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      Kingdom-wide analysis of the evolution of the plant type III polyketide synthase superfamily

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          Abstract

          The emergence of type III polyketide synthases (PKSs) was a prerequisite for the conquest of land by the green lineage. Within the PKS superfamily, chalcone synthases (CHSs) provide the entry point reaction to the flavonoid pathway, while LESS ADHESIVE POLLEN 5 and 6 (LAP5/6) provide constituents of the outer exine pollen wall. To study the deep evolutionary history of this key family, we conducted phylogenomic synteny network and phylogenetic analyses of whole-genome data from 126 species spanning the green lineage including Arabidopsis thaliana, tomato ( Solanum lycopersicum), and maize ( Zea mays). This study thereby combined study of genomic location and context with changes in gene sequences. We found that the two major clades, CHS and LAP5/6 homologs, evolved early by a segmental duplication event prior to the divergence of Bryophytes and Tracheophytes. We propose that the macroevolution of the type III PKS superfamily is governed by whole-genome duplications and triplications. The combined phylogenetic and synteny analyses in this study provide insights into changes in the genomic location and context that are retained for a longer time scale with more recent functional divergence captured by gene sequence alterations.

          Abstract

          Phylogenetic and syntenic analyses of whole genome data reveal that macroevolution of the type III polyketide synthase superfamily is mainly governed by whole-genome duplications and triplications.

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          Cytoscape is an open source software project for integrating biomolecular interaction networks with high-throughput expression data and other molecular states into a unified conceptual framework. Although applicable to any system of molecular components and interactions, Cytoscape is most powerful when used in conjunction with large databases of protein-protein, protein-DNA, and genetic interactions that are increasingly available for humans and model organisms. Cytoscape's software Core provides basic functionality to layout and query the network; to visually integrate the network with expression profiles, phenotypes, and other molecular states; and to link the network to databases of functional annotations. The Core is extensible through a straightforward plug-in architecture, allowing rapid development of additional computational analyses and features. Several case studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes in gene expression, a study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models.
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            OrthoFinder: phylogenetic orthology inference for comparative genomics

            Here, we present a major advance of the OrthoFinder method. This extends OrthoFinder’s high accuracy orthogroup inference to provide phylogenetic inference of orthologs, rooted gene trees, gene duplication events, the rooted species tree, and comparative genomics statistics. Each output is benchmarked on appropriate real or simulated datasets, and where comparable methods exist, OrthoFinder is equivalent to or outperforms these methods. Furthermore, OrthoFinder is the most accurate ortholog inference method on the Quest for Orthologs benchmark test. Finally, OrthoFinder’s comprehensive phylogenetic analysis is achieved with equivalent speed and scalability to the fastest, score-based heuristic methods. OrthoFinder is available at https://github.com/davidemms/OrthoFinder.
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              STRING v10: protein–protein interaction networks, integrated over the tree of life

              The many functional partnerships and interactions that occur between proteins are at the core of cellular processing and their systematic characterization helps to provide context in molecular systems biology. However, known and predicted interactions are scattered over multiple resources, and the available data exhibit notable differences in terms of quality and completeness. The STRING database (http://string-db.org) aims to provide a critical assessment and integration of protein–protein interactions, including direct (physical) as well as indirect (functional) associations. The new version 10.0 of STRING covers more than 2000 organisms, which has necessitated novel, scalable algorithms for transferring interaction information between organisms. For this purpose, we have introduced hierarchical and self-consistent orthology annotations for all interacting proteins, grouping the proteins into families at various levels of phylogenetic resolution. Further improvements in version 10.0 include a completely redesigned prediction pipeline for inferring protein–protein associations from co-expression data, an API interface for the R computing environment and improved statistical analysis for enrichment tests in user-provided networks.
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                Author and article information

                Journal
                Plant Physiol
                Plant Physiol
                plphys
                Plant Physiology
                Oxford University Press
                0032-0889
                1532-2548
                March 2021
                30 December 2020
                30 December 2020
                : 185
                : 3
                : 857-875
                Affiliations
                [1 ] Max Planck Institute of Molecular Plant Physiology , Am Mühlenberg 1, 14476 Potsdam, Germany
                [2 ] Department of Botany, University of Wisconsin–Madison , 430 Lincoln Drive, Madison, WI 53706, USA
                [3 ] Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, KU Leuven , Herestraat, 3000 Leuven, Belgium
                [4 ] VIB-KU Leuven Center for Microbiology, Campus Gasthuisberg, Rega Instituut , Herestraat, 3000 Leuven, Belgium
                [5 ] Nara Institute of Science and Technology , 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
                Author notes
                Author for communication: fernie@ 123456mpimp-golm.mpg.de

                Senior author.

                Author information
                https://orcid.org/0000-0003-0246-694X
                https://orcid.org/0000-0001-5555-5650
                https://orcid.org/0000-0001-9000-335X
                Article
                kiaa086
                10.1093/plphys/kiaa086
                8133574
                33793871
                ffc096c7-564d-4d7f-bdde-d08b5e60774a
                © The Author(s) 2020. Published by Oxford University Press on behalf of American Society of Plant Biologists.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 03 September 2020
                : 07 December 2020
                Page count
                Pages: 19
                Funding
                Funded by: VLAIO, DOI 10.13039/100012331;
                Award ID: HBC.2016.0556
                Funded by: National Science Foundation, DOI 10.13039/100000001;
                Award ID: IOS-1836824
                Award ID: MCB-1818040
                Categories
                Regular Issue
                Research Articles
                Biochemistry and Metabolism
                AcademicSubjects/SCI02286
                AcademicSubjects/SCI02287
                AcademicSubjects/SCI01270
                AcademicSubjects/SCI01280
                AcademicSubjects/SCI02288

                Plant science & Botany
                Plant science & Botany

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