http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.908361
MITOGENOME ANNOUNCEMENT
The complete mitogenome of the Australian land crayfish Engaeus lyelli (Clark 1936) (Crustacea: Decapoda: Parastacidae) Han Ming Gan1, Mun Hua Tan1, Yin Peng Lee1, Mark B. Schultz2, and Christopher M. Austin1 School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Petaling Jaya, Selangor, Malaysia, and 2Faculty of Medical and Dental Health Sciences, The University of Melbourne, Bio21 Research Institute, Victoria, Australia
Mitochondrial DNA Downloaded from informahealthcare.com by Kainan University on 04/20/15 For personal use only.
1
Abstract
Keywords
The complete mitochondrial genome of the enigmatic freshwater crayfish Engaeus lyelli was sequenced using the MiSeq Personal Sequencer (Illumina, San Diego, CA). The mitogenome has 16,027 bp consisting of 13 protein-coding genes, 2 ribosomal subunit genes, 23 transfer RNAs, and a non-coding AT-rich region. The base composition of E. lyelli is 29.01% for T, 27.13% for C, 31.43% for A, and 12.44% for G, with an AT bias of 60.44%. The species has the distinctive gene order characteristic of parastacid crayfish with the exception of some minor rearrangements involving the tRNA genes.
Freshwater crayfish, mitogenome, Parastacidae
Australia has a significant freshwater crayfish fauna with approximately 150 species placed in 10 genera (Crandall et al., 1999; Schultz et al., 2009). One of the most diverse and unusual of these genera is the genus Engaeus, which contains species, which burrow strongly and can complete their life cycle underground (Horwitz & Richardson, 1986). The species Engaeus lyelli (Clark, 1936) is enigmatic as it is not only one of the largest species within the genus, but almost every author who has considered the taxonomy of the species has disagreed with its designation and affinities. Schultz et al. (2009) in a molecular phylogenetic investigation inferred E. lyelli to be an ancient species (late Eocene origin) and found that it is highly divergent from all other species of Engaeus studied and worthy of placement in a new genus. In this paper, we present the complete mitochondrial genome for E. lyelli. The E. lyelli sample was collected from the Grampians, Western Victoria, Australia. The purification of genomic DNA
History Received 12 March 2014 Revised 16 March 2014 Accepted 22 March 2014 Published online 14 April 2014
from the tail 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). The partial 16S rRNA gene sequence of E. lyelli (GenBank accession number: FJ965960) was used as the initial bait for MITObim assembly. The E. lyelli mitogenome is 16,027 bp in length (GenBank accession number: HG799086) and contains 38 mitochondrial genes (13 protein-coding genes, 2 rRNAs and 23 tRNAs) and an AT-rich non-coding region of 895 bp (Table 1). The base composition is 31% A, 29% T, 12% G and 27% C and the order of genes differs slightly from Engaeus lengana, the only other Engaeus species that has had its mitogenome sequenced (Gan et al., 2014a) In E. lyelli, the trnQ gene is upstream of the rrnL gene whereas in E. lengana it is situated immediately down stream of the rrnS gene. For all five Cherax species that have full mitogenomes sequenced, the trnQ gene is located
Table 1. Annotation of the complete mitochondrial genome of E. lyelli. Gene cox1 trnL2(taa) cox2 trnK(ttt) trnD(gtc) atp8 atp6 cox3
Strand
Position
Length (bp)
H H H H H H H H
1–1534 1535–1597 1599–2288 2291–2355 2356–2418 2420–2578 2572–3246 3246–4034
1,534 63 690 65 63 159 675 789
Intergenic nucleotides 1 0 1 2 0 1 7 1
Start codon
Stop codon
ACG
ATT
ATG
TAA
Anticodon UAA UUU GUC
ATG ATG ATG
TAA TAA TAA (continued )
Correspondence: Han Ming Gan, School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 46150 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 Kainan University on 04/20/15 For personal use only.
