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      Circadian regulation of the transcriptome in a complex polyploid crop

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          Abstract

          The circadian clock is a finely balanced timekeeping mechanism that coordinates programmes of gene expression. It is currently unknown how the clock regulates expression of homoeologous genes in polyploids. Here, we generate a high-resolution time-course dataset to investigate the circadian balance between sets of 3 homoeologous genes (triads) from hexaploid bread wheat. We find a large proportion of circadian triads exhibit imbalanced rhythmic expression patterns, with no specific subgenome favoured. In wheat, period lengths of rhythmic transcripts are found to be longer and have a higher level of variance than in other plant species. Expression of transcripts associated with circadian controlled biological processes is largely conserved between wheat and Arabidopsis; however, striking differences are seen in agriculturally critical processes such as starch metabolism. Together, this work highlights the ongoing selection for balance versus diversification in circadian homoeologs and identifies clock-controlled pathways that might provide important targets for future wheat breeding.

          Abstract

          This study presents a high-resolution circadian transcriptomic time-course dataset in wheat, revealing novel insights into the balance of circadian expression in a complex polyploid crop. Over 20% of genes in wheat are circadian regulated and a large proportion of triads exhibit unbalanced rhythmicity patterns.

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          Trimmomatic: a flexible trimmer for Illumina sequence data

          Motivation: Although many next-generation sequencing (NGS) read preprocessing tools already existed, we could not find any tool or combination of tools that met our requirements in terms of flexibility, correct handling of paired-end data and high performance. We have developed Trimmomatic as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data. Results: The value of NGS read preprocessing is demonstrated for both reference-based and reference-free tasks. Trimmomatic is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested. Availability and implementation: Trimmomatic is licensed under GPL V3. It is cross-platform (Java 1.5+ required) and available at http://www.usadellab.org/cms/index.php?page=trimmomatic Contact: usadel@bio1.rwth-aachen.de Supplementary information: Supplementary data are available at Bioinformatics online.
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            RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

            Motivation: Phylogenies are increasingly used in all fields of medical and biological research. Moreover, because of the next-generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likelihood. Since the last RAxML paper in 2006, it has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community. Results: I present some of the most notable new features and extensions of RAxML, such as a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees. In addition, an up-to-date 50-page user manual covering all new RAxML options is available. Availability and implementation: The code is available under GNU GPL at https://github.com/stamatak/standard-RAxML. Contact: alexandros.stamatakis@h-its.org Supplementary information: Supplementary data are available at Bioinformatics online.
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              Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

              Rapid advances in next-generation sequencing technologies have dramatically changed our ability to perform genome-scale analyses. The human reference genome used for most genomic analyses represents only a small number of individuals, limiting its usefulness for genotyping. We designed a novel method, HISAT2, for representing and searching an expanded model of the human reference genome, in which a large catalogue of known genomic variants and haplotypes is incorporated into the data structure used for searching and alignment. This strategy for representing a population of genomes, along with a fast and memory-efficient search algorithm, enables more detailed and accurate variant analyses than previous methods. We demonstrate two initial applications of HISAT2: HLA typing, a critical need in human organ transplantation, and DNA fingerprinting, widely used in forensics. These applications are part of HISAT-genotype, with performance not only surpassing earlier computational methods, but matching or exceeding the accuracy of laboratory-based assays.
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                Author and article information

