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      Analysis of the nearly complete mitochondrial genome of Paederus fuscipes (Coleoptera: Staphylinidae)

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      Author(s): a , a , a , b
      Publication date (Electronic, pub):
      Publication date (Electronic, collection):
      Journal: Mitochondrial DNA. Part B, Resources
      Publisher: Taylor & Francis
      Keywords: Paederus fuscipes, mitochondrial genome, phylogenetic analysis

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          Abstract

          The nearly complete mitochondrial genome of Paederus fuscipes (GenBank accession no. MG581161) is 17,644 bp in size, containing 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs, and a partial control region. The gene order is similar to the typical insect mitochondrial genome. Maximum likelihood tree recovered the monophyly of Staphylininae, Pselaphinae, Paederinae and Aleocharinae. Additionally, Staphylininae is a sister group to Paederinae.

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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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            BioEdit a user-friendly biological sequences alignment editor and analysis program for Windows 9598NT

            TA HALL, T Hall, TA Hall … (1999)
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              Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study

              Qiong-Yi Zhao, Yi Wang, Yi-Meng Kong … (2011)
              Background With the fast advances in nextgen sequencing technology, high-throughput RNA sequencing has emerged as a powerful and cost-effective way for transcriptome study. De novo assembly of transcripts provides an important solution to transcriptome analysis for organisms with no reference genome. However, there lacked understanding on how the different variables affected assembly outcomes, and there was no consensus on how to approach an optimal solution by selecting software tool and suitable strategy based on the properties of RNA-Seq data. Results To reveal the performance of different programs for transcriptome assembly, this work analyzed some important factors, including k-mer values, genome complexity, coverage depth, directional reads, etc. Seven program conditions, four single k-mer assemblers (SK: SOAPdenovo, ABySS, Oases and Trinity) and three multiple k-mer methods (MK: SOAPdenovo-MK, trans-ABySS and Oases-MK) were tested. While small and large k-mer values performed better for reconstructing lowly and highly expressed transcripts, respectively, MK strategy worked well for almost all ranges of expression quintiles. Among SK tools, Trinity performed well across various conditions but took the longest running time. Oases consumed the most memory whereas SOAPdenovo required the shortest runtime but worked poorly to reconstruct full-length CDS. ABySS showed some good balance between resource usage and quality of assemblies. Conclusions Our work compared the performance of publicly available transcriptome assemblers, and analyzed important factors affecting de novo assembly. Some practical guidelines for transcript reconstruction from short-read RNA-Seq data were proposed. De novo assembly of C. sinensis transcriptome was greatly improved using some optimized methods.
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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): 5 January 2018
                Publication date (Electronic, collection): 2018
                Volume: 3
                Issue: 1
                Pages: 85-87
                Affiliations
                [a ]Department of Entomology, College of Plant Protection, Henan Agricultural University , Zhengzhou, People’s Republic of China;
                [b ]Department of Entomology, Xinyang Agriculture and Forestry University , Xinyang, People’s Republic of China
                Author notes
                CONTACT Nan Song songnan@ 123456henau.edu.cn College of Plant Protection, Henan Agricultural University , Zhengzhou, People’s Republic of China
                Article
                Publisher ID: 1422410
                DOI: 10.1080/23802359.2017.1422410
                PMC ID: 7799980
                SO-VID: 7bfe5e00-c087-4524-8b6f-dd6c6aa43cba
                Copyright statement: © 2018 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, Pages: 3, Words: 1302
                Product
                Categories
                Subject: Research Article
                Subject: Mitogenome Announcement

                Keywords: paederus fuscipes,mitochondrial genome,phylogenetic analysis
                Data availability:
                Keywords: paederus fuscipes, mitochondrial genome, phylogenetic analysis

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