http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.905853
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of Parage aegeria (Insecta: Lepidoptera: Papilionidae) Mitochondrial DNA Downloaded from informahealthcare.com by Karolinska Institutet University Library on 06/08/14 For personal use only.
Luı´s Filipe Teixeira da Costa Instituto de Cieˆncias Agra´rias e Ambientais Mediterraˆnicas (ICAAM), Universidade de E´vora, E´vora, Portugal
Abstract
Keywords
Pararge aegeria is a palearctic butterfly used as a model organism in ecology, behavior, evolution and development, with significant geographically-correlated morphological variation and two close relatives in Macaronesia. In this study, I have determined the complete mitogenome sequence of P. aegeria. The genome is 15,240 bp long, and has the typical gene organization of other lepidopteran mitogenomes. Salient features include the IMQ order of tRNA genes, a sizable (52 bp) spacer between trnQ and nad2, a CGA start codon in cox1 and the ATAGA(T)19 motif in the control region. Interestingly, this region also contains four copies of the imperfect palindrome TAAATATWTATAWATATTTA.
Lepidoptera, mitochondrial genome, model organism, Pararge aegeria
Pararge aegeria (Linnaeus, 1758) is a nymphalid butterfly found in the palearctic ecozone, and a model organism in ecology, behavior, evolution and development (Bergman et al., 2007; Carter et al., 2013; Chardon et al., 2003; Gibbs et al., 2004). It displays significant morphological variation along geographic clines (Vandewoestijne & Van Dyck, 2010), and four subspecies are currently recognized. Two of them are restricted to the UK, P. a. aegeria is found in Southwestern Europe and the Mahgreb and P. a. tircis is distributed throughout the remaining area. Intermediate forms between P. a. aegeria and P. a. tircis occur where their ranges overlap (Weingartner et al., 2006). However, genetic analyses have failed to distinguish them, despite being able to discriminate between P. a. aegeria specimens from North Africa and Europe (Weingartner et al., 2006). I therefore reasoned that the complete mitochondrial sequence of P. aegeria would be useful for more detailed studies, particularly on the ecology, population structure and evolution of this species, and potentially also of its close relatives from Macaronesia. To establish a reference sequence, I selected a single specimen of the aegeria subspecies, and PCR amplified its entire mitochondrial genome in 15 fragments, 762 to 1636 bp long, using primers designed on the basis of other lepidopteran mtDNA sequences. The deduced mitochondrial genome organization of P. aegeria is shown in Table 1. The complete genome (Genbank accession number KJ547676) is 15,240 bp long, with an A + T content of 80.5%, similar to those for other
History Received 10 March 2014 Accepted 15 March 2014 Published online 4 April 2014
Lepidoptera (Hao et al., 2012). It contains the typical complement of 37 genes found in insect mitochondrial genomes: 13 protein-coding genes (PCGs), 2 for rRNAs and 22 for tRNAs. All tRNAs were predicted to adopt a cloverleaf structure, with the exception of tRNA-Ser(AGN) which lacks a stem associated with the D-loop, as has been reported for other insects (Negrisolo et al., 2011; Zhang et al., 2013). The genome is very compact, including eleven short (510 bp) gene overlaps, totaling 34 bp, and ten short spacers, accounting for 40 bp. There was also a significantly larger (52 bp) spacer between the trnQ and nad2 genes, which, like the translocation of trnQ, has been proposed to be a synapomorphy of Lepidoptera (Cameron & Whiting, 2008; Gong et al., 2012; Hao et al., 2012). Of the PCGs, 12 started with one of the ATD codons, while for cox1 a CGA was used. This has also been hypothesized as a synapomorphic feature of Lepidoptera (Zhang et al., 2013), though that might have to be re-evaluated in light of a recently reported exception (Hao et al., 2012). Ten PCGs have TAA termination codons, while 3 have partial stop codons, which are presumed to be completed by poly-adenylation. The mitochondrial control region, located between the rrnS and trnM genes, was 410 bp long and had the highest A + T content of the genome: 94.1%. It contains a ATAGA(T)19 motif, also found in other lepidopteran mitogenomes ( Hao et al., 2012; Zhang et al., 2013), as well as four close matches to the imperfect 20 bp palindrome TAAATATWTATAWATATTTA.
