http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2015 Informa UK Ltd. DOI: 10.3109/19401736.2015.1053068
MITOGENOME ANNOUNCEMENT
The complete mitogenome of blue swimming crab Portunus pelagicus Linnaeus, 1766 (Crustacea: Decapoda: Portunidae) Xian-liang Meng, Fu-long Jia, Ping Liu, and Jian Li
Mitochondrial DNA Downloaded from informahealthcare.com by University of Otago on 07/15/15 For personal use only.
Key Laboratory of Sustainable Development of Marine Fisheries, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, People’s Republic of China Abstract
Keywords
The complete mitochondrial genome (mitogenome) of the blue swimming crab Portunus pelagicus Linnaeus, 1766 (Crustacea: Decapoda: Portunidae) was determined in this study. The full length mitogenome is 16 157 bp in size, and consists of 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a non-coding control region, with the base composition of 33.70% for A, 18.99% for C, 12.22% for G, and 35.09% for T. The gene order of P. pelagicus mainly retains as the pancrustacean ground pattern, except for a single translocation of tRNAHis gene. The mitogenome data provide a basis for further studies on population genetics and phylogenetics.
Brachyura, mitochondrial genome, Portunoidea, Portunus pelagicus, swimming crab
The blue swimming crab Portunus pelagicus, a large predatory marine brachyuran species, is naturally distributed throughout the coastal and estuarine areas of the tropical Western Pacific and Eastern Indian oceans (Xiao & Kumar, 2004). It is a commercially important crustacean species in China, but in recent years, it suffered a dramatic decline in its wild population due to overexploitation and environmental deterioration (Liao & Li, 2002; Pan & Liao, 2008). For effective conservation and fishery management of this species, it is of great importance to obtain the knowledge of its population genetics. However, few genetic studies have been conducted in this species so far (Bryars & Adams, 1999; Klinbunga et al., 2007). In this study, we report the complete sequence of mitochondrial genome for P. pelagicus. The findings will provide useful information for further studies on population genetics, as well as taxonomic and phylogenetic investigations. The P. pelagicus sample was collected from coastal waters in Guangzhou, Guangdong Province, China. The total genomic DNA was extracted from ethanol-preserved leg muscle tissue using the phenol–chloroform method. The complete mitogenome of P. pelagicus was sequenced by primer walking, and mitogenome assembly and annotation were performed as previously described by Sui et al. (2015).
Correspondence: Ping Liu, Key Laboratory of Sustainable Development of Marine Fisheries, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, People’s Republic of China. Tel/Fax: +86 532 85836605. E-mail: [email protected]
History Received 28 April 2015 Accepted 4 May 2015 Published online 14 July 2015
The mitochondrial genome of P. pelagicus is circular and consists of 16 157 bp (GenBank accession number KR153996), containing 37 mitochondrial genes (13 protein-coding genes (PCGs), two rRNAs, and 22 tRNAs) and a putative non-coding control region of 1243 bp. Twenty-three of the genes are transcribed from the heavy strand, whereas the remainder are encoded on the light strand. The gene order of P. pelagicus is largely identical to the ancestral pancrustacean ground pattern (Boore et al., 1998), except for the translocation of the tRNAHis gene. Typically the tRNAHis gene is located between ND5 and ND4 in the ancestral pancrustacea, while in P. pelagicus it lies between tRNAGlu and tRNAPhe. All the PCGs are started with the typical metazoan initiation codon ATG or ATT. The majority of the PCGs are terminated by TAA or TAG, while COI, COII, Cyt b, and ND2 are ended with the incomplete stop codon T, which can be extended to TAA by post-transcriptional polyadenylation (Ojala et al., 1981). The overall A + T content of P. pelagicus mtDNA is 68.79% (33.70% A, 18.99% C, 12.22% G, and 35.09% T), similar to that of other brachyurans (Cheng et al., 2014; Yu et al., 2014), and this pattern of base composition holds for the protein-coding, rRNA, and tRNA genes, as well as the control region. The phylogenetic position of P. pelagicus within Decapoda was reconstructed using the 13 PCGs by Bayesian inference (BI) and maximum likelihood (ML) methods. The result showed that P. pelagicus clustered with its congeneric species P. trituberculatus, Callinectes sapidus and three species of genus Scylla, forming a solid monophyletic group, which is sister to Grapsoidea, Potamoidea, and Xanthoidea (Figure 1). This result is consistence with previous morphological classification and molecular analyses (Liu, 2008; Liu & Cui, 2010; Yang et al., 2010).
Mitochondrial DNA Downloaded from informahealthcare.com by University of Otago on 07/15/15 For personal use only.
