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The complete mitochondrial genome of Artemia sinica Cai, 1989 (Crustacea: Anostraca) using next-generation sequencing

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Abstract

The complete mitochondrial genome of Artemia sinica was obtained using the next-generation sequencing (NGS) method. The mitochondrial genome is a circular molecule of 15,689 bp in length, with the typical structure of 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs) and 2 ribosomal RNA genes, and a non-coding control region (CR). The base composition is 31.53% A, 18.99% C, 16.50% G, and 32.98% T, with an A + T content of 64.51%. All tRNAs have a cloverleaf structure excepting tRNA-Ser1, that represents the D-loop structure.
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The complete mitochondrial genome of Artemia
sinica Cai, 1989 (Crustacea: Anostraca) using next-
generation sequencing
Alireza Asem, Weidong Li, Pei-Zheng Wang, Amin Eimanifar, Chun-Yang
Shen, Stephanie De Vos & Gilbert Van Stappen
To cite this article: Alireza Asem, Weidong Li, Pei-Zheng Wang, Amin Eimanifar, Chun-Yang
Shen, Stephanie De Vos & Gilbert Van Stappen (2019) The complete mitochondrial genome of
Artemia�sinica Cai, 1989 (Crustacea: Anostraca) using next-generation sequencing, Mitochondrial
DNA Part B, 4:1, 746-747, DOI: 10.1080/23802359.2019.1565933
To link to this article: https://doi.org/10.1080/23802359.2019.1565933
© 2019 The Author(s). Published by Informa
UK Limited, trading as Taylor & Francis
Group.
Published online: 08 Feb 2019.
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MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of Artemia sinica Cai, 1989 (Crustacea:
Anostraca) using next-generation sequencing
Alireza Asem
a
, Weidong Li
a
, Pei-Zheng Wang
a
, Amin Eimanifar
b
, Chun-Yang Shen
c
, Stephanie De Vos
d
and Gilbert Van Stappen
d
a
College of Life Sciences and Ecology, Hainan Tropical Ocean University, Sanya, China;
b
EAG Laboratories Inc., Easton, MD, USA;
c
Medical
College, Chengde Medical University, Chengde, China;
d
Laboratory of Aquaculture & Artemia Reference Center, Faculty of Bioscience
Engineering - Blok F, Ghent University, Gent, Belgium
ABSTRACT
The complete mitochondrial genome of Artemia sinica was obtained using the next-generation
sequencing (NGS) method. The mitochondrial genome is a circular molecule of 15,689 bp in length,
with the typical structure of 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs) and 2 ribo-
somal RNA genes, and a non-coding control region (CR). The base composition is 31.53% A, 18.99% C,
16.50% G, and 32.98% T, with an A þT content of 64.51%. All tRNAs have a cloverleaf structure except-
ing tRNA-Ser
1
, that represents the D-loop structure.
ARTICLE HISTORY
Received 19 November 2018
Accepted 5 December 2018
KEYWORDS
Mitogenome; brine shrimp;
Artemia sinica; protein-
coding genes; transfer RNA
genes; ribosomal
RNA genes
The genus Artemia consists of seven bisexual species and a
large number of parthenogenetic populations with different
ploidy degrees (Asem et al. 2010). So far, the complete mito-
genome of three bisexual species of Artemia (Artemia francis-
cana,Artemia urmiana, and Artemia tibetiana) have already
been characterized(Valverde et al. 1994; Zhang et al. 2013). In
this study, we sequenced and described the complete mito-
chondrial genome of Artemia sinica (GenBank: MK069595).
The present study is a part of a more comprehensive project
of characterizing the complete mitochondrial genome of
genus Artemia.
