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 Australian spiny crayfish Euastacus yarraensis (McCoy, 1888) (Crustacea: Decapoda: Parastacidae) Han Ming Gan, Mun Hua Tan & Christopher M. Austin To cite this article: Han Ming Gan, Mun Hua Tan & Christopher M. Austin (2014): The complete mitogenome of the Australian spiny crayfish Euastacus yarraensis (McCoy, 1888) (Crustacea: Decapoda: Parastacidae), Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2014.926490
Published online: 18 Jun 2014.
Submit your article to this journal
Article views: 20
View related articles
View Crossmark data
Citing articles: 1 View citing articles
Full Terms & Conditions of access and use can be found at http://www.tandfonline.com/action/journalInformation?journalCode=imdn20 Download by: [Deakin University Library]
Date: 05 November 2015, At: 22:09
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.926490
MITOGENOME ANNOUNCEMENT
The complete mitogenome of the Australian spiny crayfish Euastacus yarraensis (McCoy, 1888) (Crustacea: Decapoda: Parastacidae) Han Ming Gan, Mun Hua Tan, and Christopher M. Austin
Downloaded by [Deakin University Library] at 22:09 05 November 2015
School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Petaling Jaya, Selangor, Malaysia
Abstract
Keywords
The mitochondrial genome sequence of the Australian crayfish, Euastacus yarraensis, is documented and compared with other Australian crayfish genera. Euastacus yarraensis has a mitogenome of 15,548 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 E. yarraensis mitogenome is 32.39% for T, 22.45% for C, 34.43% for A, and 10.73% for G, with an AT bias of 66.82%. The mitogenome gene order conforms to what is considered the primitive arrangement for parastacid crayfish.
Freshwater crayfish, mitogenome, Parastacidae
One of the most distinctive members of Australia’s rich freshwater crayfish fauna are the spiny crayfish placed in the closely related genera Astacopsis Huxley and Euastacus Clark (Clark, 1936; Crandall et al., 1999; Riek, 1969; Shull et al., 2005). Members of these genera are generally long lived, adapted to cold waters and some can reach weights of several kilograms, making them the largest freshwater invertebrates in the world (Riek, 1969). Due to their life history (slow growing, late maturing and relatively low fecundity) and specific habitat requirements, several species are of conservation concerns (Honan & Mitchell, 1995; Horwitz, 1995). The genus Euastacus is one of the most diverse and wide ranging of all the parastacid crayfish genera and is thought to comprise over 40 species (Schultz et al., 2007). Mitogenomes of several representatives of the Australian crayfish genera have been sequenced (Austin et al., 2014a,b; Gan et al., 2014a,b,c,e; Miller et al., 2004) and they all share a distinctive gene order for the major genes (Miller et al., 2004). Minor differences between genera have been found with respect to the position of several tRNA genes (Gan et al., 2014d,e). To further explore the mitogenome evolution in freshwater crayfish, the complete mitogenome of Euastacus yarraensis was sequenced. The E. yarraensis sample was caught from Retreat Creek, east of Birregurra, Victoria, Australia (sample code: MBS183) by M. B. Schultz. The purification of genomic DNA from ethanolpreserved 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., 2014a). Sanger sequencing was performed to close a 22 bp gap located at the control region. The partial 16S rRNA gene sequence of E. yarraensis voucher KC2831 (GenBank accession number: DQ006665) was used as the initial bait for MITObim assembly. The E. yarraensis mitochondrial genome is 15,548 bp in length (GenBank accession number: HG942176), has 37 mitochondrial
Correspondence: Han Ming Gan, School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 46150 Petaling Jaya, Selangor, Malaysia. E-mail: [email protected]
History Received 27 April 2014 Accepted 9 May 2014 Published online 18 June 2014
genes (13 protein-coding genes, 2 rRNAs and 22 tRNAs) and a non-coding region of 760 bp (Table 1). This is the shortest noncoding region (putative control region) thus far reported in Table 1. Annotation of the complete mitochondrial genome of Euastacus yarraensis.
