http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.895996
MITOGENOME ANNOUNCEMENT
The complete mitogenome of the Macquarie perch, Macquaria australasica Cuvier, 1830 (Teleostei: Percichthyidae) Han Ming Gan, Mun Hua Tan, and Christopher M. Austin
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Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Petaling Jaya, Selangor, Malaysia
Abstract
Keywords
The complete mitochondrial genome of the conservationally significant Macquarie perch (Macquaria australasica) was obtained from low-coverage shotgun sequencing using the MiSeq sequencer. The M. australasica mitogenome has 16,496 base pairs (55% A + T content) made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a 819 bp noncoding AT-rich region. This is the first mitogenome sequence for the genus Macquaria, and the third to be reported for the family Percichthyidae.
Mitogenome, molecular resource, Percichthyidae
The family Percichthyidae is a distinctive group of evolutionarily significant freshwater fish and contains a number of species of conservational concern (Jerry et al., 2001; Near et al., 2012; Unmack et al., 2011). Taxonomic disputation and changes have bedeviled this group of fishes at the level of family, genus and species (Jerry et al., 2001; MacDonald, 1978; Near et al., 2012; Unmack et al., 2011). It is now generally considered that the family is restricted to a group of freshwater fishes from Australia and South America (Near et al., 2012). A number of species are of conservation concern and it is relevant in this context that there is increasing evidence of cryptic speciation in a number of the major lineages within the family (Faulks et al., 2010; Miller et al., 2004; Unmack et al., 2011). Despite a number of molecular phylogenetic studies (Jerry et al., 2001; Near et al., 2012; Unmack et al., 2011) genomic resources are limited for this family with only 2 mitogenomes are available from 2 closely related species of the genus Nannoperca (Prosdocimi et al., 2012). The Macquarie perch is listed as Endangered or Threatened by Australian states and the Australia Commonwealth (http://www.environment.gov.au/cgi-bin/sprat/public/publicspecies.pl?taxon_id¼66632). The species has a relatively restricted distribution largely limited to upland environments and is subjected to a number of threatening processes including over-fishing, habitat alteration and degradation, including river regulation and saltation, and introduced diseases and species (e.g. trout). There is also the possibility of cryptic species and diversity among isolated populations of Macquarie perch (Ingram et al., 2000). In this paper we present the complete mitogenome sequence for the Macquarie perch, Macquaria australasica, the third for the family Percichthyidae. A tissue sample of M. australasica was obtained from a fish from Dartmouth Lake, Victoria Australia. The purification of genomic DNA, partial genome sequencing (2 150 bp paired-end run), mitogenome assembly and annotation were performed as
Correspondence: Han Ming Gan, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 46150 Petaling Jaya, Selangor, Malaysia. E-mail:
[email protected]
History Received 4 February 2014 Accepted 16 February 2014 Published online 11 March 2014
previously described (Gan et al., 2014). The partial cox1 nucleotide sequence of M. ambigua (GenBank accession number: DQ107944) was used as the initial bait for MITObim assembly (Hahn et al., 2013). The complete mitogenome of M. australasica is 16,496 bp in length (GenBank accession number: HG799088) and contains 37 mitochondrial genes and a non-coding AT-rich region of 819 bp in length (Table 1). The mitogenome gene number and order is
Table 1. Annotation of the complete mitochondrial genome of M. australasica.
Gene Control region trnF(gaa) rrnS trnV(tac) rrnL trnL2(taa) nad1 trnI(gat) trnQ(ttg) trnM(cat) nad2 trnW(tca) trnA(tgc) trnN(gtt) trnC(gca) trnY(gta) cox1 trnS2(tga) trnD(gtc) cox2 trnK(ttt) atp8 atp6 cox3
Strand
Position
Length Intergenic Start Stop Anti(bp) nucleotides codon codon codon
H
1–819
819
0
H H H H H H H L H H H L L L L H L H H H H H H
821–888 889–1839 1840–1911 1927–3618 3619–3692 3693–4667 4672–4741 4741–4811 4811–4880 4881–5927 5927–5997 5999–6067 6069–6141 6179–6243 6244–6314 6316–7866 7867–7937 7941–8014 8022–8712 8713–8786 8788–8955 8946–9629 9629–10,414
68 951 72 1692 74 975 70 71 70 1047 71 69 73 65 71 1551 71 74 691 74 168 684 786
0 0 0 15 0 0 4 1 1 0 1 1 1 37 0 1 0 3 7 0 1 10 1
GAA UAC UAA ATG
TAG GAU UUG CAU
ATG
TAA UCA UGC GUU GCA GUA
GTG
TAA UGA GUC
ATG
T
ATG ATG ATG
TAA TAA TAA
UUU
(continued )
2
H. M. Gan et al.
Mitochondrial DNA, Early Online: 1–2
conflicts of interest. The authors alone are responsible for the content and writing of the paper.
Table 1. Continued
Gene
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trnG(tcc) nad3 trnR(tcg) nad4l nad4 trnH(gtg) trnS1(gct) trnL1(tag) nad5 nad6 trnE(ttc) Cob trnT(tgt) trnP(tgg)
Strand
Position
H H H H H H H H H L L H H L
10,414–10,485 10,486–10,836 10,835–10,903 10,904–11,200 11,194–12,579 12,575–12,643 12,644–12,710 12,715–12,787 12,788–14,626 14,623–15,144 15,145–15,213 15,216–16,359 16,357–16,428 16,428–16,496
Length Intergenic Start Stop Anti(bp) nucleotides codon codon codon 72 351 69 297 1386 69 67 73 1839 522 69 1144 72 70
1 0 2 0 7 5 0 4 0 4 0 2 3 1
UCC ATA
TAG UCG
ATG ATG
TAA AGA GUG GCU UAG
ATG ATG
TAA TAA
ATG
T
UUC UGU UGG
consistent with the 2 closely related species of the genus Nannoperca (Prosdocimi et al., 2012). The M. australasica mitogenome base composition is 29% A, 26% T, 16% G and 29% C. The M. australasica mitogenome shows considerable divergence from the two Nannoperca mitogenomes (84% and 85%) indicating that it will be of interest to sequence other more closely related species. We anticipate these mitochondrial sequences will be a useful genetic resource for further evolutionary, population genetic, conservation-related and taxonomic studies of M. australasica and related species and comparative mitogenome studies of members of the Percicythidae.
Acknowledgements We are grateful to Zeb Tonkin for collecting and providing us with the tissue sample for this study.
Declaration of interest This study was funded by the Monash University Malaysia, Tropical Medicine and Biology Multidisciplinary Platform. The authors report no
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