Complete mitochondrial genome of a sea star, Linckia laevigata (Echinodermata, Asteroidea, Valvatida, Ophidiasteridae)

Abstract

We determined the complete mitochondrial genome sequences of an asteroid Linckia laevigata belonging to the order Valvatida. The complete mitogenome of L. laevigata was 16,371 bp in length and consisted of 13 protein-coding genes (PCGs), two rRNA, and 22 tRNA. The orders of PCGs and rRNAs were identical to those of the recorded mitogenomes of asteroids. Phylogenetic analyses placed L. laevigata as the sister group to the species of the other Paxillosida.

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Complete mitochondrial genome of a sea star,
Linckia laevigata (Echinodermata, Asteroidea,
Valvatida, Ophidiasteridae)
Shimpei F. Hiruta, Mikihito Arai, Suchana Chavanich, Voranop Viyakarn &
Toshihiko Fujita
To cite this article: Shimpei F. Hiruta, Mikihito Arai, Suchana Chavanich, Voranop Viyakarn
& Toshihiko Fujita (2020) Complete mitochondrial genome of a sea star, Linckia�laevigata
(Echinodermata, Asteroidea, Valvatida, Ophidiasteridae), Mitochondrial DNA Part B, 5:2,
1342-1343
To link to this article: https://doi.org/10.1080/23802359.2020.1735271
© 2020 The Author(s). Published by Informa
UK Limited, trading as Taylor & Francis
Group.
Published online: 27 Apr 2020.
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MITOGENOME ANNOUNCEMENT
Complete mitochondrial genome of a sea star, Linckia laevigata (Echinodermata,
Asteroidea, Valvatida, Ophidiasteridae)
Shimpei F. Hiruta
a
, Mikihito Arai
b,c
, Suchana Chavanich
d
, Voranop Viyakarn
d
and Toshihiko Fujita
b,c
a
Center for Molecular Biodiversity Research, National Museum of Nature and Science, Tsukuba, Japan;
b
Department of Biological Sciences,
Graduate School of Science, the University of Tokyo, Bunkyo-ku, Japan;
c
Department of Zoology, National Museum of Nature and Science,
Tsukuba, Japan;
d
Department of Marine Science, Faculty of Science, Chulalongkorn University, Thailand
ABSTRACT
We determined the complete mitochondrial genome sequences of an asteroid Linckia laevigata belong-
ing to the order Valvatida. The complete mitogenome of L. laevigata was 16,371 bp in length and con-
sisted of 13 protein-coding genes (PCGs), two rRNA, and 22 tRNA. The orders of PCGs and rRNAs were
identical to those of the recorded mitogenomes of asteroids. Phylogenetic analyses placed L. laevigata
as the sister group to the species of the other Paxillosida.
ARTICLE HISTORY
Received 10 February 2020
Accepted 20 February 2020
KEYWORDS
Echinodermata; sea star;
complete mitoge-
nome; Valvatida
Linckia laevigata is a common sea star in the shallow waters
of the tropical Indo-West Pacific. Otwoma and Kochzius
(2016) conducted phylogeographic studies of the L. laevigata
to clarify the connectivity among populations in the Indo-
West Pacific. Including such a common, well-studied species,
the phylogenetic studies of the superorder Valvatacea are
ongoing (e.g. Mah and Foltz 2011), and further genetic
markers and OTUs are needed for the studies. In non-model
organisms like L. laevigata, we have to use universal primers
though these primers often fail to amplify a particular region
in PCR. To make a specific primer, genomic information of
more closely related species is necessary. Usually, mitoge-
nome is including 13 protein-coding genes and two rRNA
genes frequently used for phylogenetic reconstruction at
every taxonomic level. There was no mitogenome record for
the family Ophidiasteridae in Valvatacea, and we choose L.
laevigata for the representative of the family. We determined
the whole mitogenome sequence and also nucleic rRNA
genes by a shotgun sequencing, which is a PCR independ-
ent method.
Total DNA was extracted using DNeasy Blood & Tissue Kit
(QIAGEN) and processed using the QIAseq FX DNA Library kit
(QIAGEN). Paired-end sequencing (300 cycles) was conducted
using MiSeq (Illumina) of the National Museum of Nature and
Science, with inserts of ca. 50–200 bp for a total of approxi-
mate two million reads. Assembly was performed using CLC
Genomics Workbench ver. 12 (QIAGEN) with the default set-
ting. Ambiguous part of the contig was confirmed using
3500xL Genetic Analyzer (Thermo Fisher). Gene identification
was made using the MITOS web server (Bernt et al. 2013). A
voucher specimen with extracted DNA was deposited to the
National Museum of Nature and Science, Tokyo (NSMT
E-12913).
The mitogenome of L. laevigata (GenBank/DDBJ/EMBL
accession number LC505032) is 16,371 bp long and encodes
13 proteins, two rRNAs, and 22 tRNAs for a total of 37 gene
products. The overall A þT content of the L. laevigata mito-
chondrial genome is 63.5%, which is around average among
asteroidean species (Mu et al. 2018). Similar to other sea-star
mitogenomes, ND1 and ND2 start with GTG codon, and
ND4L starts with ATT codon, and all other protein-coding
genes (PCGs) start with the ATG start codon. Eight of PCGs
stop with the termination codon TAA, COX3 and ND6 end
with TAG codon, whereas other PCGs (COX2, CytB, and ND1)
used incomplete termination codon T—.
The maximum-likelihood phylogenetic analysis (ML) based
on 13 PCGs was conducted using RAxML-NG ver.0.9.0 (Kozlov
et al. 2019) with bootstrap analyses of 1000 replicates. The
phylogenetic tree also with posterior probability from
Bayesian analyses (BA) conducted using MrBayes 3.2.6
(Ronquist et al. 2012). Linckia laevigata make a sister clade
with species belonging to order Paxillosida (Astropecten poly-
acanthus and Luidia quinaria) with low nodal support value
(Figure 1). The family Ophidasterida, which including L. laevi-
gata, was paraphyletic in the previous study. Although
CONTACT Shimpei F. Hiruta javaboo9@gmail.com Center for Molecular Biodiversity Research, National Museum of Nature and Science, Tsukuba 305-
0005, Japan
ß2020 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
2020, VOL. 5, NO. 2, 1342–1343
https://doi.org/10.1080/23802359.2020.1735271