Gene trnG(tcc) nad3 trnA(tgc) trnR(tcg) trnN(gtt) trnS1(tct) trnE(ttc) trnF(gaa) nad5 trnH(gtg) trnT(tgt) nad6 trnP(tgg) trnQ(ttg) rrnL trnV(tac) Control region trnM(cat) nad2 trnW(tca) trnY(gta) nad4 nad4l cob trnS2(tga) nad1 trnL1(tag) rrnS trnI(gat) trnI(gat) trnC(gca)
Strand
Position
Length (bp)
Intergenic nucleotides
H H H H H H H L L L H H H L L L H H H H L L L H H L L L H H L
4033–4094 4096–4447 4447–4506 4507–4567 4567–4630 4631–4696 4696–4761 4758–4820 4827–6554 6554–6619 6626–6690 6697–7218 7220–7287 7311–7379 7355–8736 8710–8776 8711–9605 9606–9672 9674–10,675 10,675–10,743 10,746–10,808 10,814–12,139 12,133–12,393 12,487–13,621 13,621–13,689 13,700–14,620 14,643–14,710 14,713–15,551 15,670–15,732 15,901–15,963 15,963–16,026
62 352 60 61 64 66 66 63 1728 66 65 522 68 69 1382 67 895 67 1002 69 63 1326 261 1135 69 921 68 839 63 63 64
2 1 1 0 1 0 1 4 6 1 6 6 1 23 25 27 66 0 1 1 2 5 7 93 1 10 22 2 118 168 1
immediately downstream of the control region (Austin et al., 2014a, b; Gan et al., 2014b, c; Miller et al., 2004). Further, E. lyelli has two adjacent trnI genes downstream of the rrnS, which has so far not been reported in any other parastacid crayfish. The mitogenome of E. lyelli is quite divergent from the mitogenomes of E. lengana (76%) and from other Australian crayfish such as C. cainii (74%) (Austin et al., 2014b) and C. destructor (73%) (Miller et al., 2004), which is consistent with phylogenetic studies based on mitochondrial and nuclear gene fragments (Munasinghe et al., 2004; Schultz et al., 2009). Our sample of E. lyelli is almost identical (99.4% similarity) at a 493 bp fragment of the 16S rRNA region in a sample from the Grampians National Park, Victoria (GenBank accession number: AY223711) (Munasinghe, 2003). We expect our data to be a useful resource for clarifying the taxonomy and relationships of this unusual and interesting 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, 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.
Start codon
Stop codon
ATC
AAT
Anticodon UCC UGC UCG GUU UCU UUC GAA
ATG
TAA GUG UGU
ATA
TAA UGG UUG UAC CAU
ATG
TAA UCA GUA
ATG ATA ATG
TAG TAG ACT
ATA
TAA
UGA UAG GAU GAU GCA
Clark E. (1936). The freshwater and land crayfishes of Australia. Memoirs Nat 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 bioinformatcs 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 qaudricarinatus (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. Horwitz P, Richardson A. (1986). An ecological classification of the burrows of Australian freshwater crayfish. Marine Freshwater Res 37: 237–42. 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. Munasinghe DHN. (2003). Molecular systematic studies of freshwater crayfish of the genus Cherax [PhD]. Deakin University. p 227. Munasinghe 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. Schultz MB, Smith SA, Horwitz P, Richardson AM, Crandall KA, Austin CM. (2009). Evolution underground: A molecular phylogenetic investigation of Australian burrowing freshwater crayfish (Decapoda: Parastacidae) with particular focus on Engaeus Erichson. Mol Phylogenet Evol 50:580–98.
MITOGENOME ANNOUNCEMENT
The complete mitogenome of the Australian land crayfish Engaeus lyelli (Clark 1936) (Crustacea: Decapoda: Parastacidae) Han Ming Gan1, Mun Hua Tan1, Yin Peng Lee1, Mark B. Schultz2, and Christopher M. Austin1 School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Petaling Jaya, Selangor, Malaysia, and 2Faculty of Medical and Dental Health Sciences, The University of Melbourne, Bio21 Research Institute, Victoria, Australia
Mitochondrial DNA Downloaded from informahealthcare.com by Kainan University on 04/20/15 For personal use only.
1
Abstract
Keywords
The complete mitochondrial genome of the enigmatic freshwater crayfish Engaeus lyelli was sequenced using the MiSeq Personal Sequencer (Illumina, San Diego, CA). The mitogenome has 16,027 bp consisting of 13 protein-coding genes, 2 ribosomal subunit genes, 23 transfer RNAs, and a non-coding AT-rich region. The base composition of E. lyelli is 29.01% for T, 27.13% for C, 31.43% for A, and 12.44% for G, with an AT bias of 60.44%. The species has the distinctive gene order characteristic of parastacid crayfish with the exception of some minor rearrangements involving the tRNA genes.
