http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.895997
MITOGENOME ANNOUNCEMENT
The complete mitogenome of the red claw crayfish Cherax quadricarinatus (Von Martens, 1868) (Crustacea: Decapoda: Parastacidae)
Mitochondrial DNA Downloaded from informahealthcare.com by University of Maastricht on 06/27/14 For personal use only.
Han Ming Gan, Mun Hua Tan, and Christopher M. Austin Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Petaling Jaya, Selangor, Malaysia
Abstract
Keywords
The commercial freshwater crayfish Cherax quadricarinatus complete mitochondrial genome was recovered from partial genome sequencing using the MiSeq Personal Sequencer. The mitogenome has 15,869 base pairs consisting of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a non-coding AT-rich region. The base composition of C. quadricarinatus is 32.16% for T, 23.39% for C, 33.26% for A, and 11.19% for G, with an AT bias of 65.42%.
Freshwater crayfish, mitogenome, Parastacidae
The genus Cherax is a major group of freshwater crayfish in Australia and includes several large commercially important species (Huner, 1994; Saoud et al., 2013). Cherax quadricarinatus (Crustacea: Decapoda: Parastacidae) is one of the best known of these species, commonly know as the red claw, with a natural range across northern Australia that also extends into the southern most part of Papua New Guinea (Austin, 1996). In addition to its value as a commercial species for aquaculture in Australia, it has become a significant concern as an invasive species in tropical parts of the world including Africa, Asia and South America (Ahyong & Yeo, 2007; Baker et al., 2008; Saoud et al., 2013). In this study we present the complete mitogenome sequence for C. quadricarinatus, which makes it the fourth mitogenome for species of the genus Cherax. The C. quadricarinatus sample was obtained from a translocated population inhabiting a lake within the Subang Jaya
History Received 4 February 2014 Accepted 16 February 2014 Published online 11 March 2014
Recreational Park, Kuala Lumpur. Approximately 40 mg of tail muscle tissue was dissected from an ethanol-preserved specimen and cut into small pieces. The purification of genomic DNA, partial genome sequencing (2 150 bp paired-end run), mitogenome assembly and annotation were performed as previously described (Gan et al., 2014). The partial cox1 nucleotide sequence of C. quadricarinatus (GenBank accession number: EU244911) was used as the initial bait for MITObim assembly (Hahn et al., 2013). The C. quadricarinatus mitogenome is 15,869 bp in length (GenBank accession number: NC_022937) and contains the typical 37 mitochondrial genes and an AT-rich non-coding region of 925 bp (Table 1). The base composition is 33% A, 32% T, 11% G and 23% C and the order of genes is the same as in Cherax cainii and Cherax glaber (Austin et al., 2014a,b). The mitogenome of C. quadricarinatus is quite divergent from the
Table 1. Annotation of the complete mitochondrial genome of C. quadricarinatus. Gene cox1 trnL2(taa) cox2 trnK(ttt) trnD(gtc) atp8 atp6 cox3 trnG(tcc) nad3 trnA(tgc) trnR(tcg)
Strand
Position
Length (bp)
H H H H H H H H H H H H
1–1534 1535–1600 1602–2279 2289–2353 2354–2419 2421–2579 2573–3247 3247–4035 4033–4096 4098–4449 4449–4509 4510–4571
1535 66 678 65 66 159 675 789 64 352 61 62
Intergenic nucleotides 3 0 1 9 0 1 7 1 3 1 1 0
Start codon
Stop codon
ACG
T
ATG
TAA
Anticodon UAA UUU GUC
ATG ATG ATG
TAG TAA TAA
ATT
T
UCC UGC UCG (continued )
Correspondence: Han Ming Gan, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Petaling Jaya, Selangor, Malaysia. E-mail: [email protected]
2
H. M. Gan et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Continued
Mitochondrial DNA Downloaded from informahealthcare.com by University of Maastricht on 06/27/14 For personal use only.
Gene trnN(gtt) trnS1(tct) trnE(ttc) 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
H H H L L L H H H L L
4575–4639 4640–4705 4705–4770 4772–4835 4842–6569 6569–6634 6641–6705 6728–7242 7243–7306 7251–8622 8600–8667 8668–9592 9593–9661 9666–9732 9731–10,735 10,733–10,802 10,811–10,875 10,877–12,220 12,214–12,513 12,564–13,698 13,698–13,762 13,782–14,699 14,722–14,790 14,792–15,608 15,726–15,790 15,805–15,866
65 66 66 64 1728 66 65 515 64 1372 68 925 69 67 1005 70 65 1344 300 1135 65 918 69 817 65 62
3 0 1 1 6 1 6 22 0 56 23 0 0 4 2 3 8 1 7 50 1 19 22 1 117 14
L H H H L L L H H L L L H L
mitogenomes of the other commercial species, C. cainii (73.7%) and C. destructor (70.9%), which is consistent with studies based on mitochondrial gene fragments (Munasighe et al., 2004). Our sample of C. quadricarinatus is identical for a 482 bp region from the 16S rRNA gene to specimens sequenced by Baker et al. from the Calvert and McArthur Rivers (GenBank accession numbers: EU244883.1 and EU244883.2 respectively) from the eastern Northern Territory, Australia (Baker et al., 2008). We expect our data to be a valuable resource for population genetic and mitogenome comparative studies of C. quadricarinatus and related species.
