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      Complete mitochondrial genome of Biston thoracicaria (Lepidoptera: Geometridae)

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      Author(s): a , a , b
      Publication date (Electronic, pub):
      Publication date (Electronic, collection):
      Journal: Mitochondrial DNA. Part B, Resources
      Publisher: Taylor & Francis
      Keywords: Geometridae, Biston thoracicaria, mitogenome, phylogeny

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          Abstract

          The complete mitochondrial genome (mitogenome) of Biston thoracicaria (Lepidoptera: Geometridae) is 15,538 bp in length, containing 13 PCGs, 22 tRNAs, two rRNAs, and an A + T-rich region. All PCGs initiate with typical start codon of ATN and share the complete stop codon of TAA, whereas cox1 starts with CGA. The ML analysis was performed using a dataset matrix containing 13 PCGs concatenated from the mitogenomes of Geometridae species. Our study presented the phylogenetic relationship of (Larentiinae + ((Sterrhinae + (Ennominae + Geometrinae))). Within the genera Biston, B. thoracicaria grouped with other species as the sister group.

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          IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

          Lam-Tung Nguyen, Heiko Schmidt, Arndt von Haeseler … (2014)
          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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            MITOS: improved de novo metazoan mitochondrial genome annotation.

            Matthias Bernt, Alexander Donath, Frank Jühling … (2013)
            About 2000 completely sequenced mitochondrial genomes are available from the NCBI RefSeq data base together with manually curated annotations of their protein-coding genes, rRNAs, and tRNAs. This annotation information, which has accumulated over two decades, has been obtained with a diverse set of computational tools and annotation strategies. Despite all efforts of manual curation it is still plagued by misassignments of reading directions, erroneous gene names, and missing as well as false positive annotations in particular for the RNA genes. Taken together, this causes substantial problems for fully automatic pipelines that aim to use these data comprehensively for studies of animal phylogenetics and the molecular evolution of mitogenomes. The MITOS pipeline is designed to compute a consistent de novo annotation of the mitogenomic sequences. We show that the results of MITOS match RefSeq and MitoZoa in terms of annotation coverage and quality. At the same time we avoid biases, inconsistencies of nomenclature, and typos originating from manual curation strategies. The MITOS pipeline is accessible online at http://mitos.bioinf.uni-leipzig.de. Copyright © 2012 Elsevier Inc. All rights reserved.
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              GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes

              Jian-Jun Jin, Wen-Bin Yu, Jun-Bo Yang … (2020)
              GetOrganelle is a state-of-the-art toolkit to accurately assemble organelle genomes from whole genome sequencing data. It recruits organelle-associated reads using a modified “baiting and iterative mapping” approach, conducts de novo assembly, filters and disentangles the assembly graph, and produces all possible configurations of circular organelle genomes. For 50 published plant datasets, we are able to reassemble the circular plastomes from 47 datasets using GetOrganelle. GetOrganelle assemblies are more accurate than published and/or NOVOPlasty-reassembled plastomes as assessed by mapping. We also assemble complete mitochondrial genomes using GetOrganelle. GetOrganelle is freely released under a GPL-3 license (https://github.com/Kinggerm/GetOrganelle).
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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): 17 June 2021
                Publication date (Electronic, collection): 2021
                Volume: 6
                Issue: 7
                Pages: 2007-2008
                Affiliations
                [a ]College of Big data and Intelligent Engineering, Southwest Forestry University , Kunming, China
                [b ]College of Environment and Safety, Taiyuan University of Science and Technology , Taiyuan, China
                Author notes
                CONTACT You-Jie Zhao bioala@ 123456swfu.edu.cn College of Big data and Intelligent Engineering, Southwest Forestry University , Kunming, Yunnan650224, China
                Yu-peng Wu wuyupeng007@ 123456163.com College of Environment and Safety, Taiyuan University of Science and Technology , Taiyuan, Shanxi030024, China
                Article
                Publisher ID: 1939181
                DOI: 10.1080/23802359.2021.1939181
                PMC ID: 8216253
                PubMed ID: 34235271
                SO-VID: 491f864a-2ea2-4099-bcd6-79e721fb8e15
                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.

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                Page count
                Figures: 1, Tables: 0, Pages: 2, Words: 1065
                Categories
                Subject: Research Article
                Subject: Mitogenome Announcement

                Keywords: geometridae,biston thoracicaria,mitogenome,phylogeny
                Data availability:
                Keywords: geometridae, biston thoracicaria, mitogenome, phylogeny

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