http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.913147
MITOGENOME ANNOUNCEMENT
The complete mitogenome of the whale shark parasitic copepod Pandarus rhincodonicus norman, Newbound & Knott (Crustacea; Siphonostomatoida; Pandaridae) – a new gene order for the copepoda Christopher M. Austin1, Mun Hua Tan1, Yin Peng Lee1, Laurence J. Croft2, Mark G. Meekan3, Simon J. Pierce4,5, and Han Ming Gan1 Mitochondrial DNA Downloaded from informahealthcare.com by Rutgers University on 05/28/14 For personal use only.
1
School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Petaling Jaya, Selangor, Malaysia, 2Malaysian Genome Resource Centre Berhad, Kuala Lumpur, Malaysia, 3Australian Institute of Marine Science, c/o UWA Oceans Institute (MO96), Crawley, Western Australia, Australia, 4 Marine Megafauna Foundation, Truckee, California, USA, and 5Wild Me, Portland, Oregon, USA Abstract
Keywords
The complete mitochondrial genome of the parasitic copepod Pandarus rhincodonicus was obtained from a partial genome scan using the HiSeq sequencing system. The Pandarus rhincodonicus mitogenome has 14,480 base pairs (62% A+T content) made up of 12 proteincoding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a putative 384 bp non-coding AT-rich region. This Pandarus mitogenome sequence is the first for the family Pandaridae, the second for the order Siphonostomatoida and the sixth for the Copepoda.
Molecular resource, mitogenome, pandaridae
The order Siphonostomatoida, is an order of largely parasitic copepods that feed on the blood, epidermal tissue or mucus of marine fish, including elasmobranchs. The order consists of approximately 550 genera placed in nearly 40 families and includes economically important species such as sea lice that parasitise farmed fish (Boxshall, 2013a, Gunn & Pitt, 2012). The family Pandaridae comprises 16 genera thought to be almost exclusively parasitic on elasmobranchs (Boxshall, 2013b; Cressey, 1967). The genus Pandarus currently has 17 recognised species and P. rhincodonicus (Norman et al., 2000) is noteworthy as it is an ectoparasite of the largest known fish, the whale shark – Rhincodon typus. There are few genomic resources for copepods in general (5 mitogenomes) and only one mitogenome has been reported for the Siphonostomatoida (Lepeophtheirus salmonis – Caligidae). In this paper we present the complete mitogenome sequence for P. rhincodonicus. We hope these mitochondrial sequences will stimulate evolutionary and population genetic research on marine parasites. An individual of P. rhincodonicus (code – 366.1) was obtained from a whale shark in the coastal waters of Mozambique by S. Pierce. Genomic DNA was extracted using Qiagen DNAeasy Blood and Tissue Kits (Qiagen, Hilden, Germany) following the manufacturer’s instructions. The purified genomic DNA was processed using TruSeq DNA sample preparation kit (Illumina, San Diego, CA). Size estimation and quantification of the prepped
Correspondence: Han Ming Gan, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 46150 Petaling Jaya, Selangor, Malaysia. E-mail: [email protected]
History Received 27 March 2014 Accepted 5 April 2014 Published online 29 April 2014
library was performed using Bioanalyzer 2100 (Agilent, Santa Clara, CA) and KAPA Library Quantification kit (Kapa Biosystem, Cape Town, South Africa) respectively. The library was normalized to 2 nM and sequenced on the HiSeq sequencer (Illumina, San Diego, CA) at the Malaysian Genome Resource Centre Berhad (www.mgrc.com.my). The mitochondrial genome was reconstructed with MITObim using the partial cox1 gene of P. rhincodonicus from Ningaloo Reef. (GenBank accession number: KJ551843) as the initial bait (Hahn et al., 2013). The complete mitogenome was recovered, reoriented to the cox1 gene and annotated with MITOS and ORF Finder (Bernt et al., 2012; Gan et al., 2014) The complete mitogenome of P. rhincodonicus was 14,480 bp in length (GenBank accession number: HG942363) and contained 36 mitochondrial genes and a non-coding AT-rich region of 384 bp in length (Table 1). Notably, the mitogenome of P. rhincodonicus does not contain the gene coding for ATPase8, which was similarly observed in the mitogenome of the cyclopoid copepod Paracyclopina nana and the siphonostomatid, Lepeophtheirus salmonis but not for other copepods (Ki et al., 2009; Minxiao et al., 2011; Tjensvoll et al., 2005). The mitogenome gene number was similar to L. salmonis but differs in that cob and nad4l genes are found between cox1 and the rrnl genes, a gene order that has not been reported before for copepods (Ki et al., 2009; Minxiao et al., 2011; Tjensvoll et al., 2005). The P. rhincodonicus mitogenome base composition was 27% A, 35% T, 24% G and 14% C. The sequencing of the mitogenomes of additional siphonotomatid species and more copepods in general will generate interesting information for comparative studies given the diversity and ecological importance of these poorly studied groups.