2
X. Meng et al.
Mitochondrial DNA, Early Online: 1–2
Figure 1. Phylogenetic tree of decapod relationships from the dataset of 13 concatenated mitochondrial PCGs. Four stomatopods served as outgroups. Branch lengths and topologies came from the maximum likelihood (ML) analyses. Numbers besides the nodes specify bootstrap percentages from ML and Bayesian posterior probabilities (BPP). Sequence data used in the study were as following: Pseudocarcinus gigas (NC_006891), Callinectes sapidus (NC_006281), Portunus trituberculatus (NC_005037), Portunus pelagicus (KR153996), Scylla olivacea (NC_012569), Scylla tranquebarica (NC_012567), Scylla paramamosain (NC_012572), Scylla serrata (NC_012565), Geothelphusa dehaani (NC_007379), Eriocheir japonica (NC_011597), Eriocheir hepuensis (NC_011598), Eriocheir sinensis (NC_006992), Pagurus longicarpus (NC_003058), Shinkaia crosnieri (NC_011013), Cherax destructor (NC_011243), Panulirus japonicus (NC_004251), Halocaridina rubra (NC_008413), Exopalaemon carinicauda (NC_012566), Macrobrachium lanchesteri (NC_012217), Macrobrachium rosenbergii (NC_006880), Marsupenaeus japonicus (NC_007010), Fenneropenaeus chinensis (NC_009679), Penaeus monodon (NC_002184), Farfantepenaeus californiensis (NC_012738), Litopenaeus stylirostris (NC_012060), Litopenaeus vannamei (NC_009626), Gonodactylus chiragra (NC_007442), Harpiosquilla harpax (NC_006916), Lysiosquilla harpax (NC_007443), Squilla empusa (NC_007444), and Squilla mantis (NC_006081).
Declaration of interest This work is supported by the Hi-Tech Research and Development Program of China (863 Program) (No. 2012AA10A409), the Independent Innovation Foundation of Shandong Province (2013CXC80202), and National Natural Science Foundation of China (41306178). The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
References Boore JL, Lavrov DV, Brown WM. (1998). Gene translocation links insects and crustaceans. Nature 392:667. Bryars SR, Adams M. (1999). An allozyme study of the blue swimmer crab, Portunus pelagicus (Crustacea: Portunidae), in Australia: Stock delineation in southern Australia and evidence for a cryptic species in northern waters. Mar Freshwater Res 50:15–26. Cheng J, Jiang W, Shi H, Sha Z. (2014). The complete mitochondrial genome of red frog crab Ranina ranina (Crustacea: Decapoda: Brachyura: Raninidae). Mitochondrial DNA. [Epub ahead of print]. doi:10.3109/19401736.2014.947584. Klinbunga S, Khetpu K, Khamnamtong B, Menasveta P. (2007). Genetic heterogeneity of the blue swimming crab (Portunus pelagicus) in Thailand determined by AFLP analysis. Biochem Genet 45:725–36. Liao YY, Li XM. (2002). Demands of Portunus pelagicus for environmental conditions. Acta Oceanol Sin 24:140–5.
Liu JY. (2008). Checklist of marine biota of China seas. Beijing, China: Science Press. Liu Y, Cui ZX. (2010). Complete mitochondrial genome of the Asian paddle crab Charybdis japonica (Crustacea: Decapoda: Portunidae): Gene rearrangement of the marine brachyurans and phylogenetic considerations of the decapods. Mol Biol Rep 37:2559–69. Ojala D, Montoya J, Attardi G. (1981). tRNA punctuation model of RNA processing in human mitochondria. Nature 290:470–4. Pan CH, Liao YY. (2008). Observation on the morphological changes of Portunus pelagicus under artificial rearing. J Oceanol Taiwan Strait 27: 482–90. Sui X, Liang Y, He D. (2015). The complete mitochondrial genome of Rhynchocypris oxycephalus (Cypriniformes: Cyprinidae). Mitochondrial DNA. [Epub ahead of print]. doi:10.3109/19401736. 2015.1018224. Xiao Y, Kumar M. (2004). Sex ratio, and probability of sexual maturity of females at size, of the blue swimmer crab, Portunus pelagicus Linneaus, off southern Australia. Fish Res 68:271–82. Yang JS, Nagasawa H, Fujiwara Y, Tsuchida S, Yang WJ. (2010). The complete mitogenome of the hydrothermal vent crab Gandalfus yunohana (Crustacea: Decapoda: Brachyura): A link between the Bythograeoidea and Xanthoidea. Zool Scr 39:621–30. Yu YQ, Ma WM, Yang WJ, Yang JS. (2014). The complete mitogenome of the lined shore crab Pachygrapsus crassipes Randall 1840 (Crustacea: Decapoda: Grapsidae). Mitochondrial DNA 25:263–4.
