Biodiversity Data Journal : Short Communication
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Short Communication
The complete mitochondrial genome of the Arctic fairy shrimp Branchinecta paludosa (Müller, 1788) (Anostraca, Branchinectidae) from Sirius Passet, North Greenland
expand article infoJi-Hoon Kihm‡, Euna Jo§,|, Tae-Yoon S Park‡,, Bo-Mi Kim#
‡ Division of Earth Sciences, Korea Polar Research Institute, Incheon, Korea, South
§ Division of Life Sciences, Korea Polar Research Institute, Incheon, Korea, South
| Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Korea, South
¶ Polar Science, University of Science & Technology, Daejeon, Korea, South
# Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon, Korea, South
Corresponding author: Bo-Mi Kim (bomikim@kopri.re.kr)
Academic editor: Michelle Hamer
Received: 11 Jul 2022 | Accepted: 04 Oct 2022 | Published: 28 Oct 2022
© 2022 Ji-Hoon Kihm, Euna Jo, Tae-Yoon Park, Bo-Mi Kim
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation: Kihm J-H, Jo E, Park T-YS, Kim B-M (2022) The complete mitochondrial genome of the Arctic fairy shrimp Branchinecta paludosa (Müller, 1788) (Anostraca, Branchinectidae) from Sirius Passet, North Greenland. Biodiversity Data Journal 10: e90200. https://doi.org/10.3897/BDJ.10.e90200
 Open Access

Abstract

Here we report the complete mitochondrial genome of the Arctic fairy shrimp, Branchinecta paludosa (Müller, 1788) (Anostraca, Branchinectidae), which was collected in the High Arctic of North Greenland. A complete 16,059 bp mitochondrion of B. paludosa was sequenced and assembled with the Illumina next generation sequencing platform. The B. paludosa mitogenome contains 13 PCGs, 22 tRNAs and 2 rRNA genes that are commonly observed in most metazoans and shows the conserved gene arrangement pattern of Anostraca. Our results of the phylogenomic analysis are consistent with the previous phylogenetic relationship, based on nuclear 18S ribosomal DNA. The B. paludosa mitogenome will be useful for understanding the geographical distribution and phylogenetic relationship of anostracans.

Keywords

Branchinecta paludosa, Greenland anostraca, Branchinectidae, mitogenome, phylogeny

Introduction

Many branchiopod crustaceans inhabit harsh, hazardous and anomalous aquatic environments, which are even subject to drought and freeze episodes and, thus, they have frequently developed dormancy mechanisms for survival and population maintenance (Brendonck 1996). The family Branchinectidae was originally known as monogeneric with the genus Branchinecta (Rogers 2006), but a new genus Archaebranchinecta was subsequently recognised by its different gonopod and genital segment (Rogers and Coronel 2011). The genus Branchinecta consists of approximately 50 species, distributed in all continents, except for Africa and Australia (Rogers 2006). Despite their wide distribution, no complete mitochondrial genome sequence is available to date. The Arctic fairy shrimp, Branchinecta paludosa (Müller, 1788) is known as a circumpolar species inhabiting in Arctic ponds and lakes (Belk and Brtek 1995). The diapause eggs of this species normally hatch with snowmelt and fully develop during the short Arctic summer (Lindholm et al. 2015), being known as a cold stenothermic species (Lindholm et al. 2012). We here report the mitochondrial genome of B. paludosa collected from the High Arctic of North Greenland. This will not only be the first complete mitochondrial genome of the species that could be used for investigating the phylogenetic relationship with other anostracans and branchiopods, but also be the first genetic information from the High Arctic; previously, the sample from the northernmost habitat was collected from the latitude 75°N (Lindholm et al. 2016).

Material and methods

An individual male specimen of Branchinecta was sampled from a small lake near Sirius Passet, North Greenland (82°47'7.7"N, 42°13'34.34"W) on 16 July 2017. With several morphological characters, this specimen was identified as B. paludosa (Müller, 1788): i.e. a longer proximal antennomere than a distal antennomere on the second antenna, spinose second antenna medial surface and a straight and triangular distal second antennal antennomere (Rogers and Aguilar 2020). This is the northernmost record of genus Branchinecta ever reported. The voucher specimen was registered in the Korea Polar Research Institute (KOPRI; Species ID:Anostraca1; Specimen ID:Anostraca1-2) and sequenced data were deposited in the Korea Polar Data Center (https://kpdc.kopri.re.kr/search/ad5267f7-ed99-4020-9b7a-1cd8880afe6a; Dr. Bo-Mi Kim; bomikim@kopri.re.kr). Total genomic DNA was extracted from a whole body of B. paludosa using the classical phenol/chloroform method (Kim et al. 2021). A genomic DNA library was prepared using TruSeq Nano DNA kit (Macrogen, Seoul, South Korea) according to the manufacturer's instructions (Illumina, San Diego, CA, USA). After removing adapter sequences, a total of 25,345,240 reads was produced by the Illumina HiSeq platform and de novo assembly was performed using SPAdes v.3.11.1 (Bankevich et al. 2012). Genomic features and annotations were predicted using MITOS2 (Bernt et al. 2013) and tRNAscan-SE 2.0 (Lowe and Eddy 1997). The gene annotation was further confirmed using NCBI-BLAST (http://blast.ncbi.nlm.nih.gov). Nucleotide sequences of the concatenated 13 protein-coding genes and 2 ribosomal RNAs of B. paludosa and those of 14 branchiopod species were used for phylogenetic analysis. A Maximum Likelihood tree was constructed using FastTree version 2.1.10 with default parameters (Price et al. 2009). All used mtgenome’s information is incorporated in Table 1.