2
C. M. Austin et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Annotation of the complete mitochondrial genome of P. rhincodonicus.
Mitochondrial DNA Downloaded from informahealthcare.com by Rutgers University on 05/28/14 For personal use only.
Gene cox1 trnT(tgt) cob nad4l rrnL trnI(gat) trnL2(taa) trnN(gtt) trnG(tcc) trnV(tac) rrnS nad6 trnA(tgc) trnE(ttc) trnQ(ttg) trnK(ttt) trnR(tcg) Control region trnL1(tag) atp6 trnY(gta) nad4 nad2 trnS2(tga) cox3 trnP(tgg) trnW(tca) trnD(gtc) trnF(gaa) nad3 nad5 trnM(cat) trnS1(tct) trnC(gca) trnH(gtg) cox2 nad1
Strand
Position
Length (bp)
Intergenic nucleotides
Start codon
Stop codon
H L L L L L L H H H H H H H H H H H H H H L H H H H H H H H H H H H H H H
1–1548 1564–1628 1615–2739 2739–3068 3133–3642 4112–4174 4175–4238 4259–4328 4329–4390 4394–4455 4737–5044 5050–5505 5524–5571 5572–5630 5633–5692 5693–5756 5889–5938 5939–6322 6323–6385 6386–7039 7038–7100 7162–8457 8479–9402 9405–9457 9458–10,258 10,260–10,322 10,324–10,384 10,385–10,450 10,453–10,512 10,513–10,860 10,848–12,539 12,633–12,695 12,695–12,747 12,748–12,798 12,799–12,859 12,861–13,553 13,566–14,480
1548 65 1125 330 510 63 64 70 62 62 308 456 48 59 60 64 50 384 63 654 63 1296 924 53 801 63 61 66 60 348 1692 63 53 51 61 693 915
0 15 14 1 64 469 0 20 0 3 281 5 18 0 2 0 132 0 0 0 2 61 21 2 0 1 1 0 2 0 13 93 1 0 0 1 12
TTG
TAA
ATG TTG
TAA TAA
Declaration of interest Funding for this study was provided by the Monash University Malaysia Tropical Medicine and Biology Multidisciplinary Platform and the Sea World Research and Rescue Foundation (Australia). Fieldwork in Mozambique was supported by the Shark Foundation and Casa Barry Lodge. The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
References 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 7:332–6. Boxshall G. (2013a). Pandarus Leach, (1816). [Online]. Available at: http://www.marinespecies.org/copepoda/aphia.php?p¼taxdetails&id¼ 135638 (Accessed 7 March 2014). Boxshall G. (2013b). Siphonostomatoida [Online]. Available at: http:// www.marinespecies.org/copepoda/aphia.php?p¼taxdetails&id¼1104 (Accessed 22 January 2014). Cressey R. (1967). Revision of the family Pandaridae (Copepoda: Caligoida). Proc U S Nat Mus 121:1–29. Gan HM, Schultz MB, Austin CM. (2014). Integrated shotgun sequencing and bioinformatcs pipeline allows ultra-fast mitogenome recovery and
Anticodon UGU
GAU UAA GUU UCC UAC ATC
TAG UGC UUC UUG UUU UCG UAG
TTG
TAA
ATT ATT
TAG TAA
ATT
TAG
GUA UGA UGG UCA GUC GAA TTG GTG
TAG TAA CAU UCU GCA GUG
ATG TTG
TAA TAA
confirms substantial gene rearrangements in Australian freshwater crayfishes. BMC Evol Biol 14:19. Gunn A, Pitt SJ. (2012). Arthropod parasites. Parasitology: An integrated approach. Chichester, UK: John Wiley & Sons, Ltd. 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. Ki JS, Park HG, Lee JS. (2009). The complete mitochondrial genome of the cyclopoid copepod Paracyclopina nana: A highly divergent genome with novel gene order and atypical gene numbers. Gene 435: 13–22. Minxiao W, Song S, Chaolun L, Xin S. (2011). Distinctive mitochondrial genome of Calanoid copepod Calanus sinicus with multiple large non-coding regions and reshuffled gene order: Useful molecular markers for phylogenetic and population studies. BMC Genomics 12: 73. Norman BM, Newbound DR, Knott B. (2000). A new species of Pandaridae (Copepoda), from the whale shark Rhincodon typus (Smith). J Nat Hist 34:355–66. Tjensvoll K, Hodneland K, Nilsen F, Nylund A. (2005). Genetic characterization of the mitochondrial DNA from Lepeophtheirus salmonis (Crustacea; Copepoda). A new gene organization revealed. Gene 353:218–30.
