http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.908356
MITOGENOME ANNOUNCEMENT
Recombinant mitochondrial genome with standard transmission route from Mediterranean mussel Mytilus galloprovincialis Beata S´mietanka1, Monika Filipowicz1, and Artur Burzyn´ski1,2 Institute of Oceanology, Polish Academy of Sciences, Sopot, Poland and 2Institute of Biology and Environmental Protection, Pommeranian University in Sł upsk, Poland
Mitochondrial DNA Downloaded from informahealthcare.com by Ondokuz Mayis Univ. on 11/13/14 For personal use only.
1
Abstract
Keywords
Several bivalve species, including marine mussels Mytilus are atypical in having two genderspecific and highly divergent mtDNA genomes. This peculiar genetic system allows not only the recombination to occur but also facilitates its detection. Previous reports associated the existence of mosaic recombinant haplotypes with the switch of their transmission route. Here we report nearly complete sequence of a mitochondrial genome isolated from a homoplasmic female individual of Mediterranean Mytilus galloprovincialis. The genome has clear phylogenetic affinity with and organization identical to the M. galloprovincialis female haplotypes, in the coding part. However, the genome is very large, approximately 20,600 bp long, exclusively due to a long and complex control region. It contains an array of repeats, some of which are degenerated. A large part of the control region is derived from the paternal genome. This finding shows that not all haplotypes with recombinant control regions must be paternally inherited in Mytilus.
DUI, mitogenomics, recombination
The unusual system of mitochondrial DNA inheritance in marine mussels Mytilus results in the existence of two lineages of mitochondrial genomes. The genomes are either transmitted maternally (F) or paternally (M) (Skibinski et al., 1994; Zouros et al., 1994). The M genomes evolve faster than the F genomes, which could be due to relaxed selection (Stewart et al., 1996). Occasionally, an F genome may invade the paternal route, resetting their divergence to zero (masculinization, Hoeh et al., 1997). High frequency of recombinant genomes with the M-like M. edulis control region (CR) segments was observed in male Mytilus from the Baltic Sea (Burzyn´ski et al., 2006), supporting the hypothesis that a part of the M CR is necessary to masculinize the genome (Burzyn´ski et al., 2003; Cao et al., 2004; Zouros, 2000). The announced mitochondrial genome is derived from a female specimen of M. galloprovincialis. The sequence was obtained in the two step procedure involving long range PCR (S´mietanka et al., 2010). Primer sequences are available from the authors on request. It has been deposited in GenBank under accession number EF434638. Its nucleotide composition is typically biased towards A-T (62.2%), the coding part is also typical for Mytilus mitochondrial genomes and contains two
Correspondence: Artur Burzyn´ski, Institute of Oceanology, Polish Academy of Sciences, Powstan´co´w Warszawy 55, 81-712 Sopot, Poland. Tel: 48587311764. E-mail: [email protected]
History Received 3 March 2014 Revised 15 March 2014 Accepted 22 March 2014 Published online 14 April 2014
rRNA, 13 protein-coding and 23 tRNA genes including additional tRNA gene for methionine. The genetic distance from the nearest known mitochondrial genome (M. galloprovincialis F) is small, at 1.4% (2.8% from M. edulis and 18% from M. trossulus). No recombinantion signature was found in the coding part of this genome. This genome is one of the largest identified in Mytilus mussels: the total length of the obtained sequence is 18,518 bp, of which 2933 bp belong to the CR. It was impossible to sequence the whole CR due to the presence of multiple, long tandem repeats, plagued with homopolymeric runs, which seriously disrupted the sequencing. However, it was possible to amplify the whole CR with its flanks using pair of universal primers MF12S and MFCO2 (Filipowicz et al., 2008) and ascertain the overall CR structure (Figure 1). Based on this map and the sequence data it can be concluded that, the CR contains several recombination breakpoints and consists of two domains: F-specific and M-specific. The length of the F-specific part is comparable to the length of this part observed in haplotypes from 11a/15 group (Burzyn´ski et al., 2006), however, the M-like domain differs in length. In the Baltic haplogroup single M-like segment is approximately 1000 bp long. In the announced genome the CR contains an array of repeats, some of which have multiple deletion and are generally much shorter than in the Baltic case (800 bp max). This complex CR structure is consistent with the model of rearrangements proposed by Burzyn´ski et al. (2006). Under the proposed scenario the M-F recombination is one of the first steps in generating such structures. Despite its apparently long history following the recombination event, this genome is most likely inherited maternally, showing that acquisition of M-like sequences is not sufficient to switch the transmission route.
2
B. S´mietanka et al.
Mitochondrial DNA, Early Online: 1–2
Mitochondrial DNA Downloaded from informahealthcare.com by Ondokuz Mayis Univ. on 11/13/14 For personal use only.
