Complete mitochondrial genomes of two species of <i>Stichopathes</i> Brook, 1889 (Hexacorallia: Antipatharia: Antipathidae) from Rapa Nui (Easter Island)

There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

Abstract

We report the complete mitochondrial genomes of two antipatharian species, Stichopathes sp. SCBUCN-8849 and Stichopathes sp. SCBUCN-8850, collected between 120 and 180 m depth off Rapa Nui (∼ −27.1°, −109.4°). The size of the two mitogenomes are 20,389 bp (29.0% A, 15.2% C, 19.9% G, and 35.9% T) and 20,463 bp (29.0% A, 15.3% C, 19.9% G, and 35.8% T), respectively. Both mitogenomes have the classic Hexacorallia gene content of 13 protein-coding, two rRNA, and two tRNA genes plus a COX1 intron with embedded HEG as found in the Antipathidae and other antipatharian families.

Related collections

Most cited references 8

Record: found
Abstract: found
Article: found

Is Open Access

Trimmomatic: a flexible trimmer for Illumina sequence data

Anthony M. Bolger, Marc Lohse, Bjoern Usadel (2014)

Motivation: Although many next-generation sequencing (NGS) read preprocessing tools already existed, we could not find any tool or combination of tools that met our requirements in terms of flexibility, correct handling of paired-end data and high performance. We have developed Trimmomatic as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data. Results: The value of NGS read preprocessing is demonstrated for both reference-based and reference-free tasks. Trimmomatic is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested. Availability and implementation: Trimmomatic is licensed under GPL V3. It is cross-platform (Java 1.5+ required) and available at http://www.usadellab.org/cms/index.php?page=trimmomatic Contact: usadel@bio1.rwth-aachen.de Supplementary information: Supplementary data are available at Bioinformatics online.

0 comments Cited 15624 times – based on 0 reviews      Review now

Bookmark

Record: found
Abstract: found
Article: not found

SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.

Anton Bankevich, Sergey Nurk, Dmitry Antipov … (2012)

The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

0 comments Cited 6210 times – based on 0 reviews      Review now

Bookmark

Record: found
Abstract: found
Article: not found

MUSCLE: multiple sequence alignment with high accuracy and high throughput.

R. C. Edgar (2004)

We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the log-expectation score, and refinement using tree-dependent restricted partitioning. The speed and accuracy of MUSCLE are compared with T-Coffee, MAFFT and CLUSTALW on four test sets of reference alignments: BAliBASE, SABmark, SMART and a new benchmark, PREFAB. MUSCLE achieves the highest, or joint highest, rank in accuracy on each of these sets. Without refinement, MUSCLE achieves average accuracy statistically indistinguishable from T-Coffee and MAFFT, and is the fastest of the tested methods for large numbers of sequences, aligning 5000 sequences of average length 350 in 7 min on a current desktop computer. The MUSCLE program, source code and PREFAB test data are freely available at http://www.drive5. com/muscle.

0 comments Cited 6042 times – based on 0 reviews      Review now

Bookmark

All references

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): 15 October 2021

Publication date (Electronic, collection): 2021

Publication date PMC-release: 15 October 2021

Volume: 6

Issue: 11

Pages: 3226-3228

Affiliations

[a ]Departamento de Biología Marina, Facultad de Ciencias del Mar and Sala de Colecciones Biológicas, Universidad Católica del Norte, Millennium Nucleus for Ecology and Sustainable Management of Oceanic Islands (ESMOI) , Coquimbo, Chile

[b ]Conservation International, Center for Oceans , Arlington, VA, USA

[c ]School of Earth, Environmental, and Marine Sciences, University of Texas Rio Grande Valley , South Padre Island, TX, USA

Author notes

CONTACT Erin E. Easton erin.easton@ 123456utrgv.edu School of Earth, Environmental, and Marine Sciences, University of Texas Rio Grande Valley , South Padre Island, TX, USA

Supplemental data for this article is available online at https://doi.org/10.1080/23802359.2021.1990150.

Author information

Cynthia M. Asorey https://orcid.org/0000-0002-4777-421X

Javier Sellanes https://orcid.org/0000-0002-6942-0762

Daniel Wagner https://orcid.org/0000-0002-0456-4343

Erin E. Easton https://orcid.org/0000-0003-4853-6026

Article

Publisher ID: 1990150

DOI: 10.1080/23802359.2021.1990150

PMC ID: 8525922

PubMed ID: 34676296

SO-VID: 03241f9e-6fc6-46de-a4c2-1b84da38d902

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.

Complete mitochondrial genomes of two species of Stichopathes Brook, 1889 (Hexacorallia: Antipatharia: Antipathidae) from Rapa Nui (Easter Island)

Read this article at

Abstract

Related collections

SciELO Chile

Most cited references 8

Trimmomatic: a flexible trimmer for Illumina sequence data

SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.

MUSCLE: multiple sequence alignment with high accuracy and high throughput.

Author and article information

Journal

Affiliations

Author notes

Author information

Article

History

Page count

Categories

Comments

Comment on this article

Similar content 96

Cited by 4

Most referenced authors 335