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


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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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Mitochondrial DNA Part B
ISSN: (Print) 2380-2359 (Online) Journal homepage:
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,
To link to this article:
© 2020 The Author(s). Published by Informa
UK Limited, trading as Taylor & Francis
Published online: 27 Apr 2020.
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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
and Toshihiko Fujita
Center for Molecular Biodiversity Research, National Museum of Nature and Science, Tsukuba, Japan;
Department of Biological Sciences,
Graduate School of Science, the University of Tokyo, Bunkyo-ku, Japan;
Department of Zoology, National Museum of Nature and Science,
Tsukuba, Japan;
Department of Marine Science, Faculty of Science, Chulalongkorn University, Thailand
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.
Received 10 February 2020
Accepted 20 February 2020
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. 50200 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
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 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 (, which permits unrestricted use,
distribution, and reproduction in any medium, provided the original work is properly cited.
2020, VOL. 5, NO. 2, 13421343
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).
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 NMNSand
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.
Bernt M, Donath A, J
uhling F, Externbrink F, Florentz C, Fritzsch G, P
utz J,
Middendorf M, Stadler PF. 2013. MITOS: improved de novo metazoan
mitochondrial genome annotation. Mol Phylogenet Evol. 69(2):
Kozlov A, Darriba D, Flouri T, Morel B, Stamatakis A. 2019. RAxML-NG: a
fast, scalable, and user-friendly tool for maximum likelihood phylogen-
etic inference. Bioinformatics. 35(21):44534455.
Mah C, Foltz D. 2011. Molecular phylogeny of the Valvatacea (Asteroidea:
Echinodermata). Zool J Linne Soci. 161(4):769788.
Mu W, Liu J, Zhang H. 2018. The first complete mitochondrial genome of
the Mariana Trench Freyastera benthophila (Asteroidea: Brisingida:
Brisingidae) allows insights into the deep-sea adaptive evolution of
Brisingida. Ecol Evol. 8(22):1067310686.
Otwoma LM, Kochzius M. 2016. Genetic population structure of the coral
reef sea star Linckia laevigata in the Western Indian Ocean and Indo-
West Pacific. PLoS One. 11(10):e0165552.
Ronquist F, Teslenko M, Van Der Mark P, Ayres DL, Darling A, H
ohna S,
Larget B, Liu L, Suchard MA, Huelsenbeck JP. 2012. MrBayes 3.2: effi-
cient Bayesian phylogenetic inference and model choice across a large
model space. Syst Biol. 61(3):539542.
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
Distolasterias nipon
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.
... Goniasterids are the most diverse family of asteroids, including some 256 living species within 65 genera (Mah and Blake 2012). The complete mitochondrial genome of the ophidiasterid, Linckia laevigata, a species also representing the large Valvatacea cluster has recently been reported by Hiruta et al. (2020). ...
... Linchangco et al. 2017). Linckia laevigata's position here differs from its position in the tree presented by Hiruta et al. (2020) which showed it as sister to two members of Paxillosida, Luidia and Astropecten. This is likely attributable to the different number of markers used in previous studies. ...
... Furthermore, at the timing of writing, neither our tree nor that of Hiruta et al. (2020) included any members of the Velatida, the third major clade within the Asteroidea (Linchangco et al. 2017). The lack of comprehensive taxon sampling in prior studies may have resulted in Long Branch Attraction artifacts which might have led to the erroneous grouping of some OTUs (Wiens et al. 2008). ...
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The full mitogenome of an ethanol-preserved museum specimen of Ceramaster japonicus was determined using the NGS Illumina MiSeq platform. The specimen was collected from Tosa Bay, Japan, facing the Pacific Ocean (33.0781 N 134.0601 E), at 700 m depth in 2011. The mitogenome shows a typical metazoan genomic structure, with all of the 37 genes included in its 16,370 base-long mitogenome. We conducted phylogenetic analyses using a data set including 18 publicly available asteroids rooted against five ophiuroids as outgroups. The result confirms the position of C. japonicus in the order Valvatida. The complete mitogenome of C. japonicus reported here is the first reported for the family Goniasteridae Forbes, 1841.
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Motivation: Phylogenies are important for fundamental biological research, but also have numerous applications in biotechnology, agriculture, and medicine. Finding the optimal tree under the popular maximum likelihood (ML) criterion is known to be NP-hard. Thus, highly optimized and scalable codes are needed to analyze constantly growing empirical datasets. Results: We present RAxML-NG, a from scratch re-implementation of the established greedy tree search algorithm of RAxML/ExaML. RAxML-NG offers improved accuracy, flexibility, speed, scalability, and usability compared to RAxML/ExaML. On taxon-rich datasets, RAxML-NG typically finds higher-scoring trees than IQTree, an increasingly popular recent tool for ML-based phylogenetic inference (although IQ-Tree shows better stability). Finally, RAxML-NG introduces several new features, such as the detection of terraces in tree space and a the recently introduced transfer bootstrap support metric. Availability: The code is available under GNU GPL at RAxML-NG web service (maintained by Vital-IT) is available at Supplementary information: Supplementary data are available at Bioinformatics online.
