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      The larval, pupal and mitogenomic characteristics of Agrilusadelphinus Kerremans, 1895 (Coleoptera, Buprestidae) from China

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          Abstract

          In this study, the larva and pupa of Agrilus adelphinus are described and illustrated. DNA barcoding ( COI gene) was used to associate the larval and pupal stages with adults based on the maximum-likelihood method. In the resulting phylogenetic tree, species from the same species-group were found to be clustered on a branch with high support value. To better understand A. adelphinus , the complete mitochondrial genome of this species was also sequenced and annotated. Comparing this genome to the known mitogenomes of Agrilus species, the newly sequenced genome is shorter, with 15,732 bp. However, its whole mitogenome composition and gene orientation were consistent with that of most species of Buprestidae . In the mitogenome of A. adelphinus , the ATGATAG sequence was observed between ATP8 and ATP6, which is ATGATAA in other insect mitogenomes. Leu2, Phe, Ile, Gly, and Ser2 were the five most frequently encoded amino acids. The results further prove that DNA barcoding can remove the limitation of traditional taxonomy which cannot identify to species all developmental stages. This study also provides valuable molecular and morphological data for species identification and phylogenetic analyses of the genus Agrilus .

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          Most cited references87

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          PhyloSuite: An integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies

          Multigene and genomic data sets have become commonplace in the field of phylogenetics, but many existing tools are not designed for such data sets, which often makes the analysis time-consuming and tedious. Here, we present PhyloSuite, a (cross-platform, open-source, stand-alone Python graphical user interface) user-friendly workflow desktop platform dedicated to streamlining molecular sequence data management and evolutionary phylogenetics studies. It uses a plugin-based system that integrates several phylogenetic and bioinformatic tools, thereby streamlining the entire procedure, from data acquisition to phylogenetic tree annotation (in combination with iTOL). It has the following features: (a) point-and-click and drag-and-drop graphical user interface; (b) a workplace to manage and organize molecular sequence data and results of analyses; (c) GenBank entry extraction and comparative statistics; and (d) a phylogenetic workflow with batch processing capability, comprising sequence alignment (mafft and macse), alignment optimization (trimAl, HmmCleaner and Gblocks), data set concatenation, best partitioning scheme and best evolutionary model selection (PartitionFinder and modelfinder), and phylogenetic inference (MrBayes and iq-tree). PhyloSuite is designed for both beginners and experienced researchers, allowing the former to quick-start their way into phylogenetic analysis, and the latter to conduct, store and manage their work in a streamlined way, and spend more time investigating scientific questions instead of wasting it on transferring files from one software program to another.
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            Sequence and organization of the human mitochondrial genome.

            The complete sequence of the 16,569-base pair human mitochondrial genome is presented. The genes for the 12S and 16S rRNAs, 22 tRNAs, cytochrome c oxidase subunits I, II and III, ATPase subunit 6, cytochrome b and eight other predicted protein coding genes have been located. The sequence shows extreme economy in that the genes have none or only a few noncoding bases between them, and in many cases the termination codons are not coded in the DNA but are created post-transcriptionally by polyadenylation of the mRNAs.
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              tRNA punctuation model of RNA processing in human mitochondria.

              A 3'-end proximal segment of most of the putative mRNAs encoded in the heavy strand of HeLa cell mtDNA has been partially sequences and aligned with the DNA sequence. In all cases, the 3'-end nucleotide of the individual mRNA coding sequences has been found to be immediately contiguous to a tRNA gene or another mRNA coding sequence. These and previous results indicate that the heavy (H) strand sequences coding for the rRNA, poly(A)-containing RNA and tRNA species form a continuum extending over almost the entire length of this strand. We propose that the H strand is transcribed into a single polycistronic RNA molecule, which is processed later into mature species by precise endonucleolytic cleavages which occur, in most cases, immediately before and after a tRNA sequence.
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                Author and article information

                Contributors
                Role: Writing - original draftRole: Writing - review and editingRole: Data curationRole: InvestigationRole: MethodologyRole: Software
                Role: Data curation
                Role: Data curation
                Role: Data curation
                Role: ConceptualizationRole: Writing - original draftRole: Formal analysisRole: Funding acquisitionRole: Resources
                Role: ConceptualizationRole: Funding acquisitionRole: Supervision
                Journal
                Zookeys
                Zookeys
                2
                urn:lsid:arphahub.com:pub:45048D35-BB1D-5CE8-9668-537E44BD4C7E
                urn:lsid:zoobank.org:pub:91BD42D4-90F1-4B45-9350-EEF175B1727A
                ZooKeys
                Pensoft Publishers
                1313-2989
                1313-2970
                2023
                08 August 2023
                : 1174
                : 15-33
                Affiliations
                [1 ] College of Life Sciences, China West Normal University, Nanchong 637009, China China West Normal University Nanchong China
                [2 ] The Key Laboratory of Southwest China Wildlife Resources Conservation of the Ministry of Education, College of Life Sciences, China West Normal University, Nanchong 637009, China China West Normal University Nanchong China
                Author notes
                Corresponding author: Zhonghua Wei ( wzh1164@ 123456126.com)

                Academic editor: Christopher Majka

                Author information
                https://orcid.org/0000-0003-2511-7080
                https://orcid.org/0000-0001-7349-9939
                Article
                105479
                10.3897/zookeys.1174.105479
                10843335
                38318285
                fa64d246-3aa0-4272-9a40-075395b233c1
                Xuyan Huang, Yujie Gan, Lei Wang, Yanying Xu, Zhonghua Wei, Aimin Shi

                This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 25 April 2023
                : 15 July 2023
                Funding
                The Natural Science Foundation of Sichuan Province (2022NSFSC1707) and the Doctoral Scientific Research Foundation of China West Normal University (20E054).
                Categories
                Research Article
                Arthropoda
                Buprestidae
                Buprestoidea
                Coleoptera
                Hexapoda
                Insecta
                Invertebrata
                Polyphaga
                Evolutionary Biology
                Genetics
                Identification Key
                Molecular Genetics
                Molecular Systematics
                Phylogeny
                Systematics
                Taxonomy
                Cenozoic
                Asia
                Central Asia
                China
                China Seas

                Animal science & Zoology
                larva,mitogenome,pupa
                Animal science & Zoology
                larva, mitogenome, pupa

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