Origin Of Light Strand Replication Research Articles

Mitochondrial haplotype and mito-nuclear matching drive somatic mutation and selection throughout ageing

Mitochondrial genomes co-evolve with the nuclear genome over evolutionary timescales and are shaped by selection in the female germline. Here we investigate how mismatching between nuclear and mitochondrial ancestry impacts the somatic evolution of the mitochondrial genome in different tissues throughout ageing. We used ultrasensitive duplex sequencing to profile ~2.5 million mitochondrial genomes across five mitochondrial haplotypes and three tissues in young and aged mice, cataloguing ~1.2 million mitochondrial somatic and ultralow-frequency inherited mutations, of which 81,097 are unique. We identify haplotype-specific mutational patterns and several mutational hotspots, including at the light strand origin of replication, which consistently exhibits the highest mutation frequency. We show that rodents exhibit a distinct mitochondrial somatic mutational spectrum compared with primates with a surfeit of reactive oxygen species-associated G > T/C > A mutations, and that somatic mutations in protein-coding genes exhibit signatures of negative selection. Lastly, we identify an extensive enrichment in somatic reversion mutations that ‘re-align’ mito-nuclear ancestry within an organism’s lifespan. Together, our findings demonstrate that mitochondrial genomes are a dynamically evolving subcellular population shaped by somatic mutation and selection throughout organismal lifetimes.

Complete mitochondrial genome and phylogenetic analysis of Triplophysa jianchuanensis (Cypriniformes: Cobitidae)

We used the Illumina MiSeq platform to sequence the complete mitochondrial genome of Triplophysa jianchuanensis (Cypriniformes: Cobitidae). The mitochondrial genome of T. jianchuanensis is 16,569 bp in length, and its genetic constitution and arrangement are consistent with those of the teleost taxon, containing 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, an origin of light-strand replication, and a control region. The overall nucleotide base composition was 28.33% A, 27.25% T, 17.77% G, and 26.65% C. Phylogenetic analysis showed that T. jianchuanensis was grouped with T. venusta. These findings are valuable for further studies on the evolution, genetic diversity, and taxonomy of Triplophysa.

The complete mitochondrial genome of Rhinogobius szechuanensis (Gobiiformes: Ggobiidae: Gobionellinae)

Here, we sequenced the complete mitogenome of Rhinogobius szechuanensis using the Illumina HiSeq platform and submitted the genome to Genbank with accession number OM617727. Assembly circular mitogenome (16,492 bp) consisted of 54.4% AT content, 13 protein-coding genes, 22 tRNA genes, two rRNA genes, an origin of light-strand replication, and a control region. Phylogenetic analysis supported that R. szechuanensis was grouped with R. rubromaculatus and clustered with other Rhinogobius species. The basal molecular data will be essential for further genetics studies such as evolution, taxonomy, DNA barcoding, and population genetics of Rhinogobius.

Comparative analyses of the complete mitochondrial genomes of two southern African endemic guitarfish, Acroteriobatus annulatus and A. blochii

Shark-like rays (order Rhinopristiformes) are among the most threatened cartilaginous fish globally. Despite this, unresolved taxonomic issues still exist within the group. To date, no studies have used complete mitochondrial genomes to assess the phylogenetic placement of Acroteriobatus within the non-monophyletic family Rhinobatidae. The current study reports the first complete mitochondrial genomes for Acroteriobatus annulatus and A. blochii. Similar to other rhinopristiforms, the complete sequences of A. annulatus (16,773 bp) and A. blochii (16,771 bp) were circular molecules with gene organisations identical to that of the typical vertebrate mitogenome. The A + T content was higher than the G + C content, with a bias towards A and C nucleotides observed in all complete mitogenomes. The stem-and-loop secondary structures of the putative origin of light-strand replication were found to have highly conserved synthesis and stem regions, with all substitutions and indels restricted to the loop structure. The ratios of non-synonymous to synonymous substitution rates indicated that purifying selection has been the dominant driver of evolution in rhinopristiform mitogenomes. Phylogenetic reconstructions placed Acroteriobatus as a sister-group to Rhinobatos, confirming its affiliation with the family Rhinobatidae. However, based on its apparent polyphyly with the aforementioned genera, the familial assignment of Pseudobatos is not fully resolved and requires further investigation.