MITOGENOME ANNOUNCEMENT
The complete mitogenome of blue swimming crab Portunus pelagicus Linnaeus, 1766 (Crustacea: Decapoda: Portunidae) Xian-liang Meng, Fu-long Jia, Ping Liu, and Jian Li
Mitochondrial DNA Downloaded from informahealthcare.com by University of Otago on 07/15/15 For personal use only.
Key Laboratory of Sustainable Development of Marine Fisheries, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, People’s Republic of China Abstract
Keywords
The complete mitochondrial genome (mitogenome) of the blue swimming crab Portunus pelagicus Linnaeus, 1766 (Crustacea: Decapoda: Portunidae) was determined in this study. The full length mitogenome is 16 157 bp in size, and consists of 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a non-coding control region, with the base composition of 33.70% for A, 18.99% for C, 12.22% for G, and 35.09% for T. The gene order of P. pelagicus mainly retains as the pancrustacean ground pattern, except for a single translocation of tRNAHis gene. The mitogenome data provide a basis for further studies on population genetics and phylogenetics.
Brachyura, mitochondrial genome, Portunoidea, Portunus pelagicus, swimming crab
The blue swimming crab Portunus pelagicus, a large predatory marine brachyuran species, is naturally distributed throughout the coastal and estuarine areas of the tropical Western Pacific and Eastern Indian oceans (Xiao & Kumar, 2004). It is a commercially important crustacean species in China, but in recent years, it suffered a dramatic decline in its wild population due to overexploitation and environmental deterioration (Liao & Li, 2002; Pan & Liao, 2008). For effective conservation and fishery management of this species, it is of great importance to obtain the knowledge of its population genetics. However, few genetic studies have been conducted in this species so far (Bryars & Adams, 1999; Klinbunga et al., 2007). In this study, we report the complete sequence of mitochondrial genome for P. pelagicus. The findings will provide useful information for further studies on population genetics, as well as taxonomic and phylogenetic investigations. The P. pelagicus sample was collected from coastal waters in Guangzhou, Guangdong Province, China. The total genomic DNA was extracted from ethanol-preserved leg muscle tissue using the phenol–chloroform method. The complete mitogenome of P. pelagicus was sequenced by primer walking, and mitogenome assembly and annotation were performed as previously described by Sui et al. (2015).
Correspondence: Ping Liu, Key Laboratory of Sustainable Development of Marine Fisheries, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, People’s Republic of China. Tel/Fax: +86 532 85836605. E-mail: [email protected]
History Received 28 April 2015 Accepted 4 May 2015 Published online 14 July 2015
The mitochondrial genome of P. pelagicus is circular and consists of 16 157 bp (GenBank accession number KR153996), containing 37 mitochondrial genes (13 protein-coding genes (PCGs), two rRNAs, and 22 tRNAs) and a putative non-coding control region of 1243 bp. Twenty-three of the genes are transcribed from the heavy strand, whereas the remainder are encoded on the light strand. The gene order of P. pelagicus is largely identical to the ancestral pancrustacean ground pattern (Boore et al., 1998), except for the translocation of the tRNAHis gene. Typically the tRNAHis gene is located between ND5 and ND4 in the ancestral pancrustacea, while in P. pelagicus it lies between tRNAGlu and tRNAPhe. All the PCGs are started with the typical metazoan initiation codon ATG or ATT. The majority of the PCGs are terminated by TAA or TAG, while COI, COII, Cyt b, and ND2 are ended with the incomplete stop codon T, which can be extended to TAA by post-transcriptional polyadenylation (Ojala et al., 1981). The overall A + T content of P. pelagicus mtDNA is 68.79% (33.70% A, 18.99% C, 12.22% G, and 35.09% T), similar to that of other brachyurans (Cheng et al., 2014; Yu et al., 2014), and this pattern of base composition holds for the protein-coding, rRNA, and tRNA genes, as well as the control region. The phylogenetic position of P. pelagicus within Decapoda was reconstructed using the 13 PCGs by Bayesian inference (BI) and maximum likelihood (ML) methods. The result showed that P. pelagicus clustered with its congeneric species P. trituberculatus, Callinectes sapidus and three species of genus Scylla, forming a solid monophyletic group, which is sister to Grapsoidea, Potamoidea, and Xanthoidea (Figure 1). This result is consistence with previous morphological classification and molecular analyses (Liu, 2008; Liu & Cui, 2010; Yang et al., 2010).
Mitochondrial DNA Downloaded from informahealthcare.com by University of Otago on 07/15/15 For personal use only.