Freshwater crayfish, mitogenome, Parastacidae
Australia has a significant freshwater crayfish fauna with approximately 150 species placed in 10 genera (Crandall et al., 1999; Schultz et al., 2009). One of the most diverse and unusual of these genera is the genus Engaeus, which contains species, which burrow strongly and can complete their life cycle underground (Horwitz & Richardson, 1986). The species Engaeus lyelli (Clark, 1936) is enigmatic as it is not only one of the largest species within the genus, but almost every author who has considered the taxonomy of the species has disagreed with its designation and affinities. Schultz et al. (2009) in a molecular phylogenetic investigation inferred E. lyelli to be an ancient species (late Eocene origin) and found that it is highly divergent from all other species of Engaeus studied and worthy of placement in a new genus. In this paper, we present the complete mitochondrial genome for E. lyelli. The E. lyelli sample was collected from the Grampians, Western Victoria, Australia. The purification of genomic DNA
History Received 12 March 2014 Revised 16 March 2014 Accepted 22 March 2014 Published online 14 April 2014
from the tail 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). The partial 16S rRNA gene sequence of E. lyelli (GenBank accession number: FJ965960) was used as the initial bait for MITObim assembly. The E. lyelli mitogenome is 16,027 bp in length (GenBank accession number: HG799086) and contains 38 mitochondrial genes (13 protein-coding genes, 2 rRNAs and 23 tRNAs) and an AT-rich non-coding region of 895 bp (Table 1). The base composition is 31% A, 29% T, 12% G and 27% C and the order of genes differs slightly from Engaeus lengana, the only other Engaeus species that has had its mitogenome sequenced (Gan et al., 2014a) In E. lyelli, the trnQ gene is upstream of the rrnL gene whereas in E. lengana it is situated immediately down stream of the rrnS gene. For all five Cherax species that have full mitogenomes sequenced, the trnQ gene is located
Table 1. Annotation of the complete mitochondrial genome of E. lyelli. Gene cox1 trnL2(taa) cox2 trnK(ttt) trnD(gtc) atp8 atp6 cox3
Strand
Position
Length (bp)
H H H H H H H H
1–1534 1535–1597 1599–2288 2291–2355 2356–2418 2420–2578 2572–3246 3246–4034
1,534 63 690 65 63 159 675 789
Intergenic nucleotides 1 0 1 2 0 1 7 1
Start codon
Stop codon
ACG
ATT
ATG
TAA
Anticodon UAA UUU GUC
ATG ATG ATG
TAA TAA TAA (continued )
Correspondence: Han Ming Gan, School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 46150 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 Kainan University on 04/20/15 For personal use only.
Gene trnG(tcc) nad3 trnA(tgc) trnR(tcg) trnN(gtt) trnS1(tct) trnE(ttc) trnF(gaa) nad5 trnH(gtg) trnT(tgt) nad6 trnP(tgg) trnQ(ttg) rrnL trnV(tac) Control region trnM(cat) nad2 trnW(tca) trnY(gta) nad4 nad4l cob trnS2(tga) nad1 trnL1(tag) rrnS trnI(gat) trnI(gat) trnC(gca)
Strand
Position
Length (bp)
Intergenic nucleotides
H H H H H H H L L L H H H L L L H H H H L L L H H L L L H H L
4033–4094 4096–4447 4447–4506 4507–4567 4567–4630 4631–4696 4696–4761 4758–4820 4827–6554 6554–6619 6626–6690 6697–7218 7220–7287 7311–7379 7355–8736 8710–8776 8711–9605 9606–9672 9674–10,675 10,675–10,743 10,746–10,808 10,814–12,139 12,133–12,393 12,487–13,621 13,621–13,689 13,700–14,620 14,643–14,710 14,713–15,551 15,670–15,732 15,901–15,963 15,963–16,026
62 352 60 61 64 66 66 63 1728 66 65 522 68 69 1382 67 895 67 1002 69 63 1326 261 1135 69 921 68 839 63 63 64
2 1 1 0 1 0 1 4 6 1 6 6 1 23 25 27 66 0 1 1 2 5 7 93 1 10 22 2 118 168 1
immediately downstream of the control region (Austin et al., 2014a, b; Gan et al., 2014b, c; Miller et al., 2004). Further, E. lyelli has two adjacent trnI genes downstream of the rrnS, which has so far not been reported in any other parastacid crayfish. The mitogenome of E. lyelli is quite divergent from the mitogenomes of E. lengana (76%) and from other Australian crayfish such as C. cainii (74%) (Austin et al., 2014b) and C. destructor (73%) (Miller et al., 2004), which is consistent with phylogenetic studies based on mitochondrial and nuclear gene fragments (Munasinghe et al., 2004; Schultz et al., 2009). Our sample of E. lyelli is almost identical (99.4% similarity) at a 493 bp fragment of the 16S rRNA region in a sample from the Grampians National Park, Victoria (GenBank accession number: AY223711) (Munasinghe, 2003). We expect our data to be a useful resource for clarifying the taxonomy and relationships of this unusual and interesting 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, 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.
Start codon
Stop codon
ATC
AAT
Anticodon UCC UGC UCG GUU UCU UUC GAA
ATG
TAA GUG UGU
ATA
TAA UGG UUG UAC CAU
ATG
TAA UCA GUA
ATG ATA ATG
TAG TAG ACT
ATA
TAA
UGA UAG GAU GAU GCA
Clark E. (1936). The freshwater and land crayfishes of Australia. Memoirs Nat 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 bioinformatcs 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 qaudricarinatus (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. Horwitz P, Richardson A. (1986). An ecological classification of the burrows of Australian freshwater crayfish. Marine Freshwater Res 37: 237–42. 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. Munasinghe DHN. (2003). Molecular systematic studies of freshwater crayfish of the genus Cherax [PhD]. Deakin University. p 227. Munasinghe 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. Schultz MB, Smith SA, Horwitz P, Richardson AM, Crandall KA, Austin CM. (2009). Evolution underground: A molecular phylogenetic investigation of Australian burrowing freshwater crayfish (Decapoda: Parastacidae) with particular focus on Engaeus Erichson. Mol Phylogenet Evol 50:580–98.