Figure 1. Restriction fragments length polymorphism (RFLP) analysis of the PCR product containing the CR and obtained using MF12S and MFCO2 primers. DNA was digested with MboI and HpaII restriction enzymes separately, the digestion products were separated on the gel (top). Then the restriction maps were made (bottom), taking into account also the sequencing data, which spanned the regions shaded in gray.
Declaration of interest The authors are solely responsible for writing this manuscript.
References Burzyn´ski A, Zbawicka M, Skibinski DOF, Wenne R. (2003). Evidence for recombination of mtDNA in the marine mussel Mytilus trossulus from the Baltic. Mol Biol Evol 20:388–92. Burzyn´ski A, Zbawicka M, Skibinski DOF, Wenne R. (2006). Doubly uniparental inheritance is associated with high polymorphism for rearranged and recombinant control region haplotypes in Baltic Mytilus trossulus. Genetics 174:1081–94. Cao L, Kenchington E, Zouros E, Rodakis GC. (2004). Evidence that the large noncoding sequence is the main control region of maternally and paternally transmitted mitochondrial genomes of the marine mussel (Mytilus spp.). Genetics 167:835–50. Filipowicz M, Burzyn´ski A, S´mietanka B, Wenne R. (2008). Recombination in mitochondrial DNA of European mussels Mytilus. J Mol Evol 67:377–88.
Hoeh WR, Stewart DT, Saavedra C, Sutherland BW, Zouros E. (1997). Phylogenetic evidence for role-reversals of gender-associated mitochondrial DNA in Mytilus (Bivalvia: Mytilidae). Mol Biol Evol 14:959–67. Skibinski DOF, Gallagher C, Beynon CM. (1994). Mitochondrial DNA inheritance. Nature 368:817–18. S´mietanka B, Burzyn´ski A, Wenne R. (2010). Comparative genomics of marine mussels (Mytilus spp.) gender associated mtDNA: Rapidly evolving atp8. J Mol Evol 71:385–400. Stewart DT, Kenchington ER, Singh RK, Zouros E. (1996). Degree of selective constraint as an explanation of the different rates of evolution of gender-specific mitochondrial DNA lineages in the mussel Mytilus. Genetics 143:1349–57. Zouros E. (2000). The exceptional mitochondrial DNA system of the mussel family Mytilidae. Genes Genet Syst 75:313–18. Zouros E, Oberhauser Ball A, Saavedra C, Freeman KR. (1994). An unusual type of mitochondrial DNA inheritance in the blue mussel Mytilus. Proc Natl Acad Sci USA 91: 7463–7.
MITOGENOME ANNOUNCEMENT
Recombinant mitochondrial genome with standard transmission route from Mediterranean mussel Mytilus galloprovincialis Beata S´mietanka1, Monika Filipowicz1, and Artur Burzyn´ski1,2 Institute of Oceanology, Polish Academy of Sciences, Sopot, Poland and 2Institute of Biology and Environmental Protection, Pommeranian University in Sł upsk, Poland
Mitochondrial DNA Downloaded from informahealthcare.com by Ondokuz Mayis Univ. on 11/13/14 For personal use only.
1
Abstract
Keywords
Several bivalve species, including marine mussels Mytilus are atypical in having two genderspecific and highly divergent mtDNA genomes. This peculiar genetic system allows not only the recombination to occur but also facilitates its detection. Previous reports associated the existence of mosaic recombinant haplotypes with the switch of their transmission route. Here we report nearly complete sequence of a mitochondrial genome isolated from a homoplasmic female individual of Mediterranean Mytilus galloprovincialis. The genome has clear phylogenetic affinity with and organization identical to the M. galloprovincialis female haplotypes, in the coding part. However, the genome is very large, approximately 20,600 bp long, exclusively due to a long and complex control region. It contains an array of repeats, some of which are degenerated. A large part of the control region is derived from the paternal genome. This finding shows that not all haplotypes with recombinant control regions must be paternally inherited in Mytilus.
