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      Comparative transcriptomic analysis of the mechanisms underpinning ageing and fecundity in social insects

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          Abstract

          The exceptional longevity of social insect queens despite their lifelong high fecundity remains poorly understood in ageing biology. To gain insights into the mechanisms that might underlie ageing in social insects, we compared gene expression patterns between young and old castes (both queens and workers) across different lineages of social insects (two termite, two bee and two ant species). After global analyses, we paid particular attention to genes of the insulin/insulin-like growth factor 1 signalling (IIS)/target of rapamycin (TOR)/juvenile hormone (JH) network, which is well known to regulate lifespan and the trade-off between reproduction and somatic maintenance in solitary insects. Our results reveal a major role of the downstream components and target genes of this network (e.g. JH signalling, vitellogenins, major royal jelly proteins and immune genes) in affecting ageing and the caste-specific physiology of social insects, but an apparently lesser role of the upstream IIS/TOR signalling components. Together with a growing appreciation of the importance of such downstream targets, this leads us to propose the TI–J–LiFe ( TOR/ IIS– JH– Lifespan and Fecundity) network as a conceptual framework for understanding the mechanisms of ageing and fecundity in social insects and beyond.

          This article is part of the theme issue ‘Ageing and sociality: why, when and how does sociality change ageing patterns?’

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          Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

          In comparative high-throughput sequencing assays, a fundamental task is the analysis of count data, such as read counts per gene in RNA-seq, for evidence of systematic changes across experimental conditions. Small replicate numbers, discreteness, large dynamic range and the presence of outliers require a suitable statistical approach. We present DESeq2, a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates. This enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression. The DESeq2 package is available at http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0550-8) contains supplementary material, which is available to authorized users.
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            Basic local alignment search tool.

            A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score. Recent mathematical results on the stochastic properties of MSP scores allow an analysis of the performance of this method as well as the statistical significance of alignments it generates. The basic algorithm is simple and robust; it can be implemented in a number of ways and applied in a variety of contexts including straightforward DNA and protein sequence database searches, motif searches, gene identification searches, and in the analysis of multiple regions of similarity in long DNA sequences. In addition to its flexibility and tractability to mathematical analysis, BLAST is an order of magnitude faster than existing sequence comparison tools of comparable sensitivity.
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              BLAST+: architecture and applications

              Background Sequence similarity searching is a very important bioinformatics task. While Basic Local Alignment Search Tool (BLAST) outperforms exact methods through its use of heuristics, the speed of the current BLAST software is suboptimal for very long queries or database sequences. There are also some shortcomings in the user-interface of the current command-line applications. Results We describe features and improvements of rewritten BLAST software and introduce new command-line applications. Long query sequences are broken into chunks for processing, in some cases leading to dramatically shorter run times. For long database sequences, it is possible to retrieve only the relevant parts of the sequence, reducing CPU time and memory usage for searches of short queries against databases of contigs or chromosomes. The program can now retrieve masking information for database sequences from the BLAST databases. A new modular software library can now access subject sequence data from arbitrary data sources. We introduce several new features, including strategy files that allow a user to save and reuse their favorite set of options. The strategy files can be uploaded to and downloaded from the NCBI BLAST web site. Conclusion The new BLAST command-line applications, compared to the current BLAST tools, demonstrate substantial speed improvements for long queries as well as chromosome length database sequences. We have also improved the user interface of the command-line applications.
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                Author and article information

