Mitochondrial DNA The Journal of DNA Mapping, Sequencing, and Analysis
ISSN: 1940-1736 (Print) 1940-1744 (Online) Journal homepage: http://www.tandfonline.com/loi/imdn20
The complete mitogenome of Cherax monticola (Crustacea: Decapoda: Parastacidae), a large highland crayfish from New Guinea. Han Ming Gan, Mun Hua Tan, Rury Eprilurahman & Christopher M. Austin To cite this article: Han Ming Gan, Mun Hua Tan, Rury Eprilurahman & Christopher M. Austin (2014): The complete mitogenome of Cherax monticola (Crustacea: Decapoda: Parastacidae), a large highland crayfish from New Guinea., Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2014.892105
Published online: 11 Mar 2014.
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Date: 10 November 2015, At: 15:56
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.892105
MITOGENOME ANNOUNCEMENT
The complete mitogenome of Cherax monticola (Crustacea: Decapoda: Parastacidae), a large highland crayfish from New Guinea. Han Ming Gan1, Mun Hua Tan1, Rury Eprilurahman2, and Christopher M. Austin1 School of Science, Monash University Malaysia, Selangor, Malaysia and 2Faculty of Biology, Universitas Gadjah Mada, Yogyakarta, Indonesia
Downloaded by [Monash University Library] at 15:56 10 November 2015
1
Abstract
Keywords
The complete mitochondrial genome of a highland freshwater crayfish, Cherax monticola, was recovered by shotgun sequencing. The mitogenome consists of 15,917 base pairs containing 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs and a non-coding AT-rich region. The base composition of C. monticola is 33.46% for T, 21.48% for C, 33.71% for A and 11.35% for G, with an AT bias of 67.17%.
Freshwater crayfish, mitogenome, Parastacidae
Freshwater crayfish of the genus Cherax are an ecological and commercially important group of decapod crustaceans that occur widely across Australia (Austin, 1996; Austin & Knott, 1996; Munasighe et al., 2004). The genus also extends into southern New Guinea where it is represented by a diversity of species from both highland and lowland environments (Holthuis, 1982). As in Australia, several New Guinea species grow to a large size and are the subject of indigenous fisheries and traded in local markets. Cherax monticola is a large highland species with a restricted distribution in the upper Baliem Valley, in the region near Wamena in the Papua province of Indonesia. Three species of Cherax from Australia have been sequenced for their mitogenome and they were all identified as having an unusual gene order rearrangement (Austin et al., 2014a,b; Miller et al., 2004). With an increasing interest in using information from whole
History Received 31 January 2014 Accepted 4 February 2014 Published online 11 March 2014
mitochondrial genomes for phylogenetic studies (Kim et al., 2012; Liu & Cui, 2011; Masta et al., 2009; Miller & Austin, 2006; Perseke et al., 2013; Rota-Stabelli et al., 2010; Simon & Hadrys, 2013) and the emergence of interesting patterns of mitochondrial gene order that demand explanation, this study was designed to extend the studies of Miller et al. (2004) and Austin et al. (2014a,b) by sequencing an additional species of Cherax from a very different environment at the northern extreme of the distribution of the genus. The C. monticola sample was collected from a population inhabiting Baliem River, Wamena, Papua. Approximately 40 mg of tail muscle tissue was dissected from an ethanol-preserved specimen and genomics DNA extraction was done using Qiagen DNAeasy Blood and Tissue Kits (Qiagen, Hilden, Germany). Partial whole genome sequencing (2 150 bp paired-end run),
Table 1. Annotation of the complete mitochondrial genome of C. monticola. Gene cox1 trnL2(taa) cox2 trnK(ttt) trnD(gtc) atp8 atp6 cox3 trnG(tcc) nad3 trnA(tgc) trnR(tcg) trnN(gtt) trnS1(tct) trnE(ttc)
Strand H H H H H H H H H H H H H H H
