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      One Hundred Mitochondrial Genomes of Cicadas

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          Abstract

          Mitochondrial genomes can provide valuable information on the biology and evolutionary histories of their host organisms. Here, we present and characterize the complete coding regions of 107 mitochondrial genomes (mitogenomes) of cicadas (Insecta: Hemiptera: Auchenorrhyncha: Cicadoidea), representing 31 genera, 61 species, and 83 populations. We show that all cicada mitogenomes retain the organization and gene contents thought to be ancestral in insects, with some variability among cicada clades in the length of a region between the genes nad2 and cox1 , which encodes 3 tRNAs. Phylogenetic analyses using these mitogenomes recapitulate a recent 5-gene classification of cicadas into families and subfamilies, but also identify a species that falls outside of the established taxonomic framework. While protein-coding genes are under strong purifying selection, tests of relative evolutionary rates reveal significant variation in evolutionary rates across taxa, highlighting the dynamic nature of mitochondrial genome evolution in cicadas. These data will serve as a useful reference for future research into the systematics, ecology, and evolution of the superfamily Cicadoidea.

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          Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform

          Due to the increasing throughput of current DNA sequencing instruments, sample multiplexing is necessary for making economical use of available sequencing capacities. A widely used multiplexing strategy for the Illumina Genome Analyzer utilizes sample-specific indexes, which are embedded in one of the library adapters. However, this and similar multiplex approaches come with a risk of sample misidentification. By introducing indexes into both library adapters (double indexing), we have developed a method that reveals the rate of sample misidentification within current multiplex sequencing experiments. With ~0.3% these rates are orders of magnitude higher than expected and may severely confound applications in cancer genomics and other fields requiring accurate detection of rare variants. We identified the occurrence of mixed clusters on the flow as the predominant source of error. The accuracy of sample identification is further impaired if indexed oligonucleotides are cross-contaminated or if indexed libraries are amplified in bulk. Double-indexing eliminates these problems and increases both the scope and accuracy of multiplex sequencing on the Illumina platform.
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            Mitochondrial pseudogenes: evolution's misplaced witnesses.

            Nuclear copies of mitochondrial DNA (mtDNA) have contaminated PCR-based mitochondrial studies of over 64 different animal species. Since the last review of these nuclear mitochondrial pseudogenes (Numts) in animals, Numts have been found in 53 of the species studied. The recent evidence suggests that Numts are not equally abundant in all species, for example they are more common in plants than in animals, and also more numerous in humans than in Drosophila. Methods for avoiding Numts have now been tested, and several recent studies demonstrate the potential utility of Numt DNA sequences in evolutionary studies. As relics of ancient mtDNA, these pseudogenes can be used to infer ancestral states or root mitochondrial phylogenies. Where they are numerous and selectively unconstrained, Numts are ideal for the study of spontaneous mutation in nuclear genomes.
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              Eukaryotic evolution, changes and challenges.

              The idea that some eukaryotes primitively lacked mitochondria and were true intermediates in the prokaryote-to-eukaryote transition was an exciting prospect. It spawned major advances in understanding anaerobic and parasitic eukaryotes and those with previously overlooked mitochondria. But the evolutionary gap between prokaryotes and eukaryotes is now deeper, and the nature of the host that acquired the mitochondrion more obscure, than ever before.
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                Author and article information

                Journal
                Journal of Heredity
                Oxford University Press (OUP)
                0022-1503
                1465-7333
                March 2019
                March 05 2019
                December 22 2018
                March 2019
                March 05 2019
                December 22 2018
                : 110
                : 2
                : 247-256
                Affiliations
                [1 ]Division of Biological Sciences, University of Montana, Missoula, MT
                [2 ]Department of Biology, University of Hawai’i at Mānoa, Honolulu, HI
                [3 ]Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT
                [4 ]Tropical Biosphere Research Center, University of the Ryukyus, Japan
                [5 ]Centro de Investigaciones Esquel de Montaña y Estepa Patagónicas (CIEMEP), Esquel, Chubut, Argentina
                [6 ]Department of Ecological Sciences, Science Faculty, University of Chile, Santiago, Chile
                Article
                10.1093/jhered/esy068
                6784412
                30590568
                4ad9aba4-3256-4cbc-a4ca-833efa606b6b
                © 2018

                https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model

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