The cysts of A. sinica (ARC: 1166) were collected from
Ejinor Lake (Inner Mongolia, China) and stored in the Artemia
Reference Center (Ghent University, Belgium). The total DNA
was extracted from a cultured adult specimen. A genomic
library was established followed by paired-end (2 150 bp)
next-generation sequencing (10 Gb), using the Illumina HiSeq
X-ten sequencing platform. Quality checks for sequencing
reads were performed by FastQC (Andrews 2010) and the
sequences were assembled and mapped to the reference
Artemia mitochondrial genome (A. franciscana, X69067) with
Spades v3.9.0 (Bankevich et al. 2012) and bowtie v2.2.9
(Langmead and Salzberg 2012). Putative tRNA genes were
determined using the tRNAscan-SE2.0 (http://lowelab.ucsc.
edu/tRNAscan-SE/) and ARWEN (http://130.235.46.10/ARWEN/)
online software. All genes were annotated based on gene
order on the reference mitochondrial map and using BLAST
analysis (https://blast.ncbi.nlm.nih.gov). Additionally, to anno-
tate PCGs and tRNAs, the position of start and stop codons,
and secondary structures and the position of anticodons
were re-considered, respectively.
The complete mitogenome of A. sinica was 15,689 bp in
length, with 13 protein-coding genes (PCGs), 22 transfer
RNAs (tRNAs), 2 ribosomal RNAs (rRNAs), and a control region
(CR). The overall nucleotide composition of the major strand
of the A. sinica mitogenome was as follows: 31.53% A,
18.99% C, 16.50% G, and 32.98% T, with a total A þT content
of 64.51%.
Nine tRNAs (tRNA-Ile,tRNA-Gln,tRNA-Cys,tRNA-Tyr,tRNA-
Phe,tRNA-His,tRNA-Pro,tRNA-Leu, and tRNA-Val) and four
PCGs (ND5, ND4, ND4L, and ND1), as well as both rRNAs were
encoded on the light strand. Just six PCGs (ND2,COX1,ATP6,
COX3,CYTB, and ND1) began with the common ATG start
codon. Stop codons included TAA (ND2,ATP8,ATP6,ND3,
ND4L,CYTB, and ND1), TAG (ND6) and non-complete codons
T(COX1,COX2,COX3 and ND5, and ND4). The 12S rRNA and
16S rRNA were separated by the tRNA-Val.
Based on the results, the highest and lowest values of
%GC tRNA composition belong to tRNA-Lys (46.9%) and
tRNA-Glu (18.2%), respectively. Secondary structures of tRNA-
Ser
1
showed the D-loop structure. The longest and shortest
tRNAs were tRNA-Ser
2
(67 bp) and tRNA-Ala (59 bp),
respectively.
CR was located between 12S rRNA and tRNA-Met, with an
AþT content of 67.58%. The longest gap and overlapping
were determined between tRNA-Gln/tRNA-Cys (54 bp) and
tRNA-Phe/ND5 (13 bp), respectively.
CONTACT Alireza Asem asem.alireza@gmail.com; Weidong Li 542148880@qq.com College of Life Sciences and Ecology, Hainan Tropical Ocean
University, Yucai Rd., Sanya 572000, China
ß2019 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.
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.
MITOCHONDRIAL DNA PART B
2019, VOL. 4, NO. 1, 746747
https://doi.org/10.1080/23802359.2019.1565933
The phylogenetic relationship of A. sinica with members
of the genus Artemia was determined from a concatenated
dataset including the 13 PCGs and 2 rRNAs using the soft-
ware MEGA 7.0.26 v. (Kumar et al. 2016) with 1000 bootstrap
replicates and a GTR model (Figure 1). According to the
result, A. sinica was placed as a clade sister to other Asian
spp. All Asian species were clearly separated from American
A. franciscana.
Disclosure statement
No potential conflict of interest was reported by the authors.
Funding
This work was supported by the Science and Technology Major Project
of Hainan Province [ZDKJ2016009-3], Hainan Tropical Ocean University
Doctoral Research Funding [RHDXB201628].
ORCID
Alireza Asem http://orcid.org/0000-0002-8991-4903
Stephanie De Vos http://orcid.org/0000-0001-6830-6928
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Figure 1. Phylogenetic tree showing the relationship among A. sinica and three other species from the Artemia based on maximum-likelihood (ML) approach.
Numbers behind each node denote the bootstrap support values. The GenBank accession numbers are indicated on the right side of species names. Streptocephalus
sirindhornae was used as an outgroup.
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