Correspondence: Luı´s Filipe Teixeira da Costa, Instituto de Cieˆncias Agra´rias e Ambientais Mediterraˆnicas (ICAAM), Universidade de E´vora, Nu´cleo da Mitra, Apartado 94, 7002-774 E´vora, Portugal. Tel: +35 1266760885. E-mail: [email protected]; [email protected]
2
L. F. Teixeira da Costa
Mitochondrial DNA, Early Online: 1–2
Table 1. Summary of P. a. aegeria’s mitogenome.
Mitochondrial DNA Downloaded from informahealthcare.com by Karolinska Institutet University Library on 06/08/14 For personal use only.
Gene/region trnM trnI trnQ ND2 trnW trnC trnY COX1 trnL2 (UUR) COX2 trnK trnD ATP8 ATP6 COX3 trnG ND3 trnA trnR trnN trnS1 (AGN) trnE trnF ND5 trnH ND4 ND4L trnT trnP ND6 CYTB trnS2 (UCN) ND1 trnL1 (CUN) rrnL trnV rrnS Control region
Strand
Nucleotides
Size
Anticodon
Light (+) Light Heavy ( ) Light Light Heavy Heavy Light Light Light Light Light Light Light Light Light Light Light Light Light Light Light Heavy Heavy Heavy Heavy Heavy Light Heavy Light Light Light Heavy Heavy Heavy Heavy Heavy
1–67 70–134 132–200 253–1266 1265–1331 1324–1387 1388–1453 1460–2995 2991–3057 3058–3733 3734–3804 3810–3874 3875–4039 4033–4710 4710–5498 5501–5566 5567–5920 5921–5988 5990–6052 6055–6121 6119–6178 6182–6248 6249–6315 6316–8050 8051–8116 8116–9455 9455–9739 9748–9812 9813–9877 9883–10,407 10,407–11,558 11,565–11,631 11,630–12,586 12,587–12,653 12,654–13,991 13,992–14,055 14,056–14,830 14,831–15,240
67 65 69 1014 67 64 66 1536 67 676 71 65 165 678 789 66 354 68 63 67 60 67 67 1735 66 1340 285 65 65 525 1152 67 957 67 1338 64 775 410
CAT (31–33) GAT (99–101) TTG (168–170)
Start codon
Stop codon
ATT
TAA
CGA
TAA
ATG
T
ATT ATG ATG
TAA TAA TAA
ATT
TAA
ATT
T
ATG ATG
TA TAA
ATA ATG
TAA TAA
ATG
TAA
TCA (1296–1298) GCA (1355–1357) GTA (1418–1420) TAA (3021–3023) CTT (3764–3766) GTC (3840–3842)
TCC (5531–5533) TGC (5954–5956) TCG (6017–6019) GTT (6086–6088) GCT (6139–6141) TTC (6213–6215) GAA (6280–6282) GTG (8083–8085) TGT (9778–9780) TGG (9845–9847) TGA (11,595–11,597) TAG (12,622–12,624) TAC (14,024–14,026)
Declaration of interest This work was funded by Portuguese National Funds through FCT (Foundation for Science and Technology) under Cieˆncia2008-ICAAM and Strategic Project PEst-C/AGR/UI0115/2011, as well as FEDER Funds through the Operational Programme for Competitiveness Factors – COMPETE. Funding agencies had no influence on content or writing of the paper, for which the author is solely responsible.
References Bergman M, Gotthard K, Berger D, Olofsson M, Kemp DJ, Wiklund C. (2007). Mating success of resident versus non-resident males in a territorial butterfly. Proc Biol Sci 274:1659–65. Cameron SL, Whiting MF. (2008). The complete mitochondrial genome of the tobacco hornworm, Manduca sexta, (Insecta: Lepidoptera: Sphingidae), and an examination of mitochondrial gene variability within butterflies and moths. Gene 408:112–23. Carter JM, Baker SC, Pink R, Carter DR, Collins A, Tomlin J, Gibbs M, Breuker CJ. (2013). Unscrambling butterfly oogenesis. BMC Genomics 14:283. Chardon JP, Adriaesen F, Matthysen E. (2003). Incorporating landscape elements into a connectivity measure: A case study for the Speckled wood butterfly (Pararge aegeria L.). Landscape Ecol 18:561–73.