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 Ahyong ST, Yeo DCJ. (2007). Feral populations of the Australian Red-Claw crayfish (Cherax quadricarinatus von Martens) in water supply catchments of Singapore. Biol Invasions 9:943–6. Austin CM. (1996). An electrophoretic and morphological taxonomic study of the freshwater crayfish genus Cherax (Decapoda: Parastacidae) in Northern and Eastern Australia. J Zool 44:259–96.
Start codon
Stop codon
Anticodon GUU UCU UUC GAA
ATG
TAA GUG UGU
ATT
TA UGG UAC UUG CAU
ATA
TAA UCA GUA
ATG ATG ATG
TAG TAA T
ATT
TAA
UGA UAG GAU GCA
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. Baker N, De Bruyn M, Mather PB. (2008). Patterns of molecular diversity in wild stocks of the redclaw crayfish (Cherax quadricarinatus) from northern Australia and Papua New Guinea: Impacts of Plio-Pleistocene landscape evolution. Freshwater Biol 53:1592–605. Gan HM, Schultz MB, Austin CM. (2014). Integrated shotgun sequencing and bioinformatics pipeline allows ultra-fast mitogenome recovery and confirms substantial gene rearrangements in Australian freshwater crayfishes. BMC Evol Biol 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. Huner JV. (1994). Freshwater crayfish aquaculture in North America, Europe and Australia: Families Astacidae, Cambaridae and Parastacidae. New York: The Haworth Press. Munasighe DHN, Burridge CP, Austin CM. (2004). Molecular phylogeny and zoogeography of the freshwater crayfish genus Cherax Erichson (Parastacidae: Decapoda) in Australia. Biol J Linn Soc 81:553–63. Saoud IP, Ghanawi J, Thompson KR, Webster CD. (2013). A review of the culture and diseases of Redclaw Crayfish Cherax quadricarinatus (Von Martens (1868)). J World Aquac Soc 44:1–29.
MITOGENOME ANNOUNCEMENT
The complete mitogenome of the red claw crayfish Cherax quadricarinatus (Von Martens, 1868) (Crustacea: Decapoda: Parastacidae)
Mitochondrial DNA Downloaded from informahealthcare.com by University of Maastricht on 06/27/14 For personal use only.
Han Ming Gan, Mun Hua Tan, and Christopher M. Austin Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Petaling Jaya, Selangor, Malaysia
Abstract
Keywords
The commercial freshwater crayfish Cherax quadricarinatus complete mitochondrial genome was recovered from partial genome sequencing using the MiSeq Personal Sequencer. The mitogenome has 15,869 base pairs consisting of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a non-coding AT-rich region. The base composition of C. quadricarinatus is 32.16% for T, 23.39% for C, 33.26% for A, and 11.19% for G, with an AT bias of 65.42%.
Freshwater crayfish, mitogenome, Parastacidae
The genus Cherax is a major group of freshwater crayfish in Australia and includes several large commercially important species (Huner, 1994; Saoud et al., 2013). Cherax quadricarinatus (Crustacea: Decapoda: Parastacidae) is one of the best known of these species, commonly know as the red claw, with a natural range across northern Australia that also extends into the southern most part of Papua New Guinea (Austin, 1996). In addition to its value as a commercial species for aquaculture in Australia, it has become a significant concern as an invasive species in tropical parts of the world including Africa, Asia and South America (Ahyong & Yeo, 2007; Baker et al., 2008; Saoud et al., 2013). In this study we present the complete mitogenome sequence for C. quadricarinatus, which makes it the fourth mitogenome for species of the genus Cherax. The C. quadricarinatus sample was obtained from a translocated population inhabiting a lake within the Subang Jaya
History Received 4 February 2014 Accepted 16 February 2014 Published online 11 March 2014
Recreational Park, Kuala Lumpur. Approximately 40 mg of tail muscle tissue was dissected from an ethanol-preserved specimen and cut into small pieces. The purification of genomic DNA, partial genome sequencing (2 150 bp paired-end run), mitogenome assembly and annotation were performed as previously described (Gan et al., 2014). The partial cox1 nucleotide sequence of C. quadricarinatus (GenBank accession number: EU244911) was used as the initial bait for MITObim assembly (Hahn et al., 2013). The C. quadricarinatus mitogenome is 15,869 bp in length (GenBank accession number: NC_022937) and contains the typical 37 mitochondrial genes and an AT-rich non-coding region of 925 bp (Table 1). The base composition is 33% A, 32% T, 11% G and 23% C and the order of genes is the same as in Cherax cainii and Cherax glaber (Austin et al., 2014a,b). The mitogenome of C. quadricarinatus is quite divergent from the