MITOGENOME ANNOUNCEMENT
The complete mitogenome of the whale shark parasitic copepod Pandarus rhincodonicus norman, Newbound & Knott (Crustacea; Siphonostomatoida; Pandaridae) – a new gene order for the copepoda Christopher M. Austin1, Mun Hua Tan1, Yin Peng Lee1, Laurence J. Croft2, Mark G. Meekan3, Simon J. Pierce4,5, and Han Ming Gan1 Mitochondrial DNA Downloaded from informahealthcare.com by Rutgers University on 05/28/14 For personal use only.
1
School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Petaling Jaya, Selangor, Malaysia, 2Malaysian Genome Resource Centre Berhad, Kuala Lumpur, Malaysia, 3Australian Institute of Marine Science, c/o UWA Oceans Institute (MO96), Crawley, Western Australia, Australia, 4 Marine Megafauna Foundation, Truckee, California, USA, and 5Wild Me, Portland, Oregon, USA Abstract
Keywords
The complete mitochondrial genome of the parasitic copepod Pandarus rhincodonicus was obtained from a partial genome scan using the HiSeq sequencing system. The Pandarus rhincodonicus mitogenome has 14,480 base pairs (62% A+T content) made up of 12 proteincoding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a putative 384 bp non-coding AT-rich region. This Pandarus mitogenome sequence is the first for the family Pandaridae, the second for the order Siphonostomatoida and the sixth for the Copepoda.
Molecular resource, mitogenome, pandaridae
The order Siphonostomatoida, is an order of largely parasitic copepods that feed on the blood, epidermal tissue or mucus of marine fish, including elasmobranchs. The order consists of approximately 550 genera placed in nearly 40 families and includes economically important species such as sea lice that parasitise farmed fish (Boxshall, 2013a, Gunn & Pitt, 2012). The family Pandaridae comprises 16 genera thought to be almost exclusively parasitic on elasmobranchs (Boxshall, 2013b; Cressey, 1967). The genus Pandarus currently has 17 recognised species and P. rhincodonicus (Norman et al., 2000) is noteworthy as it is an ectoparasite of the largest known fish, the whale shark – Rhincodon typus. There are few genomic resources for copepods in general (5 mitogenomes) and only one mitogenome has been reported for the Siphonostomatoida (Lepeophtheirus salmonis – Caligidae). In this paper we present the complete mitogenome sequence for P. rhincodonicus. We hope these mitochondrial sequences will stimulate evolutionary and population genetic research on marine parasites. An individual of P. rhincodonicus (code – 366.1) was obtained from a whale shark in the coastal waters of Mozambique by S. Pierce. Genomic DNA was extracted using Qiagen DNAeasy Blood and Tissue Kits (Qiagen, Hilden, Germany) following the manufacturer’s instructions. The purified genomic DNA was processed using TruSeq DNA sample preparation kit (Illumina, San Diego, CA). Size estimation and quantification of the prepped
Correspondence: Han Ming Gan, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 46150 Petaling Jaya, Selangor, Malaysia. E-mail: [email protected]
History Received 27 March 2014 Accepted 5 April 2014 Published online 29 April 2014
library was performed using Bioanalyzer 2100 (Agilent, Santa Clara, CA) and KAPA Library Quantification kit (Kapa Biosystem, Cape Town, South Africa) respectively. The library was normalized to 2 nM and sequenced on the HiSeq sequencer (Illumina, San Diego, CA) at the Malaysian Genome Resource Centre Berhad (www.mgrc.com.my). The mitochondrial genome was reconstructed with MITObim using the partial cox1 gene of P. rhincodonicus from Ningaloo Reef. (GenBank accession number: KJ551843) as the initial bait (Hahn et al., 2013). The complete mitogenome was recovered, reoriented to the cox1 gene and annotated with MITOS and ORF Finder (Bernt et al., 2012; Gan et al., 2014) The complete mitogenome of P. rhincodonicus was 14,480 bp in length (GenBank accession number: HG942363) and contained 36 mitochondrial genes and a non-coding AT-rich region of 384 bp in length (Table 1). Notably, the mitogenome of P. rhincodonicus does not contain the gene coding for ATPase8, which was similarly observed in the mitogenome of the cyclopoid copepod Paracyclopina nana and the siphonostomatid, Lepeophtheirus salmonis but not for other copepods (Ki et al., 2009; Minxiao et al., 2011; Tjensvoll et al., 2005). The mitogenome gene number was similar to L. salmonis but differs in that cob and nad4l genes are found between cox1 and the rrnl genes, a gene order that has not been reported before for copepods (Ki et al., 2009; Minxiao et al., 2011; Tjensvoll et al., 2005). The P. rhincodonicus mitogenome base composition was 27% A, 35% T, 24% G and 14% C. The sequencing of the mitogenomes of additional siphonotomatid species and more copepods in general will generate interesting information for comparative studies given the diversity and ecological importance of these poorly studied groups.