Intergenic nucleotides 2 3 52 2 8 0 6 5 0 0 5 0 7 1 2 0 0 1 2 3 3 0 0 0 1 1 8 0 5 1 6 2 0 0 0 0
Gibbs M, Lace LA, Jones MJ, Moore AJ. (2004). Intraspecific competition in the speckled wood butterfly Pararge aegeria: Effect of rearing density and gender on larval life history. J Insect Sci 4:16 (1–6). Gong YJ, Shi BC, Kang ZJ, Zhang F, Wei SJ. (2012). The complete mitochondrial genome of the oriental fruit moth Grapholita molesta (Busck) (Lepidoptera: Tortricidae). Mol Biol Rep 39:2893–900. Hao J, Sun Q, Zhao H, Sun X, Gai Y, Yang Q. (2012). The complete mitochondrial genome of Ctenoptilum vasava (Lepidoptera: Hesperiidae: Pyrginae) and its phylogenetic implication. Comp Funct Genomics 2012:328049. Negrisolo E, Babbucci M, Patarnello T. (2011). The mitochondrial genome of the ascalaphid owlfly Libelloides macaronius and comparative evolutionary mitochondriomics of neuropterid insects. BMC Genomics 12:221. Vandewoestijne S, Van Dyck H. (2010). Population genetic differences along a latitudinal cline between original and recently colonized habitat in a butterfly. PLoS One 5:e13810. Weingartner E, Wahlberg N, Nylin S. (2006). Speciation in Pararge (Satyrinae: Nymphalidae) butterflies – North Africa is the source of ancestral populations of all Pararge species. Syst Entomol 31:621–32. Zhang L, Huang D, Sun X, Hao J, Peng C, Yang Q. (2013). The complete mitochondrial genome of Cupido argiades (Lepidoptera: Lycaenidae). Mitochondrial DNA 24:475–7.
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of Parage aegeria (Insecta: Lepidoptera: Papilionidae) Mitochondrial DNA Downloaded from informahealthcare.com by Karolinska Institutet University Library on 06/08/14 For personal use only.
Luı´s Filipe Teixeira da Costa Instituto de Cieˆncias Agra´rias e Ambientais Mediterraˆnicas (ICAAM), Universidade de E´vora, E´vora, Portugal
Abstract
Keywords
Pararge aegeria is a palearctic butterfly used as a model organism in ecology, behavior, evolution and development, with significant geographically-correlated morphological variation and two close relatives in Macaronesia. In this study, I have determined the complete mitogenome sequence of P. aegeria. The genome is 15,240 bp long, and has the typical gene organization of other lepidopteran mitogenomes. Salient features include the IMQ order of tRNA genes, a sizable (52 bp) spacer between trnQ and nad2, a CGA start codon in cox1 and the ATAGA(T)19 motif in the control region. Interestingly, this region also contains four copies of the imperfect palindrome TAAATATWTATAWATATTTA.