Table 1. Annotation of the complete mitochondrial genome of C. quadricarinatus. Gene cox1 trnL2(taa) cox2 trnK(ttt) trnD(gtc) atp8 atp6 cox3 trnG(tcc) nad3 trnA(tgc) trnR(tcg)
Strand
Position
Length (bp)
H H H H H H H H H H H H
1–1534 1535–1600 1602–2279 2289–2353 2354–2419 2421–2579 2573–3247 3247–4035 4033–4096 4098–4449 4449–4509 4510–4571
1535 66 678 65 66 159 675 789 64 352 61 62
Intergenic nucleotides 3 0 1 9 0 1 7 1 3 1 1 0
Start codon
Stop codon
ACG
T
ATG
TAA
Anticodon UAA UUU GUC
ATG ATG ATG
TAG TAA TAA
ATT
T
UCC UGC UCG (continued )
Correspondence: Han Ming Gan, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Petaling Jaya, Selangor, Malaysia. E-mail: [email protected]
2
H. M. Gan et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Continued
Mitochondrial DNA Downloaded from informahealthcare.com by University of Maastricht on 06/27/14 For personal use only.
Gene trnN(gtt) trnS1(tct) trnE(ttc) 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
H H H L L L H H H L L
4575–4639 4640–4705 4705–4770 4772–4835 4842–6569 6569–6634 6641–6705 6728–7242 7243–7306 7251–8622 8600–8667 8668–9592 9593–9661 9666–9732 9731–10,735 10,733–10,802 10,811–10,875 10,877–12,220 12,214–12,513 12,564–13,698 13,698–13,762 13,782–14,699 14,722–14,790 14,792–15,608 15,726–15,790 15,805–15,866
65 66 66 64 1728 66 65 515 64 1372 68 925 69 67 1005 70 65 1344 300 1135 65 918 69 817 65 62
3 0 1 1 6 1 6 22 0 56 23 0 0 4 2 3 8 1 7 50 1 19 22 1 117 14
L H H H L L L H H L L L H L
mitogenomes of the other commercial species, C. cainii (73.7%) and C. destructor (70.9%), which is consistent with studies based on mitochondrial gene fragments (Munasighe et al., 2004). Our sample of C. quadricarinatus is identical for a 482 bp region from the 16S rRNA gene to specimens sequenced by Baker et al. from the Calvert and McArthur Rivers (GenBank accession numbers: EU244883.1 and EU244883.2 respectively) from the eastern Northern Territory, Australia (Baker et al., 2008). We expect our data to be a valuable resource for population genetic and mitogenome comparative studies of C. quadricarinatus and related species.
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 Ahyong ST, Yeo DCJ. (2007). Feral populations of the Australian Red-Claw crayfish (Cherax quadricarinatus von Martens) in water supply catchments of Singapore. Biol Invasions 9:943–6. Austin CM. (1996). An electrophoretic and morphological taxonomic study of the freshwater crayfish genus Cherax (Decapoda: Parastacidae) in Northern and Eastern Australia. J Zool 44:259–96.
Start codon
Stop codon
Anticodon GUU UCU UUC GAA
ATG
TAA GUG UGU
ATT
TA UGG UAC UUG CAU
ATA
TAA UCA GUA
ATG ATG ATG
TAG TAA T
ATT
TAA
UGA UAG GAU GCA
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. Baker N, De Bruyn M, Mather PB. (2008). Patterns of molecular diversity in wild stocks of the redclaw crayfish (Cherax quadricarinatus) from northern Australia and Papua New Guinea: Impacts of Plio-Pleistocene landscape evolution. Freshwater Biol 53:1592–605. Gan HM, Schultz MB, Austin CM. (2014). Integrated shotgun sequencing and bioinformatics pipeline allows ultra-fast mitogenome recovery and confirms substantial gene rearrangements in Australian freshwater crayfishes. BMC Evol Biol 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. Huner JV. (1994). Freshwater crayfish aquaculture in North America, Europe and Australia: Families Astacidae, Cambaridae and Parastacidae. New York: The Haworth Press. Munasighe DHN, Burridge CP, Austin CM. (2004). Molecular phylogeny and zoogeography of the freshwater crayfish genus Cherax Erichson (Parastacidae: Decapoda) in Australia. Biol J Linn Soc 81:553–63. Saoud IP, Ghanawi J, Thompson KR, Webster CD. (2013). A review of the culture and diseases of Redclaw Crayfish Cherax quadricarinatus (Von Martens (1868)). J World Aquac Soc 44:1–29.
