Complete mitochondrial genome of a tropical sea cucumber, <i>Stichopus chloronotus</i>

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Abstract

In this study, we report the complete mitochondrial genome of Stichopus chloronotus. The mitogenome was 16,247 base pairs (58.55% A + T content) in length, comprising a total of 37 genes, including 13 protein-coding genes, 22 transfer RNA genes and 2 ribosomal RNA genes. To resolve the phylogenetic position of S. chloronotus, we analyzed all mitochondrial protein-coding genes from 27 species within the Echinodermata. The results showed that S. chloronotus belonged to the family Stichopodidae and was more closely related to tropical Stichopus species ( S. horrens and S. monotuberculatus) than to other species. Our results will be useful for evolutionary analysis of sea cucumber species.

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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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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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Submersible- and lander-observed community patterns in the Mariana and New Britain trenches: Influence of productivity and depth on epibenthic and scavenging communities

Natalya Gallo, James Cameron, Kevin Hardy … (2015)

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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): 31 August 2021

Publication date (Electronic, collection): 2021

Publication date PMC-release: 31 August 2021

Volume: 6

Issue: 10

Pages: 2788-2790

Affiliations

[a ]Laboratory of Aquatic Sciences, Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture in Rural Affairs, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences , Guangzhou, China

[b ]Guangdong Provincial Engineering and Technology Research Center, Doctoral Workstation of Guangdong Province, Guangdong Jinyang Biotechnology Co. Ltd , Maoming, China

Author notes

CONTACT Wen Huang huangwen549@ 123456126.com Institute of Animal Science, Guangdong Academy of Agricultural Sciences , No. 1 Dafeng 1st Street, Wushan Road, Tianhe District, Guangzhou, 510640, China

Article

Publisher ID: 1967218

DOI: 10.1080/23802359.2021.1967218

PMC ID: 8425741

SO-VID: b4b8a0fa-12dc-47b1-ad5d-22436d14aebe

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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 genome of a tropical sea cucumber, Stichopus chloronotus

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Most cited references 14

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.

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

Submersible- and lander-observed community patterns in the Mariana and New Britain trenches: Influence of productivity and depth on epibenthic and scavenging communities

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