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 the endangered freshwater crayfish Cherax tenuimanus (Smith 1912) (Crustacea: Decapoda: Parastacidae) Christopher M. Austin, Mun Hua Tan, Huan You Gan & Han Ming Gan To cite this article: Christopher M. Austin, Mun Hua Tan, Huan You Gan & Han Ming Gan (2015): The complete mitogenome of the endangered freshwater crayfish Cherax tenuimanus (Smith 1912) (Crustacea: Decapoda: Parastacidae), Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2014.1003900
Published online: 29 Jan 2015.
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Full Terms & Conditions of access and use can be found at http://www.tandfonline.com/action/journalInformation?journalCode=imdn20 Download by: [University of California Santa Barbara]
Date: 06 November 2015, At: 17:24
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2015 Informa UK Ltd. DOI: 10.3109/19401736.2014.1003900
MITOGENOME ANNOUNCEMENT
The complete mitogenome of the endangered freshwater crayfish Cherax tenuimanus (Smith 1912) (Crustacea: Decapoda: Parastacidae) Christopher M. Austin1,2, Mun Hua Tan1,2, Huan You Gan1,2, and Han Ming Gan1,2 Genomics Facility, Monash University Malaysia, Selangor, Malaysia and 2School of Science, Monash University Malaysia, Selangor, Malaysia
Downloaded by [University of California Santa Barbara] at 17:24 06 November 2015
1
Abstract
Keywords
Next-Gen sequencing was used to recover the complete mitochondrial genome of Cherax tenuimanus. The mitogenome consists of 15,797 base pairs (68.14% A + T content) containing 13 protein-coding genes, two ribosomal subunit genes, 22 transfer RNAs, and a 779 bp non-coding AT-rich region. Mitogenomes have now been recovered for all six species of Cherax native to Western Australia.
Astacidea, conservation, molecular resources
Australian freshwater crayfish includes several species of commercial significance (Huner, 1994) and several species are of conservation concern (Horwitz, 1995). One of the most threatened species of freshwater crayfish is Cherax tenuimanus, which is restricted to just a single river system, the Margaret River, in the south west of Western Australia (Austin & Ryan, 2002). The species is assessed by the IUCN as critically endangered and in decline (Austin & Bunn, 2010). The major threats to C. tenuimanus are competition and genetic introgression from its sibling species, Cherax cainii, which has invaded this river system (Austin & Ryan, 2002; Nguyen et al., 2002). In this study, we document the complete mitochondrial genome sequence for
History Received 12 December 2014 Accepted 19 December 2014 Published online 29 January 2015
C. tenuimanus, which makes it the final mitogenome to be obtained for species of the genus Cherax inhabiting the southwest of Western Australia. A tissue sample of C. tenuimanus was obtained from a sample caught from the upper Margaret River, approximately 15 km east of the Town of Margaret River, southwest of Perth, Western Australia. The purification of genomic DNA from leg muscle tissue, partial whole genome sequencing (2 150 bp paired-end run), mitogenome assembly, and annotation were performed as previously described (Gan et al., 2014). The mitochondrial genome was reconstructed with MITObim using the partial cox1 gene of C. tenuimanus (GenBank: AF510187) as the initial
Table 1. Annotation of the complete mitochondrial genome of Cherax tenuimanus.
Gene cox1 trnL2(taa) cox2 trnK(ttt) trnD(gtc) atp8 atp6 cox3 trnG(tcc) nad3 trnA(tgc) trnR(tcg) trnN(gtt)
Strand
Position
Length (bp)
H H H H H H H H H H H H H
1–1534 1536–1600 1601–2296 2312–2378 2381–2442 2443–2601 2595–3269 3269–4057 4056–4118 4119–4470 4471–4532 4533–4595 4595–4660
1534 65 696 67 62 159 675 789 63 352 62 63 66
Intergenic nucleotides 1 1 0 15 2 0 7 1 2 0 0 0 1
Start codon
Stop codon
ACG
T
ATG
TAG
Anticodon UAA UUU GUC
ATG ATG ATG
TAA TAA TAA
ATT
T
UCC UGC UCG GUU (continued )
Correspondence: Han Ming Gan, Genomics Facility, 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.
Downloaded by [University of California Santa Barbara] at 17:24 06 November 2015
Gene 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 L L L H H H L L H L H H H L L L H H L L L H L
4661–4726 4726–4792 4795–4859 4859–6586 6587–6650 6662–6725 6730–7251 7256–7321 7299–8677 8660–8729 8730–9508 9509–9577 9581–9647 9672–10,649 10,648–10,715 10,725–10,789 10,790–12,130 12,124–12,423 12,474–13,608 13,609–13,674 13,692–14,606 14,630–14,696 14,697–15,505 15,657–15,721 15,734–15,796
66 67 65 1728 64 64 522 66 1379 70 779 69 67 978 68 65 1341 300 1135 66 915 67 809 65 63
0 1 2 1 0 11 4 4 23 18 0 0 3 24 2 9 0 7 50 0 17 23 0 151 12
bait. The complete mitogenome was then annotated with MITOS and ORF Finder, and oriented starting from the cox1 gene. The base composition of the C. tenuimanus mitogenome is 34% A, 34% T, 11% G, and 21% C and is 15,797 bp in length (GenBank accession number: KP205429). The mitogenome has the typical 37 mitochondrial genes and a non-coding AT-rich region of 779 bp in length (Table 1) and the gene order is typical of that found for Cherax (Austin et al., 2014; Miller et al., 2004). The level of similarity between the C. tenuimanus and Cherax cainii complete mitogenomes is 89.9%, which is high for interspecific comparisons, but consistent with the close relationship between the two species (Munasinghe et al., 2004). This mitogenomic information will be a valuable resource for conservation genetic studies of this crayfish species.