additional OTUs are needed, this mitogenome would be
useful for reconstructing higher systematics of aster-
oid phylogeny.
Disclosure statement
No potential conflict of interest was reported by the author(s).
Funding
This work is supported by NRCT-JSPS Core-to-Core Program, B. Asia-Africa
Science Platforms; National Museum of Nature and Science Project
Researches “Collaborative research and collection building of marine inver-
tebrates in Southeast Asia developed by the core museum NMNS”and
“Biological inventory with special attention to Myanmar: Investigations of
the origin of southern elements of Japanese flora and fauna”;Thailand
Research Fund [RSA 6080087]; UNESCO-IOC/WESTPAC, UNESCO Japanese
Funds-in-Trusts; and Mubadala Petroleum (Thailand) Limited.
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0.5
Aquilonastra batheri
Styracaster yapensis
Linckia laevigata
Aphelasterias japonica
Patiria pectinifera
Acanthaster planci
Acanthaster brevispinus
Luidia quinaria
Freyastera benthophila
Astropecten polyacanthus
Pisaster ochraceus
Echinaster brasiliensis
Asterias amurensis
Forcipulatida
Brisingida
Paxillosida
Valvatida
Valvatida
Spinulosida
Distolasterias nipon
25/1.00
43/0.98
55/-
*
26/1.00
53/1.00
92/1.00
(NC_006665)
(NC_025766)
(NC_042741)
(MH473231)
(NC_039982)
(NC_041450)
(NC_006666)
(NC_006664)
(NC_037943)
(NC_001627)
(MH507076)
(NC_007788)
(NC_007789)
*
*
*
*
*
Figure 1. Maximum-likelihood tree based on the concatenated nucleotide sequence of 13 protein-coding genes of Linckia laevigata (LC505032) and 12 asteroid spe-
cies. Nodal values are ML bootstrap support values (BS) and BA posterior probabilities (PP). An asterisk () indicates 100% BS and 1.0 PP. A hyphen (-) shows the
branch not supported in the BA tree. The scale bar indicates branch length in substitutions per site.
MITOCHONDRIAL DNA PART B 1343