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Starfish (phylum Echinodermata) are ecologically important and diverse members of marine ecosystems in all of the world's oceans, from the shallow water to the hadal zone. The deep sea is recognized as an extremely harsh environment on earth. In this study, we present the mitochondrial genome sequence of Mariana Trench starfish Freyastera benthophila, and this study is the first to explore in detail the mitochondrial genome of a deep‐sea member of the order Brisingida. Similar to other starfish, it contained 13 protein‐coding genes, two ribosomal RNA genes, and 22 transfer RNA genes (duplication of two tRNAs: trnL and trnS). Twenty‐two of these genes are encoded on the positive strand, while the other 15 are encoded on the negative strand. The gene arrangement was identical to those of sequenced starfish. Phylogenetic analysis showed the deep‐sea Brisingida as a sister taxon to the traditional members of the Asteriidae. Positive selection analysis indicated that five residues (8 N and 16 I in atp8, 47 D and 196 V in nad2, 599 N in nad5) were positively selected sites with high posterior probabilities. Compared these features with shallow sea starfish, we predict that variation specifically in atp8, nad2, and nad5 may play an important role in F. benthophila's adaptation to deep‐sea environment. This study is the first determination of the mitogenome of a deep‐sea member of the order Brisingida and may shed light on the adaptive evolution of Brisingida species to the deep‐sea environment.
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The coral reef sea star Linckia laevigata is common on shallow water coral reefs of the Indo-West Pacific. Its large geographic distribution and comprehensive data from previous studies makes it suitable to examine genetic differentiation and connectivity over large geographical scales. Based on partial sequences of the mitochondrial cytochrome oxidase I (COI) gene this study investigates the genetic population structure and connectivity of L. laevigata in the Western Indian Ocean (WIO) and compares it to previous studies in the Indo-Malay-Philippines Archipelago (IMPA). A total of 138 samples were collected from nine locations in the WIO. AMOVA revealed a low but significant ΦST-value of 0.024 for the WIO populations. In the hierarchical AMOVA, the following grouping rejected the hypothesis of panmixia: (1) Kenya (Watamu, Mombasa, Diani) and Tanzanian Island populations (Misali and Jambiani) and (2) the rest of the WIO sites (mainland Tanzania and Madagascar; ΦCT = 0.03). The genetic population structure was stronger and more significant (ΦST = 0.13) in the comparative analysis of WIO and IMPA populations. Three clades were identified in the haplotype network. The strong genetic differentiation (ΦCT = 0.199, P < 0.001) suggests that Indo-West Pacific populations of L. laevigata can be grouped into four biogeographic regions: (1) WIO (2) Eastern Indian Ocean (3) IMPA and (4) Western Pacific. The findings of this study support the existence of a genetic break in the Indo-West Pacific consistent with the effect of lowered sea level during the Pleistocene, which limited gene flow between the Pacific and Indian Ocean.
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Since its introduction in 2001, MrBayes has grown in popularity as a software package for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) methods. With this note, we announce the release of version 3.2, a major upgrade to the latest official release presented in 2003. The new version provides convergence diagnostics and allows multiple analyses to be run in parallel with convergence progress monitored on the fly. The introduction of new proposals and automatic optimization of tuning parameters has improved convergence for many problems. The new version also sports significantly faster likelihood calculations through streaming single-instruction-multiple-data extensions (SSE) and support of the BEAGLE library, allowing likelihood calculations to be delegated to graphics processing units (GPUs) on compatible hardware. Speedup factors range from around 2 with SSE code to more than 50 with BEAGLE for codon problems. Checkpointing across all models allows long runs to be completed even when an analysis is prematurely terminated. New models include relaxed clocks, dating, model averaging across time-reversible substitution models, and support for hard, negative, and partial (backbone) tree constraints. Inference of species trees from gene trees is supported by full incorporation of the Bayesian estimation of species trees (BEST) algorithms. Marginal model likelihoods for Bayes factor tests can be estimated accurately across the entire model space using the stepping stone method. The new version provides more output options than previously, including samples of ancestral states, site rates, site d(N)/d(S) rations, branch rates, and node dates. A wide range of statistics on tree parameters can also be output for visualization in FigTree and compatible software.
The Valvatacea is one the most ecologically important, taxonomically diverse, and widespread groups of post-Palaeozoic (i.e. modern) Asteroidea. Classification within the group has been historically problematic. We present a comprehensively sampled, three-gene (12S, 16S, early-stage histone H3) molecular phylogenetic analysis of the Valvatacea. We include five of the six families within the Paxillosida, the monotypic Notomyotida, and 13 of the 16 families of the living Valvatida. The Solasteridae is removed from the Velatida (Spinulosacea) and joins the Ganeriidae and the Leilasteridae as members of the clade containing the Asterinidae. The Poraniidae is supported as the sister group to the large cluster of Valvatacea. Asteropseids and poraniids are phylogenetically distant, contrary to morphological evidence. Several goniasterid-like ophidiasterids, such as Fromia and Neoferdina are supported as derived goniasterids rather than as Ophidiasteridae. The Benthopectinidae (Notomyotida) are supported as members of the Paxillosida as are two members of the Pseudarchasterinae that have traditionally been considered members of the Goniasteridae. Our data suggest that Antarctic valvataceans may be derived from sister taxa in adjacent regions. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2011, 161, 769–788.