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      First Complete Mitochondrial Genome of Melyridae(Coleoptera, Cleroidea): Genome Description and Phylogenetic Implications

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          Abstract

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          Melyridae, in a broad sense including Dasytinae and Malachiinae, is the largest family of Cleroidea distributed worldwide. However, the former two subfamilies are always treated as independent families by the European coleopterists. Opposite results have been produced by the two latest molecular phylogenetic works, so the development of reliable markers for reconstructing the phylogenetic relationships between the above taxa is of great importance. Here, we present the annotated complete mitogenome of Cordylepherus sp., which is the first complete mitogenome in Melyridae. The mitogenome of Cordylepherus sp. presents the typical organization of an insect mitochondrion. Comparisons of the newly generated mitogenome of Cordylepherus sp. to all available mitochondrial genomes of other Melyridae revealed no significant differences among them in terms of the length of each protein-coding gene, AT content of different genome regions, amino acid composition and relative synonymous codon usage. Phylogenetic analyses based on 13 protein-coding genes of mitogenomes show that the monophyly of Melyridae sensu lato is not supported, and Malachiinae and Dasytinae are suggested to be independent families, which are sister groups of Prionoceridae and Cleridae, respectively. Large-scale analyses with denser locus and taxon sampling are needed to confirm the present results.

          Abstract

          To explore the characteristics of the mitogenome of Melyridae and reveal phylogenetic relationships, the mitogenome of Cordylepherus sp. was sequenced and annotated. This is the first time a complete mitochondrial genome has been generated in this family. Consistent with previous observations of Cleroidea species, the mitogenome of Cordylepherus sp. is highly conserved in gene size, organization and codon usage, and secondary structures of tRNAs. All protein-coding genes (PCGs) initiate with the standard start codon ATN, except ND1, which starts with TTG, and terminate with the complete stop codons of TAA and TAG, or incomplete forms, TA- and T-. Most tRNAs have the typical clover-leaf structure, except trnS1 (Ser, AGN), whose dihydrouridine (DHU) arm is reduced. In the A+T-rich region, three types of tandem repeat sequence units are found, including a 115 bp sequence tandemly repeated twice, a 16 bp sequence tandemly repeated three times with a partial third repeat and a 10 bp sequence tandemly repeated seven times. Phylogenetic analyses based on 13 protein-coding genes by both Bayesian inference (BI) and maximum likelihood (ML) methods suggest that Melyridae sensu lato is polyphyletic, and Dasytinae and Malchiinae are supported as independent families.

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          MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

          We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.
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            IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

            Large phylogenomics data sets require fast tree inference methods, especially for maximum-likelihood (ML) phylogenies. Fast programs exist, but due to inherent heuristics to find optimal trees, it is not clear whether the best tree is found. Thus, there is need for additional approaches that employ different search strategies to find ML trees and that are at the same time as fast as currently available ML programs. We show that a combination of hill-climbing approaches and a stochastic perturbation method can be time-efficiently implemented. If we allow the same CPU time as RAxML and PhyML, then our software IQ-TREE found higher likelihoods between 62.2% and 87.1% of the studied alignments, thus efficiently exploring the tree-space. If we use the IQ-TREE stopping rule, RAxML and PhyML are faster in 75.7% and 47.1% of the DNA alignments and 42.2% and 100% of the protein alignments, respectively. However, the range of obtaining higher likelihoods with IQ-TREE improves to 73.3-97.1%.
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              Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

              Summary: The two main functions of bioinformatics are the organization and analysis of biological data using computational resources. Geneious Basic has been designed to be an easy-to-use and flexible desktop software application framework for the organization and analysis of biological data, with a focus on molecular sequences and related data types. It integrates numerous industry-standard discovery analysis tools, with interactive visualizations to generate publication-ready images. One key contribution to researchers in the life sciences is the Geneious public application programming interface (API) that affords the ability to leverage the existing framework of the Geneious Basic software platform for virtually unlimited extension and customization. The result is an increase in the speed and quality of development of computation tools for the life sciences, due to the functionality and graphical user interface available to the developer through the public API. Geneious Basic represents an ideal platform for the bioinformatics community to leverage existing components and to integrate their own specific requirements for the discovery, analysis and visualization of biological data. Availability and implementation: Binaries and public API freely available for download at http://www.geneious.com/basic, implemented in Java and supported on Linux, Apple OSX and MS Windows. The software is also available from the Bio-Linux package repository at http://nebc.nerc.ac.uk/news/geneiousonbl. Contact: peter@biomatters.com
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                Author and article information

                Journal
                Insects
                Insects
                insects
                Insects
                MDPI
                2075-4450
                20 January 2021
                February 2021
                : 12
                : 2
                : 87
                Affiliations
                [1 ]The Key Laboratory of Zoological Systematics and Application, School of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; 201972421@ 123456yangtzeu.edu.cn (L.Y.); gexueying2020@ 123456126.com (X.G.)
                [2 ]College of Agriculture, Yangtze University, Jingzhou 434025, China; xieguanglin@ 123456yangtzeu.edu.cn
                Author notes
                [* ]Correspondence: liuhy@ 123456hbu.edu.cn (H.L.); yxyang@ 123456hbu.edu.cn (Y.Y.)
                Article
                insects-12-00087
                10.3390/insects12020087
                7909412
                33498432
                b4e7b3d0-1733-4411-8441-84bf1f323575
                © 2021 by the authors.

                Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ( http://creativecommons.org/licenses/by/4.0/).

                History
                : 28 December 2020
                : 18 January 2021
                Categories
                Article

                melyridae,mitochondrial genome,annotation,phylogenetic analysis

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