http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.880897
MITOGENOME ANNOUNCEMENT
The complete mitogenome of the crayfish Cherax glaber (Crustacea: Decapoda: Parastacidae) Mitochondrial DNA Downloaded from informahealthcare.com by Biblioteka Uniwersytetu Warszawskiego on 03/07/15 For personal use only.
Christopher M. Austin1, Mun Hua Tan1, Laurence J. Croft2, and Han Ming Gan1 1
Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Selangor, Malaysia and 2Malaysian Genome Resource Centre Berhad, Boulevard Signature Office, Kuala Lumpur, Malaysia Abstract
Keywords
The complete mitochondrial genome of Cherax glaber was sequenced using the HiSeq platform. The mitogenome consists of 15,806 base pairs containing 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs and a non-coding AT-rich region. The Cherax glaber has a base composition of 32.39% for T, 22.42% for C, 33.73% for A and 11.46% for G, with an AT bias of 66.12%.
Freshwater crayfish, mitogenome, parastacidae
Freshwater crayfish of the genus Cherax are one of the dominant faunal elements of freshwater systems in Australia and are of intrinsic interest for studying the evolution and biogeography of Australian aquatic taxa (Austin & Knott, 1996; Miller et al., 2004; Munasighe et al., 2004). Despite its aridity the State of Western Australia has a diverse freshwater crayfish fauna, albeit limited to the cooler temperate south-west (Austin & Knott, 1996). Cherax glaber is a less studied small burrowing species with one of the most restricted distribution for Cherax species from this region. In this study, we provide the complete and annotated mitochondrial genome sequence for C. glaber
History Received 30 December 2013 Accepted 5 January 2014 Published online 31 January 2014
(Table 1), which makes it the third mitogenome for species of the genus Cherax. A tissue sample of C. glaber was obtained from an individual caught in a freshwater swamp, 1 km northwest of Dunsborough, southwest of Perth, Western Australia (Austin & Knott, 1996). Approximately 40 mg of abdominal muscle tissue was dissected from an ethanol-preserved sample and cut into small pieces. Genomics DNA was extracted using Qiagen DNAeasy Blood and Tissue Kits (Qiagen, Hilden, Germany) following the manufacturer’s instructions. The purified genomics DNA was processed using TruSeq DNA sample preparation kit (Illumina,
Table 1. Annotation of the complete mitochondrial genome of C. glaber. 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) trnF(gaa) nad5
Strand
Position
Length (bp)
H H H H H H H H H H H H H H H L L
1–1534 1535–1600 1602–2297 2312–2380 2384–2446 2448–2606 2600–3274 3274–4062 4061–4123 4125–4476 4476–4535 4536–4596 4596–4660 4661–4726 4726–4794 4798–4862 4863–6593
1535 66 696 69 63 159 675 789 63 352 60 61 65 66 69 65 1731
Intergenic nucleotides 2 0 1 14 3 1 7 1 2 1 1 0 1 0 1 3 0
Start codon
Stop codon
ACG
T
ATG
TAG
Anticodon UAA UUU GUC
ATG ATG ATG
TAA TAA TAA
ATC
T
UCC UGC UCG GUU UCU UUC GAA ATA
TAA (continued )
Correspondence: Han Ming Gan, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 46150 Petaling Jaya, Selangor, Malaysia. E-mail: [email protected]
2
C. M. Austin et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Continued
Mitochondrial DNA Downloaded from informahealthcare.com by Biblioteka Uniwersytetu Warszawskiego on 03/07/15 For personal use only.
Gene 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 H H H L L
6590–6653 6666–6732 6750–7304 7266–7331 7309–8688 8661–8728 8729–9515 9516–9584 9588–9654 9656–10,657 10,655–10,722 10,728–10,793 10,795–12,135 12,129–12,428 12,473–13,610 13,610–13,678 13,697–14,611 14,634–14,699 14,700–15,516 15,667–15,730 15,742–15,804
64 67 555 66 1380 68 787 69 67 1002 68 66 1341 300 1138 69 915 66 817 64 63
4 12 17 39 23 28 0 0 3 1 3 5 1 7 44 1 18 22 0 150 11
L H H H L L L H H L L L H L
San Diego, CA). Size estimation and quantification of the prepped library was performed using Bioanalyzer 2100 (Agilent, Santa Clara, CA) and KAPA Library Quantification kit (KAPA Biosystems, Cape Town, South Africa), respectively. Subsequently, the library was normalized to 2 nM and sequenced on the HiSeq 2000 sequencing system (Illumina, San Diego, CA) by the Malaysian Genomics Resource Centre (www.mgrc. com.my). The mitochondrial genome was reconstructed with MITObim (Hahn et al., 2013) using the partial cox1 gene of C. glaber (GenBank accession number: FJ965958) as the initial bait. The complete mitogenome was recovered, reoriented to the cox1 gene and annotated with MITOS (Bernt et al., 2012) and ORF Finder. The complete mitogenome of C. glaber is 15,806 bp in length (GenBank accession number: NC_022939) and contains the typical 37 genes and an AT-rich non-coding region of 787 bp. The base composition of the C. glaber mitogenome is 34% A, 33% T, 11% G and 22% C. The order of genes and the placement of the non-coding AT-rich region in C. glaber is identical to that found for Cherax cainii by Austin et al. (2014) but differs in the placement of the tRNAval, reported by Miller et al. in the mitogenome of Cherax destructor (Miller et al., 2004). The mitogenome of C. glaber is 82.6% similar to C. cainii and 73.6% similar to C. destructor which is consistent with their phylogenetic relationships and distribution (Munasighe et al., 2004). It is anticipated that these data will support new phylogeneticand mitogenome-based investigations of Australian freshwater crayfish.