                Contributors
                Role: ConceptualizationRole: Formal analysisRole: InvestigationRole: MethodologyRole: SupervisionRole: VisualizationRole: Writing – original draftRole: Writing – review & editing
                Role: Data curationRole: Formal analysisRole: Investigation
                Role: Investigation
                Role: MethodologyRole: Validation
                Role: Validation
                Role: Data curation
                Role: Methodology
                Role: Validation
                Role: Investigation
                Role: InvestigationRole: Writing – review & editing
                Role: InvestigationRole: Writing – review & editing
                Role: ConceptualizationRole: Funding acquisitionRole: Project administrationRole: SupervisionRole: Writing – review & editing
                Role: Academic Editor
                Journal
                PLoS Biol
                PLoS Biol
                plos
                PLoS Biology
                Public Library of Science (San Francisco, CA USA )
                1544-9173
                1545-7885
                13 October 2022
                October 2022
                13 October 2022
                : 20
                : 10
                : e3001802
                Affiliations
                [1 ] Earlham Institute, Norwich Research Park, Norwich, United Kingdom
                [2 ] Royal Botanic Gardens Kew, Richmond, Surrey, United Kingdom
                [3 ] John Innes Centre, Norwich Research Park, Norwich, United Kingdom
                [4 ] School of Biological Sciences, University of Bristol, Bristol, United Kingdom
                University of California, Davis, UNITED STATES
                Author notes

                The authors have declared that no competing interests exist.