Declaration of interest Funding for this study was provided by the Monash University Malaysia Tropical Medicine and Biology Multidisciplinary Platform. The authors report that they have no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
References Austin CM, Bunn J. (2010). Cherax tenuimanus. The IUCN Red List of Threatened Species. Version 2014.3. Available at: www.iucnredlist.org (Accessed 9 December 2009).
Start codon
Stop codon
Anticodon UCU UUC GAA
ATG
TAA GUG UGU
ATA
TAA UGG UAC UUG CAU
ATA
TAA UCA GUA
ATG ATG ATG
TAA TAA T
ATA
TAA
UGA UAG GAU GCA
Austin CM, Ryan SG. (2002). Allozyme evidence for a new species of freshwater crayfish of the genus Cherax erichson (Decapoda: Parastacidae) from the south-west of Western Australia. Invertebr Syst 16:357–67. 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. 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. Horwitz P. (1995). The conservation status of Australian freshwater crayfish: Review and update. Baton Rouge, LA: Louisiana State University. Huner JV. (1994). Freshwater crayfish aquaculture in North America, Europe, and Australia: families Astacidae, Cambaridae, and Parastacidae. New York: Food Products Press. 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. Munasinghe DHN, Burridge CP, Austin CM. (2004). Molecular phylogeny and zoogeography of the freshwater crayfish genus Cherax Erichson (Decapoda: Parastacidae) in Australia. Biol J Linnean Soc 81: 553–63. Nguyen TTT, Meewan M, Ryan S, Austin CM. (2002). Genetic diversity and translocation in the marron, Cherax tenuimanus (Smith): Implications for management and conservation. Fish Manag Ecol 9: 163–73.
ISSN: 1940-1736 (Print) 1940-1744 (Online) Journal homepage: http://www.tandfonline.com/loi/imdn20
The complete mitogenome of the endangered freshwater crayfish Cherax tenuimanus (Smith 1912) (Crustacea: Decapoda: Parastacidae) Christopher M. Austin, Mun Hua Tan, Huan You Gan & Han Ming Gan To cite this article: Christopher M. Austin, Mun Hua Tan, Huan You Gan & Han Ming Gan (2015): The complete mitogenome of the endangered freshwater crayfish Cherax tenuimanus (Smith 1912) (Crustacea: Decapoda: Parastacidae), Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2014.1003900
Published online: 29 Jan 2015.
Submit your article to this journal
Article views: 15
View related articles
View Crossmark data
Full Terms & Conditions of access and use can be found at http://www.tandfonline.com/action/journalInformation?journalCode=imdn20 Download by: [University of California Santa Barbara]
Date: 06 November 2015, At: 17:24
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2015 Informa UK Ltd. DOI: 10.3109/19401736.2014.1003900
MITOGENOME ANNOUNCEMENT
The complete mitogenome of the endangered freshwater crayfish Cherax tenuimanus (Smith 1912) (Crustacea: Decapoda: Parastacidae) Christopher M. Austin1,2, Mun Hua Tan1,2, Huan You Gan1,2, and Han Ming Gan1,2 Genomics Facility, Monash University Malaysia, Selangor, Malaysia and 2School of Science, Monash University Malaysia, Selangor, Malaysia
Downloaded by [University of California Santa Barbara] at 17:24 06 November 2015
1
Abstract
Keywords
Next-Gen sequencing was used to recover the complete mitochondrial genome of Cherax tenuimanus. The mitogenome consists of 15,797 base pairs (68.14% A + T content) containing 13 protein-coding genes, two ribosomal subunit genes, 22 transfer RNAs, and a 779 bp non-coding AT-rich region. Mitogenomes have now been recovered for all six species of Cherax native to Western Australia.
