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      Complete mitochondrial genome of nipa palm hispid beetle Octodonta nipae Maulik (Coleoptera: Chrysomelidae: Cassidinae)

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          Abstract

          Octodonta nipae (Maulik 1921) is a dangerous forestry quarantine pest, which mainly harms palms. In the present study, we determined complete mitogenome of O. nipae. This mitogenome was 15,397 bp in length (GenBank Accession no. MW802252), which contained 2 ribosomal RNA genes, 22 transfer RNAs, 13 protein-coding genes (PCGs) and one non-coding AT-rich region with the length of 883 bp. All of the 22 tRNA genes displayed a typical clover-leaf structure, with the exception of tRNA Phe, tRNA Leu, tRNA Asn, tRNA Pro and tRNA Thr. Twelve PCGs were initiated by ATN codons, and NAD1 started with TTG. Ten PCGs used the typical stop codon ‘TAA’ and ‘TGA’, while three PCGs (COX2, COX3, NAD4) used the incomplete stop codons ‘TA’ or ‘T’. Phylogenetic tree demonstrated that O. nipae belongs to the family Chrysomelidae and closer to the superfamily Cassidinae.

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          MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

          Fredrik Ronquist, Maxim Teslenko, Paul van der Mark … (2012)
          Since its introduction in 2001, MrBayes has grown in popularity as a software package for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) methods. With this note, we announce the release of version 3.2, a major upgrade to the latest official release presented in 2003. The new version provides convergence diagnostics and allows multiple analyses to be run in parallel with convergence progress monitored on the fly. The introduction of new proposals and automatic optimization of tuning parameters has improved convergence for many problems. The new version also sports significantly faster likelihood calculations through streaming single-instruction-multiple-data extensions (SSE) and support of the BEAGLE library, allowing likelihood calculations to be delegated to graphics processing units (GPUs) on compatible hardware. Speedup factors range from around 2 with SSE code to more than 50 with BEAGLE for codon problems. Checkpointing across all models allows long runs to be completed even when an analysis is prematurely terminated. New models include relaxed clocks, dating, model averaging across time-reversible substitution models, and support for hard, negative, and partial (backbone) tree constraints. Inference of species trees from gene trees is supported by full incorporation of the Bayesian estimation of species trees (BEST) algorithms. Marginal model likelihoods for Bayes factor tests can be estimated accurately across the entire model space using the stepping stone method. The new version provides more output options than previously, including samples of ancestral states, site rates, site d N /d S rations, branch rates, and node dates. A wide range of statistics on tree parameters can also be output for visualization in FigTree and compatible software.
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            MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization

            Guanliang Meng, Yiyuan Li, Chentao Yang … (2019)
            Abstract Mitochondrial genome (mitogenome) plays important roles in evolutionary and ecological studies. It becomes routine to utilize multiple genes on mitogenome or the entire mitogenomes to investigate phylogeny and biodiversity of focal groups with the onset of High Throughput Sequencing (HTS) technologies. We developed a mitogenome toolkit MitoZ, consisting of independent modules of de novo assembly, findMitoScaf (find Mitochondrial Scaffolds), annotation and visualization, that can generate mitogenome assembly together with annotation and visualization results from HTS raw reads. We evaluated its performance using a total of 50 samples of which mitogenomes are publicly available. The results showed that MitoZ can recover more full-length mitogenomes with higher accuracy compared to the other available mitogenome assemblers. Overall, MitoZ provides a one-click solution to construct the annotated mitogenome from HTS raw data and will facilitate large scale ecological and evolutionary studies. MitoZ is free open source software distributed under GPLv3 license and available at https://github.com/linzhi2013/MitoZ.
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              Complete mitochondrial genome of a leaf-mining beetle, Rhadinosa nigrocyanea (Coleoptera: Chrysomelidae) with phylogenetic consideration

              Qingyun Guo, Jiasheng Xu, Xiaohua Dai … (2017)
              Abstract The complete circular mitochondrial genome (mitogenome) of Rhadinosa nigrocyanea was 17,965 bp in length, which contained 2 ribosomal RNA genes, 22 transfer RNAs, 13 protein-coding genes (PCGs) and 1 non-coding AT-rich region with the length of 3002 bp. All of the 22 tRNA genes displayed a typical clover-leaf structure, with the exception of tRNASer (TCT). 12 PCGs were initiated by ATN codons, except for ND1 started with TTG. Only six PCGs used the typical stop codon ‘TAA’ and ‘TGA’, while seven PCGs terminated with incomplete stop codons (TA or T). Phylogenetic analysis showed that R. nigrocyanea grouped with Cassidinae species, sister to Clytrinae + Cryptocephalinae.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Mitochondrial DNA B Resour
                Journal ID (iso-abbrev): Mitochondrial DNA B Resour
                Title: Mitochondrial DNA. Part B, Resources
                Publisher: Taylor & Francis
                ISSN (Electronic): 2380-2359
                Publication date (Electronic, pub): 16 August 2021
                Publication date (Electronic, collection): 2021
                Volume: 6
                Issue: 9
                Pages: 2652-2653
                Affiliations
                [a ]Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences , Haikou, China
                [b ]Ministry of Agriculture and Rural Affairs, Key Laboratory of Integrated Pest Management on Tropical Crops , Haikou, China
                [c ]College of Forestry, Hainan University , Haikou, China
                [d ]Post-Entry Quarantine Station for Tropical Plant, Haikou Customs , Haikou, China
                [e ]Hainan Province Engineering Research Center for Quarantine, Prevention and Control of Exotic Pests , Haikou, China
                Author notes
                CONTACT Baoqian Lyu lvbaoqian@ 123456hotmail.com Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences , Haikou, Hainan 571101, China
                Author information
                https://orcid.org/0000-0001-8091-0407
                Article
                Publisher ID: 1934172
                DOI: 10.1080/23802359.2021.1934172
                PMC ID: 8381925
                PubMed ID: 34435108
                SO-VID: 2d14b190-f163-46a9-9b06-75fb622ecfe7
                Copyright © © 2021 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.
                License:

                This is an Open Access article distributed under the terms of the Creative Commons Attribution 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.

                History
                Page count
                Figures: 1, Tables: 0, Pages: 2, Words: 1114
                Categories
                Subject: Research Article
                Subject: Mitogenome Announcement

                Keywords: octodonta nipae (maulik 1921),mitochondrial genome,phylogenetic relationship,phylogenetic analysis
                Data availability:
                Keywords: octodonta nipae (maulik 1921), mitochondrial genome, phylogenetic relationship, phylogenetic analysis

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