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 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)
Strand
Position
H H H H H H H H H H H H H H H L L L H H H L L H L H H H L L L H H
1–1534 1535–1599 1601–2299 2309–2373 2374–2437 2439–2597 2591–3265 3265–4053 4051–4113 4115–4466 4466–4525 4526–4586 4587–4650 4651–4716 4716–4780 4784–4847 4853–6580 6580–6645 6656–6719 6732–7268 7272–7337 7315–8681 8650–8715 8716–9212 9213–9281 9284–9350 9352–10,353 10,351–10,418 10,430–10,493 10,496–11,833 11,827–12,126 12,174–13,308 13,308–13,373
Length Intergenic Start Stop (bp) nucleotides codon codon Anticodon 1534 65 699 65 64 159 675 789 63 352 60 61 64 66 65 64 1728 66 64 537 66 1367 66 630 69 67 1002 68 64 1338 300 1135 66
11 0 1 9 0 1 7 1 3 1 1 0 0 0 1 3 5 1 10 12 3 23 32 0 0 2 1 3 11 2 7 47 1
ACG
T
ATG
TAG
UAA UUU GUC ATG ATG ATG
TAA TAA TAA
ATT
T
UCC UGC UCG GUU UCU UUC GAA ATG
TAG GUG UGU
ATA
TAA UGG UAC UUG CAU
ATG
TAG UCA GUA
ATG ATG ATG
TAG TAA T UGA
(continued )
2
H. M. Gan et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Continued
Gene
Strand
Position
L L L H L
13,404–14,318 14,339–14,403 14,417–15,251 15,401–15,465 15,475–15,537
Downloaded by [Deakin University Library] at 22:09 05 November 2015
nad1 trnL1(tag) rrnS trnI(gat) trnC(gca)
Length Intergenic Start Stop (bp) nucleotides codon codon Anticodon 915 65 835 65 63
30 20 13 149 9
ATA
TAA UAG GAU GCA
parastacid crayfish. The base composition is 34% A, 32% T, 11% G and 22% C and the order of genes is identical to Cherax (Austin et al., 2014a,b; Gan et al., 2014b,c; Miller et al., 2004) but differs slightly from Engaeus and Geocharax species with respect to the position of several tRNA genes (Gan et al., 2014a,d). Our sample of E. yarraensis is almost identical (487 out of 488 bp) for a fragment of the 16S rRNA region from a crayfish sampled from Cockatoo Ck, Victoria (GenBank accession number: DQ006664) (Shull et al., 2005). We anticipate that this mitogenome will be used with other parastacid mitogenomes to investigate mitogenome evolution in crayfish and the phylogeny of spiny crayfish.
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 paper. We are grateful to M. B. Schultz for collecting and providing the sample.
References 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. Clark E. (1936). The freshwater and land crayfishes of Australia. Mem Natl Museum Victoria 10:5–58.
Crandall KA, Fetzner J, James W, Lawler SH, Kinnersley M, Austin CM. (1999). Phylogenetic relationships among the Australian and New Zealand genera of freshwater crayfishes (Decapoda: Parastacidae). Aus J Zool 47:199–214. Gan HM, Schultz MB, Austin CM. (2014a). 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. Gan HM, Tan MH, Austin CM. (2014b). The complete mitogenome of the red claw crayfish Cherax quadricarinatus (Von Martens 1868) (Crustacea: Decapoda: Parastacidae). Mitochondrial DNA. [Epub ahead of print]. doi:10.3109/19401736.2014.895997. Gan HM, Tan MH, Eprilurahman R, Austin CM. (2014c). The complete mitogenome of Cherax monticola (Crustacea: Decapoda: Parastacidae), a large highland crayfish from New Guinea. Mitochondrial DNA. [Epub ahead of print]. doi:10.3109/ 19401736.2014.892105. Gan HM, Tan MH, Gan HY, Lee YP, Schultz MB, Austin CM. (2014d). The complete mitogenome of the Australian crayfish Geocharax gracilis Clark 1936 (Crustacea: Decapoda: Parastacidae). Mitochondrial DNA, Accepted for publication. Gan HM, Tan MH, Lee YP, Schultz MB, Austin CM. (2014e). The complete mitogenome of the Australian land crayfish Engaeus lyelli (Crustacea: Decapoda: Parastacidae). Mitochondrial DNA. [Epub ahead of print]. doi:10.3109/19401736.2014.908361. Honan JA, Mitchell BD. (1995). Growth of the large freshwater crayfish Euastacus bispinosus Clark (Decapoda: Parastacidae). Freshwater Crayfish 10:118–31. Horwitz P. (1995). The conservation status of Australian freshwater Crayfish: Review and update. Freshwater Crayfish 10:70–80. 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. Riek E. (1969). The Australian freshwater crayfish (Crustacea: Decapoda: Parastacidae), with descriptions of a new species. Aus J Zool 17: 855–918. Schultz MB, Smith SA, Richardson AMM, Horwitz P, Crandall KA, Austin CM. (2007). Cryptic diversity in Engaeus Erichson, Geocharax Clark and Gramastacus Riek (Decapoda: Parastacidae) revealed by mitochondrial 16S rDNA sequences. Invert Systematics 21:569–87. Shull HC, Perez-Losada M, Blair D, Sewell K, Sinclair EA, Lawler S, Ponniah M, Crandall KA. (2005). Phylogeny and biogeography of the freshwater crayfish Euastacus (Decapoda: Parastacidae) based on nuclear and mitochondrial DNA. Mol Phylogenet Evol 37:249–63.
