
Anton Gurkov ◽  
Maria Firulyova ◽  
...  

Abstract Background Vision is a crucial sense for the evolutionary success of many animal groups. Here we explore the diversity of visual pigments (opsins) in the transcriptomes of amphipods (Crustacea: Amphipoda) and conclude that it is restricted to middle (MWS) and long wavelength-sensitive (LWS) opsins in the overwhelming majority of examined species. Results We evidenced (i) parallel loss of MWS opsin expression in multiple species (including two independently evolved lineages from the deep and ancient Lake Baikal) and (ii) LWS opsin amplification (up to five transcripts) in both Baikal lineages. The number of LWS opsins negatively correlated with habitat depth in Baikal amphipods. Some LWS opsins in Baikal amphipods contained MWS-like substitutions, suggesting that they might have undergone spectral tuning. Conclusions This repeating two-step evolutionary scenario suggests common triggers, possibly the lack of light during the periods when Baikal was permanently covered with thick ice and its subsequent melting. Overall, this observation demonstrates the possibility of revealing climate history by following the evolutionary changes in protein families.


2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Matthew Chung ◽  
Vincent M. Bruno ◽  
David A. Rasko ◽  
Christina A. Cuomo ◽  
José F. Muñoz ◽  
...  

AbstractAdvances in transcriptome sequencing allow for simultaneous interrogation of differentially expressed genes from multiple species originating from a single RNA sample, termed dual or multi-species transcriptomics. Compared to single-species differential expression analysis, the design of multi-species differential expression experiments must account for the relative abundances of each organism of interest within the sample, often requiring enrichment methods and yielding differences in total read counts across samples. The analysis of multi-species transcriptomics datasets requires modifications to the alignment, quantification, and downstream analysis steps compared to the single-species analysis pipelines. We describe best practices for multi-species transcriptomics and differential gene expression.


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