Lepidoptera, mitochondrial genome, model organism, Pararge aegeria
Pararge aegeria (Linnaeus, 1758) is a nymphalid butterfly found in the palearctic ecozone, and a model organism in ecology, behavior, evolution and development (Bergman et al., 2007; Carter et al., 2013; Chardon et al., 2003; Gibbs et al., 2004). It displays significant morphological variation along geographic clines (Vandewoestijne & Van Dyck, 2010), and four subspecies are currently recognized. Two of them are restricted to the UK, P. a. aegeria is found in Southwestern Europe and the Mahgreb and P. a. tircis is distributed throughout the remaining area. Intermediate forms between P. a. aegeria and P. a. tircis occur where their ranges overlap (Weingartner et al., 2006). However, genetic analyses have failed to distinguish them, despite being able to discriminate between P. a. aegeria specimens from North Africa and Europe (Weingartner et al., 2006). I therefore reasoned that the complete mitochondrial sequence of P. aegeria would be useful for more detailed studies, particularly on the ecology, population structure and evolution of this species, and potentially also of its close relatives from Macaronesia. To establish a reference sequence, I selected a single specimen of the aegeria subspecies, and PCR amplified its entire mitochondrial genome in 15 fragments, 762 to 1636 bp long, using primers designed on the basis of other lepidopteran mtDNA sequences. The deduced mitochondrial genome organization of P. aegeria is shown in Table 1. The complete genome (Genbank accession number KJ547676) is 15,240 bp long, with an A + T content of 80.5%, similar to those for other
History Received 10 March 2014 Accepted 15 March 2014 Published online 4 April 2014
Lepidoptera (Hao et al., 2012). It contains the typical complement of 37 genes found in insect mitochondrial genomes: 13 protein-coding genes (PCGs), 2 for rRNAs and 22 for tRNAs. All tRNAs were predicted to adopt a cloverleaf structure, with the exception of tRNA-Ser(AGN) which lacks a stem associated with the D-loop, as has been reported for other insects (Negrisolo et al., 2011; Zhang et al., 2013). The genome is very compact, including eleven short (510 bp) gene overlaps, totaling 34 bp, and ten short spacers, accounting for 40 bp. There was also a significantly larger (52 bp) spacer between the trnQ and nad2 genes, which, like the translocation of trnQ, has been proposed to be a synapomorphy of Lepidoptera (Cameron & Whiting, 2008; Gong et al., 2012; Hao et al., 2012). Of the PCGs, 12 started with one of the ATD codons, while for cox1 a CGA was used. This has also been hypothesized as a synapomorphic feature of Lepidoptera (Zhang et al., 2013), though that might have to be re-evaluated in light of a recently reported exception (Hao et al., 2012). Ten PCGs have TAA termination codons, while 3 have partial stop codons, which are presumed to be completed by poly-adenylation. The mitochondrial control region, located between the rrnS and trnM genes, was 410 bp long and had the highest A + T content of the genome: 94.1%. It contains a ATAGA(T)19 motif, also found in other lepidopteran mitogenomes ( Hao et al., 2012; Zhang et al., 2013), as well as four close matches to the imperfect 20 bp palindrome TAAATATWTATAWATATTTA.
Correspondence: Luı´s Filipe Teixeira da Costa, Instituto de Cieˆncias Agra´rias e Ambientais Mediterraˆnicas (ICAAM), Universidade de E´vora, Nu´cleo da Mitra, Apartado 94, 7002-774 E´vora, Portugal. Tel: +35 1266760885. E-mail: [email protected]; [email protected]
2
L. F. Teixeira da Costa
Mitochondrial DNA, Early Online: 1–2
Table 1. Summary of P. a. aegeria’s mitogenome.
Mitochondrial DNA Downloaded from informahealthcare.com by Karolinska Institutet University Library on 06/08/14 For personal use only.
Gene/region trnM trnI trnQ ND2 trnW trnC trnY COX1 trnL2 (UUR) COX2 trnK trnD ATP8 ATP6 COX3 trnG ND3 trnA trnR trnN trnS1 (AGN) trnE trnF ND5 trnH ND4 ND4L trnT trnP ND6 CYTB trnS2 (UCN) ND1 trnL1 (CUN) rrnL trnV rrnS Control region