                Author information
                https://orcid.org/0000-0002-1806-020X
                Article
                PBIOLOGY-D-22-01119
                10.1371/journal.pbio.3001802
                9560141
                36227835
                5aa8ecf4-8f80-49e8-a892-ba03b52805a7
                © 2022 Rees et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 19 May 2022
                : 18 August 2022
                Page count
                Figures: 5, Tables: 2, Pages: 37
                Funding
                Funded by: funder-id http://dx.doi.org/10.13039/501100000268, Biotechnology and Biological Sciences Research Council;
                Award ID: BB/CSP1720/1
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100000268, Biotechnology and Biological Sciences Research Council;
                Award ID: BB/CSP1720/1
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100000268, Biotechnology and Biological Sciences Research Council;
                Award ID: BB/CSP1720/1
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100000268, Biotechnology and Biological Sciences Research Council;
                Award ID: BBS/E/T/000PR9819
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100000268, Biotechnology and Biological Sciences Research Council;
                Award ID: BBS/E/T/000PR9819
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100000268, Biotechnology and Biological Sciences Research Council;
                Award ID: BBS/E/T/000PR9819
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100000268, Biotechnology and Biological Sciences Research Council;
                Award ID: BB/P016855/1
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100000268, Biotechnology and Biological Sciences Research Council;
                Award ID: BB/P016855/1
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100000268, Biotechnology and Biological Sciences Research Council;
                Award ID: BB/P016855/1
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100000268, Biotechnology and Biological Sciences Research Council;
                Award ID: BBS/E/T/000PR9783
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100000268, Biotechnology and Biological Sciences Research Council;
                Award ID: BBS/E/T/000PR9783
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100000268, Biotechnology and Biological Sciences Research Council;
                Award ID: BBS/E/T/000PR9783
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100000268, Biotechnology and Biological Sciences Research Council;
                Award ID: BB/M011216/1
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100000268, Biotechnology and Biological Sciences Research Council;
                Award ID: BB/M011216/1
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100000268, Biotechnology and Biological Sciences Research Council;
                Award ID: BB/V509267/1
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100000266, Engineering and Physical Sciences Research Council;
                Award ID: EP/T001569/1
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100000268, Biotechnology and Biological Sciences Research Council;
                Award ID: BBS/E/T/000PR9816
                Funded by: funder-id http://dx.doi.org/10.13039/501100000268, Biotechnology and Biological Sciences Research Council;
                Award ID: BB/CCG1720/1
                Funded by: funder-id http://dx.doi.org/10.13039/501100000268, Biotechnology and Biological Sciences Research Council;
                Award ID: BB/N023145/1
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100000268, Biotechnology and Biological Sciences Research Council;
                Award ID: BB/P013511/1
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100000268, Biotechnology and Biological Sciences Research Council;
                Award ID: BB/P013511/1
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100000268, Biotechnology and Biological Sciences Research Council;
                Award ID: BB/M009122/1
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100000268, Biotechnology and Biological Sciences Research Council;
                Award ID: BB/P013511/1
                Award Recipient :
                H.R., R.R.P. and A.H. were funded by the BBSRC Core Strategic Programme Grant (Genomes to Food Security) BB/CSP1720/1 and its constituent work package, BBS/E/T/000PR9819 (WP2 Regulatory interactions and Complex Phenotypes). B.W., R.R.P. and A.H. was supported by the BBSRC Designing Future Wheat grant BB/P016855/1; BBS/E/T/000PR9783 (DFW WP4 Data Access and Analysis). B.C and J.C were supported by the BBSRC funded Norwich Research Park Biosciences Doctoral Training Partnership grant BB/M011216/1. C.R. by a BBSRC grant BB/V509267/1 and Wave 1 of The UKRI Strategic Priorities Fund under the EPSRC Grant EP/T001569/1, particularly the “AI for Science” theme within that grant & The Alan Turing Institute. We would also like to acknowledge BBS/E/T/000PR9816 (NC1 ‐ Supporting EI’s ISPs and the UK Community with Genomics and Single Cell Analysis) for data generation and BB/CCG1720/1 for the physical HPC infrastructure and data centre delivered via the NBI Computing infrastructure for Science (CiS) group. P.B. was supported by a BBSRC TRDF grant BB/N023145/1. A.N.D., L.L.B.D. and C.A.G. are funded by BBSRC ISP Genes in the Environment (BB/P013511/1). C.A.G. was also funded by UK BBSRC SWBIO DTP (BB/M009122/1). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Methods and Resources
                Biology and Life Sciences
                Organisms
                Eukaryota
                Plants
                Grasses
                Wheat
                Research and Analysis Methods
                Animal Studies
                Experimental Organism Systems
                Model Organisms
                Arabidopsis Thaliana
                Research and Analysis Methods
                Model Organisms
                Arabidopsis Thaliana
                Biology and Life Sciences
                Organisms
                Eukaryota
                Plants
                Brassica
                Arabidopsis Thaliana
                Research and Analysis Methods
                Animal Studies
                Experimental Organism Systems
                Plant and Algal Models
                Arabidopsis Thaliana
                Biology and Life Sciences
                Chronobiology
                Circadian Rhythms
                Biology and Life Sciences
                Biochemistry
                Circadian Oscillators
                Biology and Life Sciences
                Chronobiology
                Circadian Oscillators
                Biology and Life Sciences
                Chronobiology
                Biology and Life Sciences
                Genetics
                Gene Expression
                Physical Sciences
                Chemistry
                Chemical Compounds
                Organic Compounds
                Carbohydrates
                Starches
                Physical Sciences
                Chemistry
                Organic Chemistry
                Organic Compounds
                Carbohydrates
                Starches
                Biology and Life Sciences
                Genetics
                Genomics
                Plant Genomics
                Biology and Life Sciences
                Bioengineering
                Biotechnology
                Plant Biotechnology
                Plant Genomics
                Engineering and Technology
                Bioengineering
                Biotechnology
                Plant Biotechnology
                Plant Genomics
                Biology and Life Sciences
                Plant Science
                Plant Biotechnology
                Plant Genomics
                Biology and Life Sciences
                Genetics
                Plant Genetics
                Plant Genomics
                Biology and Life Sciences
                Plant Science
                Plant Genetics
                Plant Genomics
                Custom metadata
                Data for the recreation of all main figures in this manuscript are available in S1 Data. Data for the recreation of all supplementary figures in this manuscript are available in S2 Data. Fastq data from the RNA-seq circadian time course are available to view from the Grassroots Data Repository: https://opendata.earlham.ac.uk/opendata/data/wheat_circadian_Rees_2021. A summary csv table with expression of wheat genes (TPM), Metacycle estimates, gene annotations and triad balance classification can be viewed in S11 Table is available here: https://opendata.earlham.ac.uk/opendata/data/wheat_circadian_Rees_2021. A TPM expression matrix at the individual replicate level with triad IDs information is also available: S12 Table: https://opendata.earlham.ac.uk/opendata/data/wheat_circadian_Rees_2021. Code for creating Loom plots, the cross-correlation analysis and the clustering analysis are available from our groups GitHub repository: https://github.com/AHallLab/circadian_transcriptome_regulation_paper_2022/tree/main.

                Life sciences
                Life sciences

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