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      Comparative analysis of the complete mitochondrial genomes of five Achilidae species (Hemiptera: Fulgoroidea) and other Fulgoroidea reveals conserved mitochondrial genome organization

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      PeerJ
      PeerJ Inc.
      Achilidae, Fulgoroidea, Mitochondrial genome, Phylogeny

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          Abstract

          In the present study, the complete mitochondrial genomes (mitogenomes) of five Achilidae (Hemiptera: Fulgoroidea), Betatropis formosana, two new species ( Magadhaideus luodiana sp. nov and Peltatavertexalis horizontalis sp. nov), Plectoderini sp. and Paracatonidia sp., were sequenced for the first time through next-generation sequencing. The five mitogenomes ranged from 15,214 to 16,216 bp in length, with the typical gene content and arrangement usually observed in Hexapods. The motif “ATGATAA” between atp8 and atp6 was found in all the analyzed species. An overlap “AAGCTTA” between trnW and trnC was observed in the mitogenomes of most Fulgoroidea. The structural and compositional analyses of 26 Fulgoroidea mitogenomes, including the gene rearrangement of five tRNAs ( trnW, trnC and trnY; trnT and trnP), the A + T content and AT-skew of the whole mitogenomes, and the nuclear acid and amino acid compositions of the protein-coding genes (PCGs), revealed family-level differences between Delphacidae and other families (Achilidae, Flatidae, Fulgoridae, Issidae and Ricaniidae). Phylogenetic analyses of 13 protein-coding genes from 26 Fulgoroidea species by maximum likelihood and Bayesian Inference were consistent and well supported the basal position of Delphacidae, a close affinity among the families Flatidae, Issidae and Ricaniidae, and a close relationship between Achilidae and Fulgoridae.

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          Toward almost closed genomes with GapFiller

          De novo assembly is a commonly used application of next-generation sequencing experiments. The ultimate goal is to puzzle millions of reads into one complete genome, although draft assemblies usually result in a number of gapped scaffold sequences. In this paper we propose an automated strategy, called GapFiller, to reliably close gaps within scaffolds using paired reads. The method shows good results on both bacterial and eukaryotic datasets, allowing only few errors. As a consequence, the amount of additional wetlab work needed to close a genome is drastically reduced. The software is available at http://www.baseclear.com/bioinformatics-tools/.
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            Windows 95/98/NT

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              Evolutionary genomics in Metazoa: the mitochondrial DNA as a model system.

              One of the most important aspects of mitochondrial (mt) genome evolution in Metazoa is constancy of size and gene content of mtDNA, whose plasticity is maintained through a great variety of gene rearrangements probably mediated by tRNA genes. The trend of mtDNA to maintain the same genetic structure within a phylum (e.g., Chordata) is generally accepted, although more recent reports show that a considerable number of transpositions are observed also between closely related organisms. Base composition of mtDNA is extremely variable. Genome GC content is often low and, when it increases, the two complementary bases distribute asymmetrically, creating, particularly in vertebrates, a negative GC-skew. In mammals, we have found coding strand base composition and average degree of gene conservation to be related to the asymmetric replication mechanism of mtDNA. A quantitative measurement of mtDNA evolutionary rate has revealed that each of the various components has a different evolutionary rate. Non-synonymous rates are gene specific and fall in a range comparable to that of nuclear genes, whereas synonymous rates are about 22-fold higher in mt than in nuclear genes. tRNA genes are among the most conserved but, when compared to their nuclear counterparts, they evolve 100 times faster. Finally, we describe some molecular phylogenetic reconstructions which have produced unexpected outcomes, and might change our vision of the classification of living organisms.
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                Author and article information

                Contributors
                Journal
                PeerJ
                PeerJ
                PeerJ
                PeerJ
                PeerJ
                PeerJ Inc. (San Diego, USA )
                2167-8359
                26 March 2019
                2019
                : 7
                : e6659
                Affiliations
                [1 ]Institute of Entomology, Special Key Laboratory for Development and Utilization of Insect Resources of Guizhou, Guizhou University , Guiyang, Guizhou, China
                [2 ]College of Animal Sciences, Guizhou University , Guiyang, Guizhou, China
                Article
                6659
                10.7717/peerj.6659
                6440461
                30941275
                f61a7789-b6f5-45d0-8a90-3f9607950d99
                © 2019 Xu et al.

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.

                History
                : 25 October 2018
                : 19 February 2019
                Funding
                Funded by: National Natural Science Foundation of China
                Award ID: 31601886 and 31093430
                Funded by: Program of Science and Technology Innovation Talents Team, Guizhou Province
                Award ID: 20144001
                Funded by: Program of Excellent Innovation Talents, Guizhou Province
                Award ID: 20154021
                Funded by: Provincial Outstanding Graduate Program for Agricultural Entomology and Pest Control
                Award ID: ZYRC-2013
                Funded by: International cooperation base for insect evolutionary biology and pest control
                Award ID: 20165802
                This work was supported by the National Natural Science Foundation of China (No. 31601886 and 31093430); the Program of Science and Technology Innovation Talents Team, Guizhou Province (No. 20144001); the Program of Excellent Innovation Talents, Guizhou Province (No. 20154021); the Provincial Outstanding Graduate Program for Agricultural Entomology and Pest Control (ZYRC-2013); and the International cooperation base for insect evolutionary biology and pest control (No. 20165802). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Entomology
                Genomics
                Molecular Biology
                Taxonomy

                achilidae,fulgoroidea,mitochondrial genome,phylogeny
                achilidae, fulgoroidea, mitochondrial genome, phylogeny

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