Position 1–1535 1536–1601 1603–2280 2298–2363 2364–2429 2431–2589 2583–3257 3257–4045 4043–4106 4162–4459 4459–4522 4523–4585 4589–4656 4657–4722 4722–4788
Length (bp) 1536 66 678 66 66 159 675 789 64 298 64 63 68 66 67
Intergenic nucleotides 2 0 1 17 0 1 7 1 3 55 1 0 3 0 1
Start codon
Stop codon
ACG
T
ATG
TAA
Anticodon UAA UUU GUC
ATG ATG ATG
TAA TAA TAA
ATA
T
UCC UGC UCG GUU UCU UUC (continued )
Correspondence: Han Ming Gan, School of Science, Monash Universiti Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Malaysia. E-mail: [email protected]
2
H. M. Gan et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Continued
Downloaded by [Monash University Library] at 15:56 10 November 2015
Gene trnF(gaa) nad5 trnH(gtg) trnT(tgt) nad6 trnP(tgg) rrnL trnV(tac) Control region trnQ(ttg) trnM(cat) nad2 trnW(tca) trnY(gta) nad4 nad4l cob trnS2(tga) nad1 trnL1(tag) rrnS trnI(gat) trnC(gca)
Strand
Position
Length (bp)
Intergenic nucleotides
L L L H H H L L – L H H H L L L H H L L L H L
4790–4853 4859–6583 6586–6650 6655–6718 6722–7255 7256–7322 7263–8653 8619–8686 8687–9627 9628–9696 9703–9768 9767–10,771 10,769–10,838 10,847–10,911 10,913–12,253 12,247–12,546 12,595–13,729 13,729–13,793 13,813–14,727 14,755–14,822 14,824–15,644 15,771–15,836 15,853–15,915
64 1725 65 64 534 67 1391 68 941 69 66 1005 70 65 1341 300 1135 65 915 68 821 66 63
1 5 2 4 3 0 60 35 0 0 6 2 3 8 1 7 48 1 19 27 1 126 16
mitogenome assembly and annotation were performed as previously described (Gan et al., 2014). The partial cox1 nucleotide sequence of C. quadricarinatus (GenBank accession number: DQ006294) was used as the initial bait for MITObim assembly (Hahn et al., 2013). The complete mitogenome of C. monticola is 15,917 bp in length (GenBank accession number: KF649851) and contains the typical 37 mitochondrial genes and an AT-rich non-coding region of 941 bp (Table 1). The base composition is 34% A, 33% T, 11% G and 21% C. The gene order in C. monticola is identical to that found in the currently available Cherax mitogenome, suggesting that the unusual gene order may be a common feature of the genus Cherax. Compared with the three well-known commercial species, C. motincola shows the highest similarity with the northern species, C. quadricarinatus (82.4%) and the least similarity with C. destructor (71.8%). It is expected that the present data will contribute to further phylogenetic and mitogenome-based comparative studies of freshwater crayfish.
Declaration of interest Funding for this study provided by the Monash University Malaysia Tropical Medicine and Biology Multidisciplinary Platform. The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
References Austin CM, Knott B. (1996). Sytematics of the freshwater crayfish genus Cherax (Decapo: Paratacidae) in south western Australia: Electrophoretic, morphological and habitat variation. Aust J Zool 44: 223–58. Austin CM, Tan MH, Croft LJ, Gan HM. (2014a). The complete mitogenome of the crayfish Cherax glaber (Crustacea: Decapoda: Parastacidae). Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/19401736.2014.880897. Austin CM, Tan MH, Croft LJ, Gan HM. (2014b). The complete mitogenome of the freshwater crayfish Cherax cainii (Crustacea: Decapoda: Parastacidae). Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/19401736.2013.878907. Austin CM. (1996). An electrophoretic and morphological taxonomic study of the freshwater crayfish genus Cherax
Start codon
Stop codon
TTG
TAG
Anticodon GAA GUG UGU
ATA
TAA UGG UAC UUG CAU
ATA
TAA UCA GUA
ATG ATG ATG
TAG TAA T
ATA
TAA
UGA UAG GAU GCA
