Conservation of structural elements in the mitochondrial control region of Daphnia

Kuhn, Kerstin; Streit, Bruno; Schwenk, Klaus

doi:10.1016/j.gene.2008.05.020

Cited by 29 publications

(9 citation statements)

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“…In addition to the customary characteristics used to identify the mitochondrial control region of replication in animals (i.e., the largest noncoding region, increased AT content, and presence of repetitive elements and secondary structures) (Boore 1999;Saccone et al 2002;Cao et al 2004a;Saito et al 2005;Kuhn et al 2006;Oliveira et al 2007;Brugler and France 2008), we also used AT-skew values of protein-coding genes at fourfold redundant sites to locate the origins of heavy (O H ) and light (O L ) strand replication in freshwater bivalves. In most metazoans, the mitochondrial DNA genome replicates with a strand-asynchronous, asymmetric mechanism during which the parental heavy (H) strand becomes temporarily single-stranded DNA (ssDNA) while the nascent H strand is synthesized, and when the heavy strand synthesis reaches two-thirds of the genome, it exposes the O L and initiates the synthesis of a new light (L) strand in the opposite direction (Clayton 1982;Reyes et al 1998).…”

Section: Methodsmentioning

confidence: 99%

“…Typically, the main control region of animal mitochondrial genomes corresponds to (i) the longest noncoding region, (ii) a region in which repetitive elements and secondary structures frequently occur, (iii) a region containing relatively high A 1 T content, and/or (iv) a region associated with abrupt changes in base composition bias (Lewis et al 1994;Boore 1999;Saccone et al 2002;Serb and Lydeard 2003;Cao et al 2004a;Saito et al 2005;Kuhn et al 2006;Oliveira et al 2007;Brugler and France 2008). In the mytiloid mussel Mytilus, for example, the putative control region has been identified as such because it is the largest noncoding region, and it is capable of producing characteristic secondary structures (Cao et al 2004a).…”

Section: Regions B C and A)mentioning

confidence: 99%

“…In the F genome of this species, F nd5-trnQ is 1196 bp long (i.e., 910 bp longer than the second largest unassigned region in trnE-trnW) and it has a higher A 1 T content (67.5%) compared to the other parts of the genome (Tables 1 and 3; A 1 T for trnE-trnW ¼ 51%). High A 1 T content is also a characteristic typically used to identify origins of replication (e.g., Lewis et al 1994;Serb and Lydeard 2003;Kuhn et al 2006). There are eight consecutive repeats of a 106-bp element with the potential to form stem-loop structures, with an additional incomplete repeat on each side of the eightrepeat cluster.…”

Section: Regions B C and A)mentioning

confidence: 99%

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Comparative Mitochondrial Genomics of Freshwater Mussels (Bivalvia: Unionoida) With Doubly Uniparental Inheritance of mtDNA: Gender-Specific Open Reading Frames and Putative Origins of Replication

et al. 2009

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Doubly uniparental inheritance (DUI) of mitochondrial DNA in marine mussels (Mytiloida), freshwater mussels (Unionoida), and marine clams (Veneroida) is the only known exception to the general rule of strict maternal transmission of mtDNA in animals. DUI is characterized by the presence of genderassociated mitochondrial DNA lineages that are inherited through males (male-transmitted or M types) or females (female-transmitted or F types), respectively. This unusual system constitutes an excellent model for studying basic aspects of mitochondrial DNA inheritance and the evolution of mtDNA genomes in general.Here we compare published mitochondrial genomes of unionoid bivalve species with DUI, with an emphasis on characterizing unassigned regions, to identify regions of the F and M mtDNA genomes that could (i) play a role in replication or transcription of the mtDNA molecule and/or (ii) determine whether a genome will be transmitted via the female or the male gamete. Our results reveal the presence of one Fspecific and one M-specific open reading frames (ORFs), and we hypothesize that they play a role in the transmission and/or gender-specific adaptive functions of the M and F mtDNA genomes in unionoid bivalves. Three major unassigned regions shared among all F and M unionoid genomes have also been identified, and our results indicate that (i) two of them are potential heavy-strand control regions (O H ) for regulating replication and/or transcription and that (ii) multiple and potentially bidirectional light-strand origins of replication (O L ) are present in unionoid F and M mitochondrial genomes. We propose that unassigned regions are the most promising candidate sequences in which to find regulatory and/or genderspecific sequences that could determine whether a mitochondrial genome will be maternally or paternally transmitted.

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Section: Methodsmentioning

confidence: 99%

Section: Regions B C and A)mentioning

confidence: 99%

Section: Regions B C and A)mentioning

confidence: 99%

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Comparative Mitochondrial Genomics of Freshwater Mussels (Bivalvia: Unionoida) With Doubly Uniparental Inheritance of mtDNA: Gender-Specific Open Reading Frames and Putative Origins of Replication

et al. 2009

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“…The mt genome in animals typically contains 37 genes (13 protein-coding, two ribosomal, and 22 transfer RNA genes) and one major non-coding region, the displacement loop or D-loop. The D-loop is the control region with a number of regulatory elements, such as extended termination-associated sequences (ETASs) and conserved sequence blocks (CSBs) that are responsible for replication and transcription of the mtDNA [16][17][18][19][20][21][22]. Although, overall, animal mt genomes are highly conserved in size and protein-coding components, substantial variations, including substitutions and indels [22,23], do exist, providing clues for functional differentiation.…”

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confidence: 99%

Mitochondrial genome sequences of Artemia tibetiana and Artemia urmiana: assessing molecular changes for high plateau adaptation

Zhang

Luo

Sun

et al. 2013

Sci. China Life Sci.