ISSN: 1940-1736 (Print) 1940-1744 (Online) Journal homepage: http://www.tandfonline.com/loi/imdn20
The complete mitogenome of the Australian spiny crayfish Euastacus yarraensis (McCoy, 1888) (Crustacea: Decapoda: Parastacidae) Han Ming Gan, Mun Hua Tan & Christopher M. Austin To cite this article: Han Ming Gan, Mun Hua Tan & Christopher M. Austin (2014): The complete mitogenome of the Australian spiny crayfish Euastacus yarraensis (McCoy, 1888) (Crustacea: Decapoda: Parastacidae), Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2014.926490
Published online: 18 Jun 2014.
Submit your article to this journal
Article views: 20
View related articles
View Crossmark data
Citing articles: 1 View citing articles
Full Terms & Conditions of access and use can be found at http://www.tandfonline.com/action/journalInformation?journalCode=imdn20 Download by: [Deakin University Library]
Date: 05 November 2015, At: 22:09
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.926490
MITOGENOME ANNOUNCEMENT
The complete mitogenome of the Australian spiny crayfish Euastacus yarraensis (McCoy, 1888) (Crustacea: Decapoda: Parastacidae) Han Ming Gan, Mun Hua Tan, and Christopher M. Austin
Downloaded by [Deakin University Library] at 22:09 05 November 2015
School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Petaling Jaya, Selangor, Malaysia
Abstract
Keywords
The mitochondrial genome sequence of the Australian crayfish, Euastacus yarraensis, is documented and compared with other Australian crayfish genera. Euastacus yarraensis has a mitogenome of 15,548 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 E. yarraensis mitogenome is 32.39% for T, 22.45% for C, 34.43% for A, and 10.73% for G, with an AT bias of 66.82%. The mitogenome gene order conforms to what is considered the primitive arrangement for parastacid crayfish.
Freshwater crayfish, mitogenome, Parastacidae
One of the most distinctive members of Australia’s rich freshwater crayfish fauna are the spiny crayfish placed in the closely related genera Astacopsis Huxley and Euastacus Clark (Clark, 1936; Crandall et al., 1999; Riek, 1969; Shull et al., 2005). Members of these genera are generally long lived, adapted to cold waters and some can reach weights of several kilograms, making them the largest freshwater invertebrates in the world (Riek, 1969). Due to their life history (slow growing, late maturing and relatively low fecundity) and specific habitat requirements, several species are of conservation concerns (Honan & Mitchell, 1995; Horwitz, 1995). The genus Euastacus is one of the most diverse and wide ranging of all the parastacid crayfish genera and is thought to comprise over 40 species (Schultz et al., 2007). Mitogenomes of several representatives of the Australian crayfish genera have been sequenced (Austin et al., 2014a,b; Gan et al., 2014a,b,c,e; Miller et al., 2004) and they all share a distinctive gene order for the major genes (Miller et al., 2004). Minor differences between genera have been found with respect to the position of several tRNA genes (Gan et al., 2014d,e). To further explore the mitogenome evolution in freshwater crayfish, the complete mitogenome of Euastacus yarraensis was sequenced. The E. yarraensis sample was caught from Retreat Creek, east of Birregurra, Victoria, Australia (sample code: MBS183) by M. B. Schultz. The purification of genomic DNA from ethanolpreserved 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., 2014a). Sanger sequencing was performed to close a 22 bp gap located at the control region. The partial 16S rRNA gene sequence of E. yarraensis voucher KC2831 (GenBank accession number: DQ006665) was used as the initial bait for MITObim assembly. The E. yarraensis mitochondrial genome is 15,548 bp in length (GenBank accession number: HG942176), has 37 mitochondrial
Correspondence: Han Ming Gan, School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 46150 Petaling Jaya, Selangor, Malaysia. E-mail: [email protected]
History Received 27 April 2014 Accepted 9 May 2014 Published online 18 June 2014
genes (13 protein-coding genes, 2 rRNAs and 22 tRNAs) and a non-coding region of 760 bp (Table 1). This is the shortest noncoding region (putative control region) thus far reported in Table 1. Annotation of the complete mitochondrial genome of Euastacus yarraensis.