2
X. Meng et al.
Mitochondrial DNA, Early Online: 1–2
Figure 1. Phylogenetic tree of decapod relationships from the dataset of 13 concatenated mitochondrial PCGs. Four stomatopods served as outgroups. Branch lengths and topologies came from the maximum likelihood (ML) analyses. Numbers besides the nodes specify bootstrap percentages from ML and Bayesian posterior probabilities (BPP). Sequence data used in the study were as following: Pseudocarcinus gigas (NC_006891), Callinectes sapidus (NC_006281), Portunus trituberculatus (NC_005037), Portunus pelagicus (KR153996), Scylla olivacea (NC_012569), Scylla tranquebarica (NC_012567), Scylla paramamosain (NC_012572), Scylla serrata (NC_012565), Geothelphusa dehaani (NC_007379), Eriocheir japonica (NC_011597), Eriocheir hepuensis (NC_011598), Eriocheir sinensis (NC_006992), Pagurus longicarpus (NC_003058), Shinkaia crosnieri (NC_011013), Cherax destructor (NC_011243), Panulirus japonicus (NC_004251), Halocaridina rubra (NC_008413), Exopalaemon carinicauda (NC_012566), Macrobrachium lanchesteri (NC_012217), Macrobrachium rosenbergii (NC_006880), Marsupenaeus japonicus (NC_007010), Fenneropenaeus chinensis (NC_009679), Penaeus monodon (NC_002184), Farfantepenaeus californiensis (NC_012738), Litopenaeus stylirostris (NC_012060), Litopenaeus vannamei (NC_009626), Gonodactylus chiragra (NC_007442), Harpiosquilla harpax (NC_006916), Lysiosquilla harpax (NC_007443), Squilla empusa (NC_007444), and Squilla mantis (NC_006081).
Declaration of interest This work is supported by the Hi-Tech Research and Development Program of China (863 Program) (No. 2012AA10A409), the Independent Innovation Foundation of Shandong Province (2013CXC80202), and National Natural Science Foundation of China (41306178). The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
References Boore JL, Lavrov DV, Brown WM. (1998). Gene translocation links insects and crustaceans. Nature 392:667. Bryars SR, Adams M. (1999). An allozyme study of the blue swimmer crab, Portunus pelagicus (Crustacea: Portunidae), in Australia: Stock delineation in southern Australia and evidence for a cryptic species in northern waters. Mar Freshwater Res 50:15–26. Cheng J, Jiang W, Shi H, Sha Z. (2014). The complete mitochondrial genome of red frog crab Ranina ranina (Crustacea: Decapoda: Brachyura: Raninidae). Mitochondrial DNA. [Epub ahead of print]. doi:10.3109/19401736.2014.947584. Klinbunga S, Khetpu K, Khamnamtong B, Menasveta P. (2007). Genetic heterogeneity of the blue swimming crab (Portunus pelagicus) in Thailand determined by AFLP analysis. Biochem Genet 45:725–36. Liao YY, Li XM. (2002). Demands of Portunus pelagicus for environmental conditions. Acta Oceanol Sin 24:140–5.
Liu JY. (2008). Checklist of marine biota of China seas. Beijing, China: Science Press. Liu Y, Cui ZX. (2010). Complete mitochondrial genome of the Asian paddle crab Charybdis japonica (Crustacea: Decapoda: Portunidae): Gene rearrangement of the marine brachyurans and phylogenetic considerations of the decapods. Mol Biol Rep 37:2559–69. Ojala D, Montoya J, Attardi G. (1981). tRNA punctuation model of RNA processing in human mitochondria. Nature 290:470–4. Pan CH, Liao YY. (2008). Observation on the morphological changes of Portunus pelagicus under artificial rearing. J Oceanol Taiwan Strait 27: 482–90. Sui X, Liang Y, He D. (2015). The complete mitochondrial genome of Rhynchocypris oxycephalus (Cypriniformes: Cyprinidae). Mitochondrial DNA. [Epub ahead of print]. doi:10.3109/19401736. 2015.1018224. Xiao Y, Kumar M. (2004). Sex ratio, and probability of sexual maturity of females at size, of the blue swimmer crab, Portunus pelagicus Linneaus, off southern Australia. Fish Res 68:271–82. Yang JS, Nagasawa H, Fujiwara Y, Tsuchida S, Yang WJ. (2010). The complete mitogenome of the hydrothermal vent crab Gandalfus yunohana (Crustacea: Decapoda: Brachyura): A link between the Bythograeoidea and Xanthoidea. Zool Scr 39:621–30. Yu YQ, Ma WM, Yang WJ, Yang JS. (2014). The complete mitogenome of the lined shore crab Pachygrapsus crassipes Randall 1840 (Crustacea: Decapoda: Grapsidae). Mitochondrial DNA 25:263–4.