2
C. M. Austin et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Annotation of the complete mitochondrial genome of P. rhincodonicus.
Mitochondrial DNA Downloaded from informahealthcare.com by Rutgers University on 05/28/14 For personal use only.
Gene cox1 trnT(tgt) cob nad4l rrnL trnI(gat) trnL2(taa) trnN(gtt) trnG(tcc) trnV(tac) rrnS nad6 trnA(tgc) trnE(ttc) trnQ(ttg) trnK(ttt) trnR(tcg) Control region trnL1(tag) atp6 trnY(gta) nad4 nad2 trnS2(tga) cox3 trnP(tgg) trnW(tca) trnD(gtc) trnF(gaa) nad3 nad5 trnM(cat) trnS1(tct) trnC(gca) trnH(gtg) cox2 nad1
Strand
Position
Length (bp)
Intergenic nucleotides
Start codon
Stop codon
H L L L L L L H H H H H H H H H H H H H H L H H H H H H H H H H H H H H H
1–1548 1564–1628 1615–2739 2739–3068 3133–3642 4112–4174 4175–4238 4259–4328 4329–4390 4394–4455 4737–5044 5050–5505 5524–5571 5572–5630 5633–5692 5693–5756 5889–5938 5939–6322 6323–6385 6386–7039 7038–7100 7162–8457 8479–9402 9405–9457 9458–10,258 10,260–10,322 10,324–10,384 10,385–10,450 10,453–10,512 10,513–10,860 10,848–12,539 12,633–12,695 12,695–12,747 12,748–12,798 12,799–12,859 12,861–13,553 13,566–14,480
1548 65 1125 330 510 63 64 70 62 62 308 456 48 59 60 64 50 384 63 654 63 1296 924 53 801 63 61 66 60 348 1692 63 53 51 61 693 915
0 15 14 1 64 469 0 20 0 3 281 5 18 0 2 0 132 0 0 0 2 61 21 2 0 1 1 0 2 0 13 93 1 0 0 1 12
TTG
TAA
ATG TTG
TAA TAA
Declaration of interest Funding for this study was provided by the Monash University Malaysia Tropical Medicine and Biology Multidisciplinary Platform and the Sea World Research and Rescue Foundation (Australia). Fieldwork in Mozambique was supported by the Shark Foundation and Casa Barry Lodge. The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
References 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 7:332–6. Boxshall G. (2013a). Pandarus Leach, (1816). [Online]. Available at: http://www.marinespecies.org/copepoda/aphia.php?p¼taxdetails&id¼ 135638 (Accessed 7 March 2014). Boxshall G. (2013b). Siphonostomatoida [Online]. Available at: http:// www.marinespecies.org/copepoda/aphia.php?p¼taxdetails&id¼1104 (Accessed 22 January 2014). Cressey R. (1967). Revision of the family Pandaridae (Copepoda: Caligoida). Proc U S Nat Mus 121:1–29. Gan HM, Schultz MB, Austin CM. (2014). Integrated shotgun sequencing and bioinformatcs pipeline allows ultra-fast mitogenome recovery and
Anticodon UGU
GAU UAA GUU UCC UAC ATC
TAG UGC UUC UUG UUU UCG UAG
TTG
TAA
ATT ATT
TAG TAA
ATT
TAG
GUA UGA UGG UCA GUC GAA TTG GTG
TAG TAA CAU UCU GCA GUG
ATG TTG
TAA TAA
confirms substantial gene rearrangements in Australian freshwater crayfishes. BMC Evol Biol 14:19. Gunn A, Pitt SJ. (2012). Arthropod parasites. Parasitology: An integrated approach. Chichester, UK: John Wiley & Sons, Ltd. 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. Ki JS, Park HG, Lee JS. (2009). The complete mitochondrial genome of the cyclopoid copepod Paracyclopina nana: A highly divergent genome with novel gene order and atypical gene numbers. Gene 435: 13–22. Minxiao W, Song S, Chaolun L, Xin S. (2011). Distinctive mitochondrial genome of Calanoid copepod Calanus sinicus with multiple large non-coding regions and reshuffled gene order: Useful molecular markers for phylogenetic and population studies. BMC Genomics 12: 73. Norman BM, Newbound DR, Knott B. (2000). A new species of Pandaridae (Copepoda), from the whale shark Rhincodon typus (Smith). J Nat Hist 34:355–66. Tjensvoll K, Hodneland K, Nilsen F, Nylund A. (2005). Genetic characterization of the mitochondrial DNA from Lepeophtheirus salmonis (Crustacea; Copepoda). A new gene organization revealed. Gene 353:218–30.