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 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)
Strand
Position
H H H H H H H H H H H H H H H L L L H H H L L H L H H H L L L H H
1–1534 1535–1599 1601–2299 2309–2373 2374–2437 2439–2597 2591–3265 3265–4053 4051–4113 4115–4466 4466–4525 4526–4586 4587–4650 4651–4716 4716–4780 4784–4847 4853–6580 6580–6645 6656–6719 6732–7268 7272–7337 7315–8681 8650–8715 8716–9212 9213–9281 9284–9350 9352–10,353 10,351–10,418 10,430–10,493 10,496–11,833 11,827–12,126 12,174–13,308 13,308–13,373
Length Intergenic Start Stop (bp) nucleotides codon codon Anticodon 1534 65 699 65 64 159 675 789 63 352 60 61 64 66 65 64 1728 66 64 537 66 1367 66 630 69 67 1002 68 64 1338 300 1135 66
11 0 1 9 0 1 7 1 3 1 1 0 0 0 1 3 5 1 10 12 3 23 32 0 0 2 1 3 11 2 7 47 1
ACG
T
ATG
TAG
UAA UUU GUC ATG ATG ATG
TAA TAA TAA
ATT
T
UCC UGC UCG GUU UCU UUC GAA ATG
TAG GUG UGU
ATA
TAA UGG UAC UUG CAU
ATG
TAG UCA GUA
ATG ATG ATG
TAG TAA T UGA
(continued )
2
H. M. Gan et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Continued
Gene
Strand
Position
L L L H L
13,404–14,318 14,339–14,403 14,417–15,251 15,401–15,465 15,475–15,537
Downloaded by [Deakin University Library] at 22:09 05 November 2015
nad1 trnL1(tag) rrnS trnI(gat) trnC(gca)
Length Intergenic Start Stop (bp) nucleotides codon codon Anticodon 915 65 835 65 63
30 20 13 149 9
ATA
TAA UAG GAU GCA
parastacid crayfish. The base composition is 34% A, 32% T, 11% G and 22% C and the order of genes is identical to Cherax (Austin et al., 2014a,b; Gan et al., 2014b,c; Miller et al., 2004) but differs slightly from Engaeus and Geocharax species with respect to the position of several tRNA genes (Gan et al., 2014a,d). Our sample of E. yarraensis is almost identical (487 out of 488 bp) for a fragment of the 16S rRNA region from a crayfish sampled from Cockatoo Ck, Victoria (GenBank accession number: DQ006664) (Shull et al., 2005). We anticipate that this mitogenome will be used with other parastacid mitogenomes to investigate mitogenome evolution in crayfish and the phylogeny of spiny crayfish.
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 paper. We are grateful to M. B. Schultz for collecting and providing the sample.
References 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. Clark E. (1936). The freshwater and land crayfishes of Australia. Mem Natl Museum Victoria 10:5–58.
Crandall KA, Fetzner J, James W, Lawler SH, Kinnersley M, Austin CM. (1999). Phylogenetic relationships among the Australian and New Zealand genera of freshwater crayfishes (Decapoda: Parastacidae). Aus J Zool 47:199–214. Gan HM, Schultz MB, Austin CM. (2014a). 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. Gan HM, Tan MH, Austin CM. (2014b). The complete mitogenome of the red claw crayfish Cherax quadricarinatus (Von Martens 1868) (Crustacea: Decapoda: Parastacidae). Mitochondrial DNA. [Epub ahead of print]. doi:10.3109/19401736.2014.895997. Gan HM, Tan MH, Eprilurahman R, Austin CM. (2014c). The complete mitogenome of Cherax monticola (Crustacea: Decapoda: Parastacidae), a large highland crayfish from New Guinea. Mitochondrial DNA. [Epub ahead of print]. doi:10.3109/ 19401736.2014.892105. Gan HM, Tan MH, Gan HY, Lee YP, Schultz MB, Austin CM. (2014d). The complete mitogenome of the Australian crayfish Geocharax gracilis Clark 1936 (Crustacea: Decapoda: Parastacidae). Mitochondrial DNA, Accepted for publication. Gan HM, Tan MH, Lee YP, Schultz MB, Austin CM. (2014e). The complete mitogenome of the Australian land crayfish Engaeus lyelli (Crustacea: Decapoda: Parastacidae). Mitochondrial DNA. [Epub ahead of print]. doi:10.3109/19401736.2014.908361. Honan JA, Mitchell BD. (1995). Growth of the large freshwater crayfish Euastacus bispinosus Clark (Decapoda: Parastacidae). Freshwater Crayfish 10:118–31. Horwitz P. (1995). The conservation status of Australian freshwater Crayfish: Review and update. Freshwater Crayfish 10:70–80. 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. Riek E. (1969). The Australian freshwater crayfish (Crustacea: Decapoda: Parastacidae), with descriptions of a new species. Aus J Zool 17: 855–918. Schultz MB, Smith SA, Richardson AMM, Horwitz P, Crandall KA, Austin CM. (2007). Cryptic diversity in Engaeus Erichson, Geocharax Clark and Gramastacus Riek (Decapoda: Parastacidae) revealed by mitochondrial 16S rDNA sequences. Invert Systematics 21:569–87. Shull HC, Perez-Losada M, Blair D, Sewell K, Sinclair EA, Lawler S, Ponniah M, Crandall KA. (2005). Phylogeny and biogeography of the freshwater crayfish Euastacus (Decapoda: Parastacidae) based on nuclear and mitochondrial DNA. Mol Phylogenet Evol 37:249–63.