Start codon
Stop codon
Anticodon GUG UGU
ATC
TAA UGG UAC UUG CAU
ATG
TAA UCA GUA
ATG ATG ATA
TAG TAA T
ATG
TAA
UGA UAG GAU GCA
Declaration of interest Funding for this study was 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 article.
References Austin CM, Knott B. (1996). Sytematics of the freshwater crayfish genus Cherax (Decapo: Paratacidae) in south western Australia: Electrophoretic, morphological and habitat variation. Austra J Zool 44:223–58. Austin CM, Tan MH, Croft LJ, Gan HM. (2014). The complete mitogenome of the freshwater crayfish Cherax cainii (Crustacea: Decapoda: Parastacidae). Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/19401736.2013.878907. Bernt M, Donath A, Juhling F, Externbrink F, Florentz C, Fritzsch G, Putz J, et al. (2012). MITOS: Improved de novo metazoan mitochondrial genome annotation. Mol Phylogenet Evol 69:313–19. 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 41:9. doi: 10.1093/nar/gkt371.. Miller AD, Nguyen TT, Burridge CP, Austin CM. (2004). Complete mitochondrial DNA sequence of the Australian freshwater crayfish, Cherax destructor (Crustacea: Decapoda: 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.
MITOGENOME ANNOUNCEMENT
The complete mitogenome of the crayfish Cherax glaber (Crustacea: Decapoda: Parastacidae) Mitochondrial DNA Downloaded from informahealthcare.com by Biblioteka Uniwersytetu Warszawskiego on 03/07/15 For personal use only.
Christopher M. Austin1, Mun Hua Tan1, Laurence J. Croft2, and Han Ming Gan1 1
Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Selangor, Malaysia and 2Malaysian Genome Resource Centre Berhad, Boulevard Signature Office, Kuala Lumpur, Malaysia Abstract
Keywords
The complete mitochondrial genome of Cherax glaber was sequenced using the HiSeq platform. The mitogenome consists of 15,806 base pairs containing 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs and a non-coding AT-rich region. The Cherax glaber has a base composition of 32.39% for T, 22.42% for C, 33.73% for A and 11.46% for G, with an AT bias of 66.12%.
Freshwater crayfish, mitogenome, parastacidae
Freshwater crayfish of the genus Cherax are one of the dominant faunal elements of freshwater systems in Australia and are of intrinsic interest for studying the evolution and biogeography of Australian aquatic taxa (Austin & Knott, 1996; Miller et al., 2004; Munasighe et al., 2004). Despite its aridity the State of Western Australia has a diverse freshwater crayfish fauna, albeit limited to the cooler temperate south-west (Austin & Knott, 1996). Cherax glaber is a less studied small burrowing species with one of the most restricted distribution for Cherax species from this region. In this study, we provide the complete and annotated mitochondrial genome sequence for C. glaber
History Received 30 December 2013 Accepted 5 January 2014 Published online 31 January 2014
(Table 1), which makes it the third mitogenome for species of the genus Cherax. A tissue sample of C. glaber was obtained from an individual caught in a freshwater swamp, 1 km northwest of Dunsborough, southwest of Perth, Western Australia (Austin & Knott, 1996). Approximately 40 mg of abdominal muscle tissue was dissected from an ethanol-preserved sample and cut into small pieces. Genomics DNA was extracted using Qiagen DNAeasy Blood and Tissue Kits (Qiagen, Hilden, Germany) following the manufacturer’s instructions. The purified genomics DNA was processed using TruSeq DNA sample preparation kit (Illumina,
Table 1. Annotation of the complete mitochondrial genome of C. glaber. 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) trnF(gaa) nad5
Strand
Position
Length (bp)
H H H H H H H H H H H H H H H L L
1–1534 1535–1600 1602–2297 2312–2380 2384–2446 2448–2606 2600–3274 3274–4062 4061–4123 4125–4476 4476–4535 4536–4596 4596–4660 4661–4726 4726–4794 4798–4862 4863–6593
1535 66 696 69 63 159 675 789 63 352 60 61 65 66 69 65 1731
Intergenic nucleotides 2 0 1 14 3 1 7 1 2 1 1 0 1 0 1 3 0
Start codon
Stop codon
ACG
T
ATG
TAG
Anticodon UAA UUU GUC
ATG ATG ATG
TAA TAA TAA
ATC
T
UCC UGC UCG GUU UCU UUC GAA ATA
TAA (continued )
Correspondence: Han Ming Gan, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 46150 Petaling Jaya, Selangor, Malaysia. E-mail: [email protected]
2
C. M. Austin et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Continued
Mitochondrial DNA Downloaded from informahealthcare.com by Biblioteka Uniwersytetu Warszawskiego on 03/07/15 For personal use only.
