The complete mitochondrial genome of the tropical oyster  Saccostrea echinata  (Bivalvia: Ostreidae) from the South China Sea

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Abstract

Saccostrea echinata is a rock perched oyster with wide distribution and tremendous potential for commercial mariculture. However, the taxonomy of this genus is confused. In this study, we described the complete mitochondrial genome of medium-sized form of Saccostrea echinata. The genome is 16,282 bp in length, encoding the standard set of 12 protein-coding genes (PCGs), 23 tRNA genes, and two rRNA genes, with circular organization. The overall base composition of the whole mitochondrial genome was A (26.78%), T (36.64%), G (21.99%), and C (14.59%) with an AT bias of 63.42%. The longest PCG of these species was ND5, whereas the shortest was ND4L.

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Most cited references 13

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Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads—a baiting and iterative mapping approach

Christoph Hahn, Lutz Bachmann, Bastien Chevreux (2013)

We present an in silico approach for the reconstruction of complete mitochondrial genomes of non-model organisms directly from next-generation sequencing (NGS) data—mitochondrial baiting and iterative mapping (MITObim). The method is straightforward even if only (i) distantly related mitochondrial genomes or (ii) mitochondrial barcode sequences are available as starting-reference sequences or seeds, respectively. We demonstrate the efficiency of the approach in case studies using real NGS data sets of the two monogenean ectoparasites species Gyrodactylus thymalli and Gyrodactylus derjavinoides including their respective teleost hosts European grayling (Thymallus thymallus) and Rainbow trout (Oncorhynchus mykiss). MITObim appeared superior to existing tools in terms of accuracy, runtime and memory requirements and fully automatically recovered mitochondrial genomes exceeding 99.5% accuracy from total genomic DNA derived NGS data sets in <24 h using a standard desktop computer. The approach overcomes the limitations of traditional strategies for obtaining mitochondrial genomes for species with little or no mitochondrial sequence information at hand and represents a fast and highly efficient in silico alternative to laborious conventional strategies relying on initial long-range PCR. We furthermore demonstrate the applicability of MITObim for metagenomic/pooled data sets using simulated data. MITObim is an easy to use tool even for biologists with modest bioinformatics experience. The software is made available as open source pipeline under the MIT license at https://github.com/chrishah/MITObim.

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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): 8 February 2021

Publication date (Electronic, collection): 2021

Volume: 6

Issue: 2

Pages: 384-386

Affiliations

[a ]South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangdong Provincial Key Laboratory of Fishery Ecology and Environment , Guangzhou, China

[b ]Ministry of Agriculture, Key Laboratory of South China Sea Fishery Resources Development and Utilization , Guangzhou, China

Author notes

CONTACT Feiyan Du feiyanegg@ 123456163.com South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangdong Provincial Key Laboratory of Fishery Ecology and Environment , Guangzhou, China

Article

Publisher ID: 1869610

DOI: 10.1080/23802359.2020.1869610

PMC ID: 7872523

PubMed ID: 33659685

SO-VID: f45d40e5-c717-4145-bc38-9277899d5971

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, Tables: 0, Pages: 3, Words: 1405

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