(Decapoda: Parastacidae) in Northern and Eastern Australia. J Zool 44:259–96. Gan HM, Schultz MB, Austin CM. (2014). Integrated shotgun sequencing and bioinformatcs pipeline allows ultra-fast mitogenome recovery and confirms substantial gene rearrangements in Australian freshwater crayfishes. BMC Evol Biol 14:19. doi: 10.1186/1471-2148-14-19. Hahn C, Bachmann L, Chevreux B. (2013). Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads – A baiting and iterative mapping approach. Nucleic Acids Res 41:e129. doi: 10.1093/nar/gkt371. Holthuis LB. (1982). Freshwater crustacea decapoda of New Guinea. In: Gressit JL, editor. Monographiae biologicae. New York City: Springer. p 609–19. Kim S, Park M-H, Jung J-H, Ahn D-H, Sultana T, Kim S, Park J-K, et al. (2012). The mitochondrial genomes of Cambaroides similis and Procambarus clarkii (Decapoda: Astacidea: Cambaridae): The phylogenetic implications for Reptantia. Zool Scripta 41:281–92. Liu Y, Cui Z. (2011). Complete mitochondrial genome of the Chinese spiny lobster Panulirus stimpsoni (Crustacea: Decapoda): Genome characterization and phylogenetic considerations. Mol Biol Rep 38: 403–10. Masta SE, Longhorn SJ, Boore JL. (2009). Arachnid relationships based on mitochondrial genomes: Asymmetric nucleotide and amino acid bias affects phylogenetic analyses. Mol Phylogenet Evol 50:117–28. Miller AD, Austin CM. (2006). The complete mitochondrial genome of the mantid shrimp Harpiosquilla harpax, and a phylogenetic investigation of the Decapoda using mitochondrial sequences. Mol Phylogenet Evol 38:565–74. Miller AD, Nguyen TT, Burridge CP, Austin CM. (2004). Complete mitochondrial DNA sequence of the Australian freshwater crayfish, Cherax destructor (Crustacea: Decapodo: Parastacidae): A novel gene order revealed. Gene 331:65–72. Munasighe DHN, Burridge CP, Austin CM. (2004). Molecular phylogeny and zoogeography of the freshwater crayfish genus Cherax Erichson (Parastacidae: Decapoda) in Australia. Biol J Linnean Soc 81:553–63. Perseke M, Golombek A, Schlegel M, Struck TH. (2013). The impact of mitochondrial genome analyses on the understanding of deuterostome phylogeny. Mol Phylogenet Evol 66:898–905. Rota-Stabelli O, Kayal E, Gleeson D, Daub J, Boore JL, Telford MJ, Pisani D, et al. (2010). Ecdysozoan mitogenomics: Evidence for a common origin of the legged invertebrates, the Panarthropoda. Genome Biol Evol 2:425–40. Simon S, Hadrys H. (2013). A comparative analysis of complete mitochondrial genomes among Hexapoda. Mol Phylogenet Evol 15: 00155–3.
ISSN: 1940-1736 (Print) 1940-1744 (Online) Journal homepage: http://www.tandfonline.com/loi/imdn20
The complete mitogenome of Cherax monticola (Crustacea: Decapoda: Parastacidae), a large highland crayfish from New Guinea. Han Ming Gan, Mun Hua Tan, Rury Eprilurahman & Christopher M. Austin To cite this article: Han Ming Gan, Mun Hua Tan, Rury Eprilurahman & Christopher M. Austin (2014): The complete mitogenome of Cherax monticola (Crustacea: Decapoda: Parastacidae), a large highland crayfish from New Guinea., Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2014.892105
Published online: 11 Mar 2014.
Submit your article to this journal
Article views: 22
View related articles
View Crossmark data
Citing articles: 5 View citing articles
Full Terms & Conditions of access and use can be found at http://www.tandfonline.com/action/journalInformation?journalCode=imdn20 Download by: [Monash University Library]
Date: 10 November 2015, At: 15:56
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.892105
MITOGENOME ANNOUNCEMENT
The complete mitogenome of Cherax monticola (Crustacea: Decapoda: Parastacidae), a large highland crayfish from New Guinea. Han Ming Gan1, Mun Hua Tan1, Rury Eprilurahman2, and Christopher M. Austin1 School of Science, Monash University Malaysia, Selangor, Malaysia and 2Faculty of Biology, Universitas Gadjah Mada, Yogyakarta, Indonesia
Downloaded by [Monash University Library] at 15:56 10 November 2015
1
Abstract
Keywords
The complete mitochondrial genome of a highland freshwater crayfish, Cherax monticola, was recovered by shotgun sequencing. The mitogenome consists of 15,917 base pairs containing 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs and a non-coding AT-rich region. The base composition of C. monticola is 33.46% for T, 21.48% for C, 33.71% for A and 11.35% for G, with an AT bias of 67.17%.