Astacidea, conservation, molecular resources
Australian freshwater crayfish includes several species of commercial significance (Huner, 1994) and several species are of conservation concern (Horwitz, 1995). One of the most threatened species of freshwater crayfish is Cherax tenuimanus, which is restricted to just a single river system, the Margaret River, in the south west of Western Australia (Austin & Ryan, 2002). The species is assessed by the IUCN as critically endangered and in decline (Austin & Bunn, 2010). The major threats to C. tenuimanus are competition and genetic introgression from its sibling species, Cherax cainii, which has invaded this river system (Austin & Ryan, 2002; Nguyen et al., 2002). In this study, we document the complete mitochondrial genome sequence for
History Received 12 December 2014 Accepted 19 December 2014 Published online 29 January 2015
C. tenuimanus, which makes it the final mitogenome to be obtained for species of the genus Cherax inhabiting the southwest of Western Australia. A tissue sample of C. tenuimanus was obtained from a sample caught from the upper Margaret River, approximately 15 km east of the Town of Margaret River, southwest of Perth, Western Australia. The purification of genomic DNA from leg muscle tissue, partial whole genome sequencing (2 150 bp paired-end run), mitogenome assembly, and annotation were performed as previously described (Gan et al., 2014). The mitochondrial genome was reconstructed with MITObim using the partial cox1 gene of C. tenuimanus (GenBank: AF510187) as the initial
Table 1. Annotation of the complete mitochondrial genome of Cherax tenuimanus.
Gene cox1 trnL2(taa) cox2 trnK(ttt) trnD(gtc) atp8 atp6 cox3 trnG(tcc) nad3 trnA(tgc) trnR(tcg) trnN(gtt)
Strand
Position
Length (bp)
H H H H H H H H H H H H H
1–1534 1536–1600 1601–2296 2312–2378 2381–2442 2443–2601 2595–3269 3269–4057 4056–4118 4119–4470 4471–4532 4533–4595 4595–4660
1534 65 696 67 62 159 675 789 63 352 62 63 66
Intergenic nucleotides 1 1 0 15 2 0 7 1 2 0 0 0 1
Start codon
Stop codon
ACG
T
ATG
TAG
Anticodon UAA UUU GUC
ATG ATG ATG
TAA TAA TAA
ATT
T
UCC UGC UCG GUU (continued )
Correspondence: Han Ming Gan, Genomics Facility, 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.
Downloaded by [University of California Santa Barbara] at 17:24 06 November 2015
Gene 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 L L L H H H L L H L H H H L L L H H L L L H L
4661–4726 4726–4792 4795–4859 4859–6586 6587–6650 6662–6725 6730–7251 7256–7321 7299–8677 8660–8729 8730–9508 9509–9577 9581–9647 9672–10,649 10,648–10,715 10,725–10,789 10,790–12,130 12,124–12,423 12,474–13,608 13,609–13,674 13,692–14,606 14,630–14,696 14,697–15,505 15,657–15,721 15,734–15,796
66 67 65 1728 64 64 522 66 1379 70 779 69 67 978 68 65 1341 300 1135 66 915 67 809 65 63
0 1 2 1 0 11 4 4 23 18 0 0 3 24 2 9 0 7 50 0 17 23 0 151 12
bait. The complete mitogenome was then annotated with MITOS and ORF Finder, and oriented starting from the cox1 gene. The base composition of the C. tenuimanus mitogenome is 34% A, 34% T, 11% G, and 21% C and is 15,797 bp in length (GenBank accession number: KP205429). The mitogenome has the typical 37 mitochondrial genes and a non-coding AT-rich region of 779 bp in length (Table 1) and the gene order is typical of that found for Cherax (Austin et al., 2014; Miller et al., 2004). The level of similarity between the C. tenuimanus and Cherax cainii complete mitogenomes is 89.9%, which is high for interspecific comparisons, but consistent with the close relationship between the two species (Munasinghe et al., 2004). This mitogenomic information will be a valuable resource for conservation genetic studies of this crayfish species.
Declaration of interest Funding for this study was provided by the Monash University Malaysia Tropical Medicine and Biology Multidisciplinary Platform. The authors report that they have no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
References Austin CM, Bunn J. (2010). Cherax tenuimanus. The IUCN Red List of Threatened Species. Version 2014.3. Available at: www.iucnredlist.org (Accessed 9 December 2009).
Start codon
Stop codon
Anticodon UCU UUC GAA
ATG
TAA GUG UGU
ATA
TAA UGG UAC UUG CAU
ATA
TAA UCA GUA
ATG ATG ATG
TAA TAA T
ATA
TAA
UGA UAG GAU GCA
Austin CM, Ryan SG. (2002). Allozyme evidence for a new species of freshwater crayfish of the genus Cherax erichson (Decapoda: Parastacidae) from the south-west of Western Australia. Invertebr Syst 16:357–67. 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. 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. Horwitz P. (1995). The conservation status of Australian freshwater crayfish: Review and update. Baton Rouge, LA: Louisiana State University. Huner JV. (1994). Freshwater crayfish aquaculture in North America, Europe, and Australia: families Astacidae, Cambaridae, and Parastacidae. New York: Food Products Press. 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. Munasinghe DHN, Burridge CP, Austin CM. (2004). Molecular phylogeny and zoogeography of the freshwater crayfish genus Cherax Erichson (Decapoda: Parastacidae) in Australia. Biol J Linnean Soc 81: 553–63. Nguyen TTT, Meewan M, Ryan S, Austin CM. (2002). Genetic diversity and translocation in the marron, Cherax tenuimanus (Smith): Implications for management and conservation. Fish Manag Ecol 9: 163–73.