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Brine shrimps, Artemia (Crustacea, Anostraca), inhabit hypersaline environments and have a broad geographical distribution from sea level to high plateaus. Artemia therefore possess significant genetic diversity, which gives them their outstanding adaptability. To understand this remarkable plasticity, we sequenced the mitochondrial genomes of two Artemia tibetiana isolates from the Tibetan Plateau in China and one Artemia urmiana isolate from Lake Urmia in Iran and compared them with the genome of a low-altitude Artemia, A. franciscana. We compared the ratio of the rate of nonsynonymous (Ka) and synonymous (Ks) substitutions (Ka/Ks ratio) in the mitochondrial protein-coding gene sequences and found that atp8 had the highest Ka/Ks ratios in comparisons of A. franciscana with either A. tibetiana or A. urmiana and that atp6 had the highest Ka/Ks ratio between A. tibetiana and A. urmiana. Atp6 may have experienced strong selective pressure for high-altitude adaptation because although A. tibetiana and A. urmiana are closely related they live at different altitudes. We identified two extended termination-associated sequences and three conserved sequence blocks in the D-loop region of the mitochondrial genomes. We propose that sequence variations in the D-loop region and in the subunits of the respiratory chain complexes independently or collectively contribute to the adaptation of Artemia to different altitudes. mitochondrial genome, Artemia tibetiana, sequence variation, high plateau species Citation:Zhang H X, Luo Q B, Sun J, et al. Mitochondrial genome sequences of Artemia tibetiana and Artemia urmiana: assessing molecular changes for high plateau adaptation. Sci China Life Sci, 2013Sci, , 56: 440 -452, doi: 10.1007 Brine shrimps, Artemia (Crustacea, Anostraca), have a broad geographical distribution and inhabit hypersaline environments that vary considerably in their anionic composition, climate, and altitude. The major anions that contribute to anionic composition include chloride, sulfate, carbonate, or combinations of up to all three [1]. Artemia species can be found in altitudes from sea level to over 4000 m above sea level; for example, in Tibet (4000 m) and in the East African Plateau (over 5000 m). Artemia can survive in harsh environments other than in high salinity, including low atmospheric pressure, rarefied air, cold temperature, and long winters, as well as in climatological conditions that range from humid to arid [2]. Artemia species are capable of switching their reproduction strategies between sexual and parthenogenetic forms in a single life cycle [1,3,4], and populations can survive through cold winters by producing diapause cysts [5][6][7]. Because of their distinct features, Ar- Zhang H X, et al. Sci China Life Sci May (2013) Vol.56 No.5 441 temia draw significant scientific interest from several areas including ecology, aquaculture, physiology, ecotoxicology, and genetics [8][9][10][11][12]. Animal mitochondrial (mt) genomes are circular DNA molecules ~17 kb in length that encode the ma...

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“…In comparison with the mitogenomes of R. flavipes, the rate of sequence conservation varied considerably among different gene regions (Table 4). In particular, CR is known to show much more genetic variation than other mitochondrial regions and is appropriate for population genetics studies below species level (Vila and Björklund, 2004;Kuhn et al, 2008). Thus, more detailed phylogeographic analyses using additional mitochondrial sequences from a wider area should provide information useful for the understanding of the origin and distribution of C. formosanus.…”

Section: Discussionmentioning

confidence: 99%

The complete mitogenome of the Formosan termite, Coptotermes formosanus Shiraki

2011

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The Formosan termite Coptotermes formosanus Shiraki is a well-known invasive pest that causes severe damage to wooden structures in many parts of the world.Although several studies examined its phylogeographic patterns using a few mitochondrial genes, the phylogenetic relationships among C. formosanus are poorly understood because of the small number of mutations known among its mitochondrial genes. To provide a useful genetic tool for further analyses, we analyzed the complete mitochondrial genome sequence of C. formosanus using specimens collected from three isolated islands in the Ryukyu Archipelago of Japan. The circular mitogenome of these termites consisted of genes encoding 22 transfer RNAs, two ribosomal RNAs, and 13 mitochondrial proteins, as is the case for most animal mitochondrial genomes. The G ? C content was 34.1%, and the total length varied slightly between 16,234 and 16,236 base pairs. The complete mitochondrial genomes of the three populations were more than 99.9% identical to each other and showed differences at six nucleotide positions. The COII, 12S rRNA, and 16S rRNA genes that are commonly used for phylogenetic analyses revealed only one substitution or no substitutions. The mitogenome sequences determined here should contribute to the design of new molecular markers for the clarification of the historical distribution process of C. formosanus and for further phylogenetic analyses with this and related termite species.

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Conservation of structural elements in the mitochondrial control region of Daphnia

Cited by 29 publications

References 43 publications

Comparative Mitochondrial Genomics of Freshwater Mussels (Bivalvia: Unionoida) With Doubly Uniparental Inheritance of mtDNA: Gender-Specific Open Reading Frames and Putative Origins of Replication

Comparative Mitochondrial Genomics of Freshwater Mussels (Bivalvia: Unionoida) With Doubly Uniparental Inheritance of mtDNA: Gender-Specific Open Reading Frames and Putative Origins of Replication

Mitochondrial genome sequences of Artemia tibetiana and Artemia urmiana: assessing molecular changes for high plateau adaptation

The complete mitogenome of the Formosan termite, Coptotermes formosanus Shiraki

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