Freshwater crayfish, mitogenome, Parastacidae
Freshwater crayfish of the genus Cherax are an ecological and commercially important group of decapod crustaceans that occur widely across Australia (Austin, 1996; Austin & Knott, 1996; Munasighe et al., 2004). The genus also extends into southern New Guinea where it is represented by a diversity of species from both highland and lowland environments (Holthuis, 1982). As in Australia, several New Guinea species grow to a large size and are the subject of indigenous fisheries and traded in local markets. Cherax monticola is a large highland species with a restricted distribution in the upper Baliem Valley, in the region near Wamena in the Papua province of Indonesia. Three species of Cherax from Australia have been sequenced for their mitogenome and they were all identified as having an unusual gene order rearrangement (Austin et al., 2014a,b; Miller et al., 2004). With an increasing interest in using information from whole
History Received 31 January 2014 Accepted 4 February 2014 Published online 11 March 2014
mitochondrial genomes for phylogenetic studies (Kim et al., 2012; Liu & Cui, 2011; Masta et al., 2009; Miller & Austin, 2006; Perseke et al., 2013; Rota-Stabelli et al., 2010; Simon & Hadrys, 2013) and the emergence of interesting patterns of mitochondrial gene order that demand explanation, this study was designed to extend the studies of Miller et al. (2004) and Austin et al. (2014a,b) by sequencing an additional species of Cherax from a very different environment at the northern extreme of the distribution of the genus. The C. monticola sample was collected from a population inhabiting Baliem River, Wamena, Papua. Approximately 40 mg of tail muscle tissue was dissected from an ethanol-preserved specimen and genomics DNA extraction was done using Qiagen DNAeasy Blood and Tissue Kits (Qiagen, Hilden, Germany). Partial whole genome sequencing (2 150 bp paired-end run),
Table 1. Annotation of the complete mitochondrial genome of C. monticola. Gene cox1 trnL2(taa) cox2 trnK(ttt) trnD(gtc) atp8 atp6 cox3 trnG(tcc) nad3 trnA(tgc) trnR(tcg) trnN(gtt) trnS1(tct) trnE(ttc)
Strand H H H H H H H H H H H H H H H
Position 1–1535 1536–1601 1603–2280 2298–2363 2364–2429 2431–2589 2583–3257 3257–4045 4043–4106 4162–4459 4459–4522 4523–4585 4589–4656 4657–4722 4722–4788
Length (bp) 1536 66 678 66 66 159 675 789 64 298 64 63 68 66 67
Intergenic nucleotides 2 0 1 17 0 1 7 1 3 55 1 0 3 0 1
Start codon
Stop codon
ACG
T
ATG
TAA
Anticodon UAA UUU GUC
ATG ATG ATG
TAA TAA TAA
ATA
T
UCC UGC UCG GUU UCU UUC (continued )
Correspondence: Han Ming Gan, School of Science, Monash Universiti Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Malaysia. E-mail: [email protected]
2
H. M. Gan et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Continued
Downloaded by [Monash University Library] at 15:56 10 November 2015
Gene trnF(gaa) nad5 trnH(gtg) trnT(tgt) nad6 trnP(tgg) rrnL trnV(tac) Control region trnQ(ttg) trnM(cat) nad2 trnW(tca) trnY(gta) nad4 nad4l cob trnS2(tga) nad1 trnL1(tag) rrnS trnI(gat) trnC(gca)
Strand
Position
Length (bp)
Intergenic nucleotides
L L L H H H L L – L H H H L L L H H L L L H L
4790–4853 4859–6583 6586–6650 6655–6718 6722–7255 7256–7322 7263–8653 8619–8686 8687–9627 9628–9696 9703–9768 9767–10,771 10,769–10,838 10,847–10,911 10,913–12,253 12,247–12,546 12,595–13,729 13,729–13,793 13,813–14,727 14,755–14,822 14,824–15,644 15,771–15,836 15,853–15,915
64 1725 65 64 534 67 1391 68 941 69 66 1005 70 65 1341 300 1135 65 915 68 821 66 63
1 5 2 4 3 0 60 35 0 0 6 2 3 8 1 7 48 1 19 27 1 126 16
mitogenome assembly and annotation were performed as previously described (Gan et al., 2014). The partial cox1 nucleotide sequence of C. quadricarinatus (GenBank accession number: DQ006294) was used as the initial bait for MITObim assembly (Hahn et al., 2013). The complete mitogenome of C. monticola is 15,917 bp in length (GenBank accession number: KF649851) and contains the typical 37 mitochondrial genes and an AT-rich non-coding region of 941 bp (Table 1). The base composition is 34% A, 33% T, 11% G and 21% C. The gene order in C. monticola is identical to that found in the currently available Cherax mitogenome, suggesting that the unusual gene order may be a common feature of the genus Cherax. Compared with the three well-known commercial species, C. motincola shows the highest similarity with the northern species, C. quadricarinatus (82.4%) and the least similarity with C. destructor (71.8%). It is expected that the present data will contribute to further phylogenetic and mitogenome-based comparative studies of freshwater crayfish.