Strand
Nucleotides
Size
Anticodon
Light (+) Light Heavy ( ) Light Light Heavy Heavy Light Light Light Light Light Light Light Light Light Light Light Light Light Light Light Heavy Heavy Heavy Heavy Heavy Light Heavy Light Light Light Heavy Heavy Heavy Heavy Heavy
1–67 70–134 132–200 253–1266 1265–1331 1324–1387 1388–1453 1460–2995 2991–3057 3058–3733 3734–3804 3810–3874 3875–4039 4033–4710 4710–5498 5501–5566 5567–5920 5921–5988 5990–6052 6055–6121 6119–6178 6182–6248 6249–6315 6316–8050 8051–8116 8116–9455 9455–9739 9748–9812 9813–9877 9883–10,407 10,407–11,558 11,565–11,631 11,630–12,586 12,587–12,653 12,654–13,991 13,992–14,055 14,056–14,830 14,831–15,240
67 65 69 1014 67 64 66 1536 67 676 71 65 165 678 789 66 354 68 63 67 60 67 67 1735 66 1340 285 65 65 525 1152 67 957 67 1338 64 775 410
CAT (31–33) GAT (99–101) TTG (168–170)
Start codon
Stop codon
ATT
TAA
CGA
TAA
ATG
T
ATT ATG ATG
TAA TAA TAA
ATT
TAA
ATT
T
ATG ATG
TA TAA
ATA ATG
TAA TAA
ATG
TAA
TCA (1296–1298) GCA (1355–1357) GTA (1418–1420) TAA (3021–3023) CTT (3764–3766) GTC (3840–3842)
TCC (5531–5533) TGC (5954–5956) TCG (6017–6019) GTT (6086–6088) GCT (6139–6141) TTC (6213–6215) GAA (6280–6282) GTG (8083–8085) TGT (9778–9780) TGG (9845–9847) TGA (11,595–11,597) TAG (12,622–12,624) TAC (14,024–14,026)
Declaration of interest This work was funded by Portuguese National Funds through FCT (Foundation for Science and Technology) under Cieˆncia2008-ICAAM and Strategic Project PEst-C/AGR/UI0115/2011, as well as FEDER Funds through the Operational Programme for Competitiveness Factors – COMPETE. Funding agencies had no influence on content or writing of the paper, for which the author is solely responsible.
References Bergman M, Gotthard K, Berger D, Olofsson M, Kemp DJ, Wiklund C. (2007). Mating success of resident versus non-resident males in a territorial butterfly. Proc Biol Sci 274:1659–65. Cameron SL, Whiting MF. (2008). The complete mitochondrial genome of the tobacco hornworm, Manduca sexta, (Insecta: Lepidoptera: Sphingidae), and an examination of mitochondrial gene variability within butterflies and moths. Gene 408:112–23. Carter JM, Baker SC, Pink R, Carter DR, Collins A, Tomlin J, Gibbs M, Breuker CJ. (2013). Unscrambling butterfly oogenesis. BMC Genomics 14:283. Chardon JP, Adriaesen F, Matthysen E. (2003). Incorporating landscape elements into a connectivity measure: A case study for the Speckled wood butterfly (Pararge aegeria L.). Landscape Ecol 18:561–73.
Intergenic nucleotides 2 3 52 2 8 0 6 5 0 0 5 0 7 1 2 0 0 1 2 3 3 0 0 0 1 1 8 0 5 1 6 2 0 0 0 0
Gibbs M, Lace LA, Jones MJ, Moore AJ. (2004). Intraspecific competition in the speckled wood butterfly Pararge aegeria: Effect of rearing density and gender on larval life history. J Insect Sci 4:16 (1–6). Gong YJ, Shi BC, Kang ZJ, Zhang F, Wei SJ. (2012). The complete mitochondrial genome of the oriental fruit moth Grapholita molesta (Busck) (Lepidoptera: Tortricidae). Mol Biol Rep 39:2893–900. Hao J, Sun Q, Zhao H, Sun X, Gai Y, Yang Q. (2012). The complete mitochondrial genome of Ctenoptilum vasava (Lepidoptera: Hesperiidae: Pyrginae) and its phylogenetic implication. Comp Funct Genomics 2012:328049. Negrisolo E, Babbucci M, Patarnello T. (2011). The mitochondrial genome of the ascalaphid owlfly Libelloides macaronius and comparative evolutionary mitochondriomics of neuropterid insects. BMC Genomics 12:221. Vandewoestijne S, Van Dyck H. (2010). Population genetic differences along a latitudinal cline between original and recently colonized habitat in a butterfly. PLoS One 5:e13810. Weingartner E, Wahlberg N, Nylin S. (2006). Speciation in Pararge (Satyrinae: Nymphalidae) butterflies – North Africa is the source of ancestral populations of all Pararge species. Syst Entomol 31:621–32. Zhang L, Huang D, Sun X, Hao J, Peng C, Yang Q. (2013). The complete mitochondrial genome of Cupido argiades (Lepidoptera: Lycaenidae). Mitochondrial DNA 24:475–7.