Gene 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 H H H L L
6590–6653 6666–6732 6750–7304 7266–7331 7309–8688 8661–8728 8729–9515 9516–9584 9588–9654 9656–10,657 10,655–10,722 10,728–10,793 10,795–12,135 12,129–12,428 12,473–13,610 13,610–13,678 13,697–14,611 14,634–14,699 14,700–15,516 15,667–15,730 15,742–15,804
64 67 555 66 1380 68 787 69 67 1002 68 66 1341 300 1138 69 915 66 817 64 63
4 12 17 39 23 28 0 0 3 1 3 5 1 7 44 1 18 22 0 150 11
L H H H L L L H H L L L H L
San Diego, CA). Size estimation and quantification of the prepped library was performed using Bioanalyzer 2100 (Agilent, Santa Clara, CA) and KAPA Library Quantification kit (KAPA Biosystems, Cape Town, South Africa), respectively. Subsequently, the library was normalized to 2 nM and sequenced on the HiSeq 2000 sequencing system (Illumina, San Diego, CA) by the Malaysian Genomics Resource Centre (www.mgrc. com.my). The mitochondrial genome was reconstructed with MITObim (Hahn et al., 2013) using the partial cox1 gene of C. glaber (GenBank accession number: FJ965958) as the initial bait. The complete mitogenome was recovered, reoriented to the cox1 gene and annotated with MITOS (Bernt et al., 2012) and ORF Finder. The complete mitogenome of C. glaber is 15,806 bp in length (GenBank accession number: NC_022939) and contains the typical 37 genes and an AT-rich non-coding region of 787 bp. The base composition of the C. glaber mitogenome is 34% A, 33% T, 11% G and 22% C. The order of genes and the placement of the non-coding AT-rich region in C. glaber is identical to that found for Cherax cainii by Austin et al. (2014) but differs in the placement of the tRNAval, reported by Miller et al. in the mitogenome of Cherax destructor (Miller et al., 2004). The mitogenome of C. glaber is 82.6% similar to C. cainii and 73.6% similar to C. destructor which is consistent with their phylogenetic relationships and distribution (Munasighe et al., 2004). It is anticipated that these data will support new phylogeneticand mitogenome-based investigations of Australian freshwater crayfish.
Start codon
Stop codon
Anticodon GUG UGU
ATC
TAA UGG UAC UUG CAU
ATG
TAA UCA GUA
ATG ATG ATA
TAG TAA T
ATG
TAA
UGA UAG GAU GCA
Declaration of interest Funding for this study was 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 article.
References Austin CM, Knott B. (1996). Sytematics of the freshwater crayfish genus Cherax (Decapo: Paratacidae) in south western Australia: Electrophoretic, morphological and habitat variation. Austra J Zool 44:223–58. Austin CM, Tan MH, Croft LJ, Gan HM. (2014). The complete mitogenome of the freshwater crayfish Cherax cainii (Crustacea: Decapoda: Parastacidae). Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/19401736.2013.878907. Bernt M, Donath A, Juhling F, Externbrink F, Florentz C, Fritzsch G, Putz J, et al. (2012). MITOS: Improved de novo metazoan mitochondrial genome annotation. Mol Phylogenet Evol 69:313–19. 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 41:9. doi: 10.1093/nar/gkt371.. Miller AD, Nguyen TT, Burridge CP, Austin CM. (2004). Complete mitochondrial DNA sequence of the Australian freshwater crayfish, Cherax destructor (Crustacea: Decapoda: 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.
