The complete mitochondrial genome of <i>Hyperhalosydna striata</i> (Kinberg, 1856) (Annelida: Polynoidae) collected from Jejudo Island, Korea

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Abstract

The mitogenome sequence of Hyperhalosydna striata was determined for the first time in the present study. The genome is 15,226 bp long and contains 13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), and 22 transfer RNA genes (tRNA). The overall base composition was 28.0% A, 21.9% C, 13.0% G, and 37.1% T. A phylogenetic tree was constructed to infer the phylogenetic position of H. striata among polynoid species whose mitochondrial genome sequences are available in GenBank. Hyperhalosydna striata was closely related to the species of subfamily Lepidonotinae.

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Most cited references 20

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MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.

Sudhir Kumar, Glen Stecher, Michael KaWah Li … (2018)

The Molecular Evolutionary Genetics Analysis (Mega) software implements many analytical methods and tools for phylogenomics and phylomedicine. Here, we report a transformation of Mega to enable cross-platform use on Microsoft Windows and Linux operating systems. Mega X does not require virtualization or emulation software and provides a uniform user experience across platforms. Mega X has additionally been upgraded to use multiple computing cores for many molecular evolutionary analyses. Mega X is available in two interfaces (graphical and command line) and can be downloaded from www.megasoftware.net free of charge.

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NOVOPlasty: de novo assembly of organelle genomes from whole genome data

Nicolas Dierckxsens, Patrick Mardulyn, Guillaume Smits (2016)

Abstract The evolution in next-generation sequencing (NGS) technology has led to the development of many different assembly algorithms, but few of them focus on assembling the organelle genomes. These genomes are used in phylogenetic studies, food identification and are the most deposited eukaryotic genomes in GenBank. Producing organelle genome assembly from whole genome sequencing (WGS) data would be the most accurate and least laborious approach, but a tool specifically designed for this task is lacking. We developed a seed-and-extend algorithm that assembles organelle genomes from whole genome sequencing (WGS) data, starting from a related or distant single seed sequence. The algorithm has been tested on several new (Gonioctena intermedia and Avicennia marina) and public (Arabidopsis thaliana and Oryza sativa) whole genome Illumina data sets where it outperforms known assemblers in assembly accuracy and coverage. In our benchmark, NOVOPlasty assembled all tested circular genomes in less than 30 min with a maximum memory requirement of 16 GB and an accuracy over 99.99%. In conclusion, NOVOPlasty is the sole de novo assembler that provides a fast and straightforward extraction of the extranuclear genomes from WGS data in one circular high quality contig. The software is open source and can be downloaded at https://github.com/ndierckx/NOVOPlasty.

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GeSeq – versatile and accurate annotation of organelle genomes

Michael Tillich, Pascal Lehwark, Tommaso Pellizzer … (2017)

Abstract We have developed the web application GeSeq (https://chlorobox.mpimp-golm.mpg.de/geseq.html) for the rapid and accurate annotation of organellar genome sequences, in particular chloroplast genomes. In contrast to existing tools, GeSeq combines batch processing with a fully customizable reference sequence selection of organellar genome records from NCBI and/or references uploaded by the user. For the annotation of chloroplast genomes, the application additionally provides an integrated database of manually curated reference sequences. GeSeq identifies genes or other feature-encoding regions by BLAT-based homology searches and additionally, by profile HMM searches for protein and rRNA coding genes and two de novo predictors for tRNA genes. These unique features enable the user to conveniently compare the annotations of different state-of-the-art methods, thus supporting high-quality annotations. The main output of GeSeq is a GenBank file that usually requires only little curation and is instantly visualized by OGDRAW. GeSeq also offers a variety of optional additional outputs that facilitate downstream analyzes, for example comparative genomic or phylogenetic studies.

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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): 13 March 2024

Publication date (Electronic, collection): 2024

Publication date PMC-release: 13 March 2024

Volume: 9

Issue: 3

Pages: 338-341

Affiliations

[a ]National Institute of Biological Resources , Incheon, Republic of Korea

[b ]Research Institute of EcoScience, Ewha Womans University , Seoul, South Korea

Author notes

Supplemental data for this article can be accessed online at https://doi.org/10.1080/23802359.2024.2324929.

CONTACT Taeseo Park polychaeta@ 123456gmail.com National Institute of Biological Resources , Hwangyeong-ro 42, Seo-gu, Incheon 22689, Republic of Korea

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Kwang-Soo Kim https://orcid.org/0000-0001-6132-8745

Jiseon Park https://orcid.org/0000-0003-4041-6812

Taeseo Park https://orcid.org/0000-0003-2057-9411

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Publisher ID: 2324929

DOI: 10.1080/23802359.2024.2324929

PMC ID: 10939100

PubMed ID: 38487810

SO-VID: 09040f9c-c4e9-4e9c-87b3-be1cfd104877

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This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License ( http://creativecommons.org/licenses/by-nc/4.0/), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. The terms on which this article has been published allow the posting of the Accepted Manuscript in a repository by the author(s) or with their consent.

The complete mitochondrial genome of Hyperhalosydna striata (Kinberg, 1856) (Annelida: Polynoidae) collected from Jejudo Island, Korea

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Most cited references 20

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.

NOVOPlasty: de novo assembly of organelle genomes from whole genome data

GeSeq – versatile and accurate annotation of organelle genomes

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