The complete mitochondrial genome of  Neritina violacea

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Abstract

Neritina violacea is a common and important component of mangrove ecosystem. In this study, the mitogenome of N. violacea was determined for the first time using next-generation sequencing; the overall base components of mitogenome consisting of 15,710 bp was 31.37% for A, 34.91% for T, 19.47% for G, 14.25% for C, and its GC content was 33.72%. The mitogenome was composed of 13 protein-coding genes, 22 tranfer RNAs, and 2 ribosomal RNAs. Polygenetic analysis showed that the N. violacea was more close to N. Usnea and Theodoxus fluviatilis. We speculated that the N. violacea was evolved from freshwater species.

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RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

Alexandros Stamatakis (2014)

Motivation: Phylogenies are increasingly used in all fields of medical and biological research. Moreover, because of the next-generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likelihood. Since the last RAxML paper in 2006, it has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community. Results: I present some of the most notable new features and extensions of RAxML, such as a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees. In addition, an up-to-date 50-page user manual covering all new RAxML options is available. Availability and implementation: The code is available under GNU GPL at https://github.com/stamatak/standard-RAxML. Contact: alexandros.stamatakis@h-its.org Supplementary information: Supplementary data are available at Bioinformatics online.

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jModelTest 2: more models, new heuristics and parallel computing.

Diego Darriba, Guillermo Taboada, Ramón Doallo … (2012)

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tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes

Todd Lowe, Patricia P. Chan (2016)

High-throughput genome sequencing continues to grow the need for rapid, accurate genome annotation and tRNA genes constitute the largest family of essential, ever-present non-coding RNA genes. Newly developed tRNAscan-SE 2.0 has advanced the state-of-the-art methodology in tRNA gene detection and functional prediction, captured by rich new content of the companion Genomic tRNA Database. Previously, web-server tRNA detection was isolated from knowledge of existing tRNAs and their annotation. In this update of the tRNAscan-SE On-line resource, we tie together improvements in tRNA classification with greatly enhanced biological context via dynamically generated links between web server search results, the most relevant genes in the GtRNAdb and interactive, rich genome context provided by UCSC genome browsers. The tRNAscan-SE On-line web server can be accessed at http://trna.ucsc.edu/tRNAscan-SE/.

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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): 11 September 2019

Publication date (Electronic, collection): 2019

Volume: 4

Issue: 2

Pages: 2942-2943

Affiliations

Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Beibu Gulf University , Qinzhou, China

Author notes

CONTACT Haiping Wu wuhaipingsky@ 123456163.com ;

Youhou Xu 36714447@ 123456qq.com Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Beibu Gulf University , No. 12, Binhai Avenue, Qinnan District, Qinzhou City, Guangxi Autonomous Regions, China

Article

Publisher ID: 1662744

DOI: 10.1080/23802359.2019.1662744

PMC ID: 7707012

PubMed ID: 33365803

SO-VID: b58cc8c7-64ea-418e-9fd4-a2c97ca67090

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.

The complete mitochondrial genome of Neritina violacea

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Genome Integrity

Most cited references 7

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

jModelTest 2: more models, new heuristics and parallel computing.

tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes

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