DUI, mitogenomics, recombination
The unusual system of mitochondrial DNA inheritance in marine mussels Mytilus results in the existence of two lineages of mitochondrial genomes. The genomes are either transmitted maternally (F) or paternally (M) (Skibinski et al., 1994; Zouros et al., 1994). The M genomes evolve faster than the F genomes, which could be due to relaxed selection (Stewart et al., 1996). Occasionally, an F genome may invade the paternal route, resetting their divergence to zero (masculinization, Hoeh et al., 1997). High frequency of recombinant genomes with the M-like M. edulis control region (CR) segments was observed in male Mytilus from the Baltic Sea (Burzyn´ski et al., 2006), supporting the hypothesis that a part of the M CR is necessary to masculinize the genome (Burzyn´ski et al., 2003; Cao et al., 2004; Zouros, 2000). The announced mitochondrial genome is derived from a female specimen of M. galloprovincialis. The sequence was obtained in the two step procedure involving long range PCR (S´mietanka et al., 2010). Primer sequences are available from the authors on request. It has been deposited in GenBank under accession number EF434638. Its nucleotide composition is typically biased towards A-T (62.2%), the coding part is also typical for Mytilus mitochondrial genomes and contains two
Correspondence: Artur Burzyn´ski, Institute of Oceanology, Polish Academy of Sciences, Powstan´co´w Warszawy 55, 81-712 Sopot, Poland. Tel: 48587311764. E-mail: [email protected]
History Received 3 March 2014 Revised 15 March 2014 Accepted 22 March 2014 Published online 14 April 2014
rRNA, 13 protein-coding and 23 tRNA genes including additional tRNA gene for methionine. The genetic distance from the nearest known mitochondrial genome (M. galloprovincialis F) is small, at 1.4% (2.8% from M. edulis and 18% from M. trossulus). No recombinantion signature was found in the coding part of this genome. This genome is one of the largest identified in Mytilus mussels: the total length of the obtained sequence is 18,518 bp, of which 2933 bp belong to the CR. It was impossible to sequence the whole CR due to the presence of multiple, long tandem repeats, plagued with homopolymeric runs, which seriously disrupted the sequencing. However, it was possible to amplify the whole CR with its flanks using pair of universal primers MF12S and MFCO2 (Filipowicz et al., 2008) and ascertain the overall CR structure (Figure 1). Based on this map and the sequence data it can be concluded that, the CR contains several recombination breakpoints and consists of two domains: F-specific and M-specific. The length of the F-specific part is comparable to the length of this part observed in haplotypes from 11a/15 group (Burzyn´ski et al., 2006), however, the M-like domain differs in length. In the Baltic haplogroup single M-like segment is approximately 1000 bp long. In the announced genome the CR contains an array of repeats, some of which have multiple deletion and are generally much shorter than in the Baltic case (800 bp max). This complex CR structure is consistent with the model of rearrangements proposed by Burzyn´ski et al. (2006). Under the proposed scenario the M-F recombination is one of the first steps in generating such structures. Despite its apparently long history following the recombination event, this genome is most likely inherited maternally, showing that acquisition of M-like sequences is not sufficient to switch the transmission route.
2
B. S´mietanka et al.
Mitochondrial DNA, Early Online: 1–2
Mitochondrial DNA Downloaded from informahealthcare.com by Ondokuz Mayis Univ. on 11/13/14 For personal use only.
Figure 1. Restriction fragments length polymorphism (RFLP) analysis of the PCR product containing the CR and obtained using MF12S and MFCO2 primers. DNA was digested with MboI and HpaII restriction enzymes separately, the digestion products were separated on the gel (top). Then the restriction maps were made (bottom), taking into account also the sequencing data, which spanned the regions shaded in gray.
Declaration of interest The authors are solely responsible for writing this manuscript.
References Burzyn´ski A, Zbawicka M, Skibinski DOF, Wenne R. (2003). Evidence for recombination of mtDNA in the marine mussel Mytilus trossulus from the Baltic. Mol Biol Evol 20:388–92. Burzyn´ski A, Zbawicka M, Skibinski DOF, Wenne R. (2006). Doubly uniparental inheritance is associated with high polymorphism for rearranged and recombinant control region haplotypes in Baltic Mytilus trossulus. Genetics 174:1081–94. Cao L, Kenchington E, Zouros E, Rodakis GC. (2004). Evidence that the large noncoding sequence is the main control region of maternally and paternally transmitted mitochondrial genomes of the marine mussel (Mytilus spp.). Genetics 167:835–50. Filipowicz M, Burzyn´ski A, S´mietanka B, Wenne R. (2008). Recombination in mitochondrial DNA of European mussels Mytilus. J Mol Evol 67:377–88.
Hoeh WR, Stewart DT, Saavedra C, Sutherland BW, Zouros E. (1997). Phylogenetic evidence for role-reversals of gender-associated mitochondrial DNA in Mytilus (Bivalvia: Mytilidae). Mol Biol Evol 14:959–67. Skibinski DOF, Gallagher C, Beynon CM. (1994). Mitochondrial DNA inheritance. Nature 368:817–18. S´mietanka B, Burzyn´ski A, Wenne R. (2010). Comparative genomics of marine mussels (Mytilus spp.) gender associated mtDNA: Rapidly evolving atp8. J Mol Evol 71:385–400. Stewart DT, Kenchington ER, Singh RK, Zouros E. (1996). Degree of selective constraint as an explanation of the different rates of evolution of gender-specific mitochondrial DNA lineages in the mussel Mytilus. Genetics 143:1349–57. Zouros E. (2000). The exceptional mitochondrial DNA system of the mussel family Mytilidae. Genes Genet Syst 75:313–18. Zouros E, Oberhauser Ball A, Saavedra C, Freeman KR. (1994). An unusual type of mitochondrial DNA inheritance in the blue mussel Mytilus. Proc Natl Acad Sci USA 91: 7463–7.