                Contributors
                Journal
                Philos Trans R Soc Lond B Biol Sci
                Philos Trans R Soc Lond B Biol Sci
                RSTB
                royptb
                Philosophical Transactions of the Royal Society B: Biological Sciences
                The Royal Society
                0962-8436
                1471-2970
                April 26, 2021
                March 8, 2021
                March 8, 2021
                : 376
                : 1823 , Theme issue ‘Ageing and sociality: why, when and how does sociality change ageing patterns?’ compiled and edited by Judith Korb and Jürgen Heinze
                : 20190728
                Affiliations
                [ 1 ]Department of Evolutionary Biology and Ecology, Institute of Biology I (Zoology), University of Freiburg, , Hauptstraße 1, D-79104 Freiburg (Breisgau), Germany
                [ 2 ]Australian National Insect Collection, CSIRO National Research Collections Australia, , Clunies Ross Street, Canberra, Acton 2601, Australia
                [ 3 ]Developmental Zoology, Molecular Ecology Research Group, , Hoher Weg 4, D-06099 Halle (Saale), Germany
                [ 4 ]Zoology/Evolutionary Biology, University of Regensburg, , Universitätsstraße 31, D-93040 Regensburg, Germany
                [ 5 ]Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Molecular Ecology, , Senckenberg, Georg-Voigt-Straße 14-16, D-60325 Frankfurt, Germany
                [ 6 ]Institute of Organismic and Molecular Evolution (IOME), Johannes Gutenberg University Mainz, , Hanns-Dieter-Hüsch-Weg 15, D-55128 Mainz, Germany
                [ 7 ]Institute for Biology, Martin Luther University Halle-Wittenberg, , Hoher Weg 8, 06120 Halle, Germany
                [ 8 ]Institute for Evolution and Biodiversity, University of Münster, , Hüfferstraße 1, 48149 Münster, Germany
                [ 9 ]Department of Biology, University of Fribourg, , Chemin du Musée 10, CH-1700 Fribourg, Switzerland
                Author notes
                [†]

                These authors contributed equally to the study.

                Electronic supplementary material is available online at https://doi.org/10.6084/m9.figshare.c.5303452.

                Author information
                http://orcid.org/0000-0001-9577-9376
                http://orcid.org/0000-0002-7590-4851
                http://orcid.org/0000-0001-5600-587X
                http://orcid.org/0000-0002-0413-7245
                http://orcid.org/0000-0001-8161-6306
                http://orcid.org/0000-0002-9403-5946
                http://orcid.org/0000-0003-4397-000X
                http://orcid.org/0000-0002-6206-5198
                http://orcid.org/0000-0002-4748-8854
                http://orcid.org/0000-0002-0494-1428
                http://orcid.org/0000-0003-2517-1351
                http://orcid.org/0000-0001-5159-5815
                http://orcid.org/0000-0003-2410-4413
                http://orcid.org/0000-0002-5990-1503
                Article
                rstb20190728
                10.1098/rstb.2019.0728
                7938167
                33678016
                629cada7-2b33-4fed-9773-b8df04305cf3
                © 2021 The Authors.

                Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original author and source are credited.

                History
                : January 4, 2021
                Funding
                Funded by: Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung, http://dx.doi.org/10.13039/501100001711;
                Award ID: 310030E-164207
                Award ID: 31003A_182262
                Funded by: Deutsche Forschungsgemeinschaft, http://dx.doi.org/10.13039/501100001659;
                Award ID: BE6684/1-1
                Award ID: FE1333/6-1
                Award ID: FE1333/6-2
                Award ID: FO298/19-1
                Award ID: FO298/19-2
                Award ID: He1623/37
                Award ID: KO1895/16-1
                Award ID: KO1895/19-1
                Award ID: KO1895/20-1
                Award ID: KO1895/20-2
                Award ID: LI 3051/3-1
                Award ID: NE1969/4-1
                Award ID: PA632/9 -1
                Award ID: PA632/9 -2
                Funded by: Novartis Foundation, http://dx.doi.org/10.13039/100008273;
                Award ID: grant 19B149
                Categories
                1001
                70
                14
                129
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                Research Articles
                Custom metadata
                April 26, 2021

                Philosophy of science
                social insects,longevity,insulin,tor,juvenile hormone,transcriptomics
                Philosophy of science
                social insects, longevity, insulin, tor, juvenile hormone, transcriptomics

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