Table 1.
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Taxonomy, mitogenome sizes, length of the input sequence for phylogetic analysis and GenBank accession numbers used in this study.

Order

Species

Mitogenome size (bp)

Length of PCGs+rRNAs (bp)

GenBank ID

Reference

Anostraca

Artemia franciscana

15,822

12,452

NC_001620.1

Perez et al. 1994

Anostraca

Artemia sinica

15,689

12,397

NC_042147.1

Asem et al. 2019

Anostraca

Artemia tibetiana

15,742

12,439

NC_021383.1

Zhang et al. 2013

Anostraca

Artemia urmiana

15,945

12,441

NC_021382.1

Zhang et al. 2013

Anostraca

Branchinecta paludosa

16,059

12,661

MZ853171

This study

Anostraca

Branchinella kugenumaensis

15,127

12,502

MN660045.1

Yang and Chen 2020

Anostraca

Eubranchipus grubii

16,328

12,595

NC_050310.1

NC_050310.1

Anostraca

Phallocryptus tserensodnomi

16,493

12,513

NC_026710.1

Fan et al. 2016

Anostraca

Streptocephalus cafer

17,020

12,574

NC_046688.1

Tladi et al. 2020

Anostraca

Streptocephalus sirindhornae

16,887

12,634

NC_026704.1

Liu et al. 2016

Brachypoda

Hutchinsoniella macracantha

16,491

13,329

AY456189.1

Lavrov et al. 2004

Diplostraca

Daphnia magna

14,948

13,210

NC_026914.1

Cheng et al. 2016

Diplostraca

Daphnia pulex

15,333

13,143

NC_000844.1

Crease 1999

Notostraca

Lepidurus apus

15,635

13,175

NC_044646.1

Luchetti et al. 2019

Notostraca

Lepidurus arcticus

15,223

13,181

NC_044654.1

Luchetti et al. 2019

Notostraca

Triops cancriformis

15,101

13,167

NC_004465.1

Luchetti et al. 2019

Results and Discussion

The assembly produced a complete consensus sequence with 16,059 bp, which contained 13 protein-coding genes (PCGs), 22 tRNAs, 2 rRNAs and one putative control region (MZ853171) (Fig. 1). Eleven PCGs (ND1, ND6, ND4L, ATP8 and COI with ATT; CYTB, ND4, ND3, COIII and COII with ATG; ND2 with ATC) have typical ATN as a start codon. However, two genes, ND5 and ATP6, possess TTG and GTG as a start codon, respectively. Ten PCGs have TAA or TAG as a stop codon, whereas three genes, CYTB, COII and COI have an incomplete stop codon T (two nucleotides are missing). Two distinct gene arrangements in tRNA structures have been recognised in Crustacea: the ancestral pancrustacean pattern and the anostracan pattern (Cook et al. 2005) (Fig. 2). The gene arrangement of the B. paludosa tRNAs also complies with the typical pattern of anostracans as observed in the mitogenomes of Eubranchipus grubii, two species of Streptocephalus and Phallocryptus tserensodnomi. In anostracans mitogenomes, a gene coding for tRNATrp shows a rearrangement pattern in Branchinella kugenumaensis. Overall, this result supports the hypothesis of the ancestral gene rearrangement in anostracan mitochondrial genomes (Cook et al. 2005, Yang and Chen 2020).

Figure 1.  

Circular map of the complete mitochondrial genome of Branchinecta paludosa. The map was drawn with OrganellarGenomeDRAW (OGDRAW) version 1.3.1 (Greiner et al. 2019).

Figure 2.  

Maximum Likelihood phylogeny of 15 species of Branchiopoda with one species of Cephalocarida as an outgroup analysed with the concatenated nucleotide sequences of 13 PCGs and 2 rRNAs. Numbers on the branches indicate ML bootstrap percentages (100 replicates). The black arrow indicates the B. paludosa analysed in this study. A schematic diagram for the partial genomic structure of each mitogenome is appended on the right side of the phylogenetic tree. Other regions were omitted due to their same organisation. Genes on the major stand are shown in grey. Gene names for entire tRNAs are abbreviated as single-letter codes.

The results of the phylogenetic analysis using mitogenome show that the B. paludosa is clustered within other anostracans, with Eubranchipus grubii being the closest species (Fig. 2). The complete mitogenome of B. paludosa here in this study will provide essential information for understanding the potential correlation between the geographic distribution including the High Arctic and the phylogenetic relationship within Anostraca.

Acknowledgements

Sampling was executed under permission from the Greenland government (permission no. C-17-4). We thank Mr. Man Jung and the Villum Research Station and the Station Nord for logistic support.

Grant title

This research was supported by Korea Polar Research Institute (PE22060).

Hosting institution

Korea Polar Research Institute

Conflicts of interest

The authors report no conflicts of interest and are solely responsible for the content and writing of this manuscript.

References

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