Declaration of interest Funding for this study provided by the Monash University Malaysia Tropical Medicine and Biology Multidisciplinary Platform. The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
References Austin CM, Knott B. (1996). Sytematics of the freshwater crayfish genus Cherax (Decapo: Paratacidae) in south western Australia: Electrophoretic, morphological and habitat variation. Aust J Zool 44: 223–58. Austin CM, Tan MH, Croft LJ, Gan HM. (2014a). The complete mitogenome of the crayfish Cherax glaber (Crustacea: Decapoda: Parastacidae). Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/19401736.2014.880897. Austin CM, Tan MH, Croft LJ, Gan HM. (2014b). The complete mitogenome of the freshwater crayfish Cherax cainii (Crustacea: Decapoda: Parastacidae). Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/19401736.2013.878907. Austin CM. (1996). An electrophoretic and morphological taxonomic study of the freshwater crayfish genus Cherax
Start codon
Stop codon
TTG
TAG
Anticodon GAA GUG UGU
ATA
TAA UGG UAC UUG CAU
ATA
TAA UCA GUA
ATG ATG ATG
TAG TAA T
ATA
TAA
UGA UAG GAU GCA
(Decapoda: Parastacidae) in Northern and Eastern Australia. J Zool 44:259–96. Gan HM, Schultz MB, Austin CM. (2014). Integrated shotgun sequencing and bioinformatcs pipeline allows ultra-fast mitogenome recovery and confirms substantial gene rearrangements in Australian freshwater crayfishes. BMC Evol Biol 14:19. doi: 10.1186/1471-2148-14-19. Hahn C, Bachmann L, Chevreux B. (2013). Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads – A baiting and iterative mapping approach. Nucleic Acids Res 41:e129. doi: 10.1093/nar/gkt371. Holthuis LB. (1982). Freshwater crustacea decapoda of New Guinea. In: Gressit JL, editor. Monographiae biologicae. New York City: Springer. p 609–19. Kim S, Park M-H, Jung J-H, Ahn D-H, Sultana T, Kim S, Park J-K, et al. (2012). The mitochondrial genomes of Cambaroides similis and Procambarus clarkii (Decapoda: Astacidea: Cambaridae): The phylogenetic implications for Reptantia. Zool Scripta 41:281–92. Liu Y, Cui Z. (2011). Complete mitochondrial genome of the Chinese spiny lobster Panulirus stimpsoni (Crustacea: Decapoda): Genome characterization and phylogenetic considerations. Mol Biol Rep 38: 403–10. Masta SE, Longhorn SJ, Boore JL. (2009). Arachnid relationships based on mitochondrial genomes: Asymmetric nucleotide and amino acid bias affects phylogenetic analyses. Mol Phylogenet Evol 50:117–28. Miller AD, Austin CM. (2006). The complete mitochondrial genome of the mantid shrimp Harpiosquilla harpax, and a phylogenetic investigation of the Decapoda using mitochondrial sequences. Mol Phylogenet Evol 38:565–74. Miller AD, Nguyen TT, Burridge CP, Austin CM. (2004). Complete mitochondrial DNA sequence of the Australian freshwater crayfish, Cherax destructor (Crustacea: Decapodo: Parastacidae): A novel gene order revealed. Gene 331:65–72. Munasighe DHN, Burridge CP, Austin CM. (2004). Molecular phylogeny and zoogeography of the freshwater crayfish genus Cherax Erichson (Parastacidae: Decapoda) in Australia. Biol J Linnean Soc 81:553–63. Perseke M, Golombek A, Schlegel M, Struck TH. (2013). The impact of mitochondrial genome analyses on the understanding of deuterostome phylogeny. Mol Phylogenet Evol 66:898–905. Rota-Stabelli O, Kayal E, Gleeson D, Daub J, Boore JL, Telford MJ, Pisani D, et al. (2010). Ecdysozoan mitogenomics: Evidence for a common origin of the legged invertebrates, the Panarthropoda. Genome Biol Evol 2:425–40. Simon S, Hadrys H. (2013). A comparative analysis of complete mitochondrial genomes among Hexapoda. Mol Phylogenet Evol 15: 00155–3.
