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      Genome Analyses of a New Mycoplasma Species from the Scorpion Centruroides vittatus

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          Abstract

          Arthropod Mycoplasma are little known endosymbionts in insects, primarily known as plant disease vectors. Mycoplasma in other arthropods such as arachnids are unknown. We report the first complete Mycoplasma genome sequenced, identified, and annotated from a scorpion, Centruroides vittatus, and designate it as Mycoplasma vittatus. We find the genome is at least a 683,827 bp single circular chromosome with a GC content of 42.7% and with 987 protein-coding genes. The putative virulence determinants include 11 genes associated with the virulence operon associated with protein synthesis or DNA transcription and ten genes with antibiotic and toxic compound resistance. Comparative analysis revealed that the M. vittatus genome is smaller than other Mycoplasma genomes and exhibits a higher GC content. Phylogenetic analysis shows M. vittatus as part of the Hominis group of Mycoplasma. As arthropod genomes accumulate, further novel Mycoplasma genomes may be identified and characterized.

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          The house spider genome reveals an ancient whole-genome duplication during arachnid evolution

          Background The duplication of genes can occur through various mechanisms and is thought to make a major contribution to the evolutionary diversification of organisms. There is increasing evidence for a large-scale duplication of genes in some chelicerate lineages including two rounds of whole genome duplication (WGD) in horseshoe crabs. To investigate this further, we sequenced and analyzed the genome of the common house spider Parasteatoda tepidariorum. Results We found pervasive duplication of both coding and non-coding genes in this spider, including two clusters of Hox genes. Analysis of synteny conservation across the P. tepidariorum genome suggests that there has been an ancient WGD in spiders. Comparison with the genomes of other chelicerates, including that of the newly sequenced bark scorpion Centruroides sculpturatus, suggests that this event occurred in the common ancestor of spiders and scorpions, and is probably independent of the WGDs in horseshoe crabs. Furthermore, characterization of the sequence and expression of the Hox paralogs in P. tepidariorum suggests that many have been subject to neo-functionalization and/or sub-functionalization since their duplication. Conclusions Our results reveal that spiders and scorpions are likely the descendants of a polyploid ancestor that lived more than 450 MYA. Given the extensive morphological diversity and ecological adaptations found among these animals, rivaling those of vertebrates, our study of the ancient WGD event in Arachnopulmonata provides a new comparative platform to explore common and divergent evolutionary outcomes of polyploidization events across eukaryotes. Electronic supplementary material The online version of this article (doi:10.1186/s12915-017-0399-x) contains supplementary material, which is available to authorized users.
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            Comparative Genomics of Mycoplasma: Analysis of Conserved Essential Genes and Diversity of the Pan-Genome

            Mycoplasma, the smallest self-replicating organism with a minimal metabolism and little genomic redundancy, is expected to be a close approximation to the minimal set of genes needed to sustain bacterial life. This study employs comparative evolutionary analysis of twenty Mycoplasma genomes to gain an improved understanding of essential genes. By analyzing the core genome of mycoplasmas, we finally revealed the conserved essential genes set for mycoplasma survival. Further analysis showed that the core genome set has many characteristics in common with experimentally identified essential genes. Several key genes, which are related to DNA replication and repair and can be disrupted in transposon mutagenesis studies, may be critical for bacteria survival especially over long period natural selection. Phylogenomic reconstructions based on 3,355 homologous groups allowed robust estimation of phylogenetic relatedness among mycoplasma strains. To obtain deeper insight into the relative roles of molecular evolution in pathogen adaptation to their hosts, we also analyzed the positive selection pressures on particular sites and lineages. There appears to be an approximate correlation between the divergence of species and the level of positive selection detected in corresponding lineages.
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              Towards a genome based taxonomy of Mycoplasmas.

              Mycoplasmas are Gram-positive wall-less bacteria with a wide environmental and host distribution, causing disease in man and in (wild and farmed) animals. The aim of this study was to analyze the usefulness of a genomic taxonomic approach in Mycoplasma systematics. Multilocus Sequence Analysis (MLSA), average amino acid identity (AAI), and Karlin genomic signature allowed a clear identification of species. For instance, Mycoplasma pneumoniae and Mycoplasma genitalium had only 71% MLSA similarity, 67% AAI, and 88 for Karlin genomic signature. Codon usage (Nc) of the phylogenetically distantly related species Mycoplasma conjunctivae and Mycoplasma gallisepticum was identical, in spite of clear differences in MLSA, AAI, and Karlin, suggesting that these two species were subjected to convergent adaptation due to similar environmental conditions. We suggest that a Mycoplasma species may be better defined based on genomic features. In our hands, a Mycoplasma species is defined as a group of strains that share ≥ 97% DNA identity in MLSA, ≥ 93.9% AAI and ≤ 8 in Karlin genomic signature. This new definition may be useful to advance the taxonomy of Mycoplasmas. Copyright © 2011 Elsevier B.V. All rights reserved.
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                Author and article information

                Journal
                G3 (Bethesda)
                Genetics
                G3: Genes, Genomes, Genetics
                G3: Genes, Genomes, Genetics
                G3: Genes, Genomes, Genetics
                G3: Genes|Genomes|Genetics
                Genetics Society of America
                2160-1836
                14 February 2019
                April 2019
                : 9
                : 4
                : 993-997
                Affiliations
                [* ]Department of Biological Sciences, Arkansas Tech University, Russellville, AR 72801
                []Department of Biological Sciences, University of Arkansas-Fayetteville, Fayetteville, AR 72701
                []High Performance Computing Center, University of Arkansas-Fayetteville, Fayetteville, AR 72701
                Author notes
                [1 ]Corresponding Author: Dept. of Biological Sciences, Arkansas Tech University, 1701 N. Boulder Ave., Russellville, AR 72801, E-mail: tyamashita@ 123456atu.edu
                Article
                GGG_200858
                10.1534/g3.118.200858
                6469414
                30765418
                Copyright © 2019 Yamashita et al.

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

                Page count
                Figures: 2, Tables: 0, Equations: 0, References: 14, Pages: 5
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                Categories
                Genome Report

                Genetics

                arachnid, scorpions, mycoplasma, genome

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