Comparative Mitogenomics of Two Sympatric Catfishes of Exostoma (Siluriformes: Sisoridae) from the Lower Yarlung Tsangpo River and Its Application for Phylogenetic Consideration.

The genus Exostoma is a group of stenotopic and rheophilic glyptosternine catfishes distributed in South and Southeast Asia. So far, comprehensive studies on mitogenomics referring to this genus are very scarce. In this study, we first sequenced and annotated the complete mitochondrial genomes of Exostoma tibetanum and Exostoma tenuicaudatum—two sympatric congeners from the lower Yarlung Tsangpo River, Tibet, China. The mitogenomes of both species contained 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, one light-strand origin of replication, and one control region, with lengths of 16,528 bp and 16,533 bp, respectively. The mitogenome architecture, nucleotide composition, and codon usage of protein-coding genes were almost identical between the two Exostoma species, although some estimated parameters varied. Phylogenetic analysis strongly supported the monophyly of Exostoma in the subfamily Glyptosternae, and Exostoma tibetanum had the closest relationship to Exostoma tenuicaudatum. The divergence time estimation demonstrated that these two species diverged approximately 1.51 Ma during the early Pleistocene, which was speculated to be triggered by the river system changes caused by the uplift of the southeastern Tibetan Plateau. Selection pressure analyses indicated that all protein-coding genes of Exostoma species underwent a strong purifying selection, while minority positive sites from NADH dehydrogenase complex genes were detected. These findings are expected to promote our understanding of the molecular phylogeny of the genus Exostoma and provide valuable mitogenomic resources for the subfamily Glyptosternae.

Evolution of the Noncoding Features of Sea Snake Mitochondrial Genomes within Elapidae.

Mitochondrial genomes of four elapid snakes (three marine species [Emydocephalus ijimae, Hydrophis ornatus, and Hydrophis melanocephalus], and one terrestrial species [Sinomicrurus japonicus]) were completely sequenced by a combination of Sanger sequencing, next-generation sequencing and Nanopore sequencing. Nanopore sequencing was especially effective in accurately reading through long tandem repeats in these genomes. This led us to show that major noncoding regions in the mitochondrial genomes of those three sea snakes contain considerably long tandem duplications, unlike the mitochondrial genomes previously reported for same and other sea snake species. We also found a transposition of the light-strand replication origin within a tRNA gene cluster for the three sea snakes. This change can be explained by the Tandem Duplication—Random Loss model, which was further supported by remnant intervening sequences between tRNA genes. Mitochondrial genomes of true snakes (Alethinophidia) have been shown to contain duplicate major noncoding regions, each of which includes the control region necessary for regulating the heavy-strand replication and transcription from both strands. However, the control region completely disappeared from one of the two major noncoding regions for two Hydrophis sea snakes, posing evolutionary questions on the roles of duplicate control regions in snake mitochondrial genomes. The timing and molecular mechanisms for these changes are discussed based on the elapid phylogeny.

The complete mitochondrial genomes and phylogenetic analysis of two Nycteribiidae bat flies (Diptera: Hippoboscoidea)

We sequenced the complete mitochondrial genomes of two bat fly species within the Nycteribiidae (Diptera: Hippoboscoidea) – Dipseliopoda setosa (Cyclopodiinae) and Basilia ansifera (Nycteribiinae). Both mitogenomes were complete and contained 13 protein-coding genes, 22 tRNAs, and two rRNAs. Relative to the inferred ancestral gene order of dipteran mitochondrial genomes, no rearrangements were identified in either species. There were large differences in size between the two genomes, with D. setosa having a larger genome (19,164 bp) than B. ansifera (16,964 bp); both species had larger genomes than two previously published Streblidae bat fly species (e.g., Paradyschiria parvula and Paratrichobius longicrus). The increased genome sizes were due to expansions in the control region and the non-coding region downstream of the light-strand origin of replication. Additional differences between the two mitogenomes included a significantly longer cox3 gene in B. ansifera and a longer nad1 gene in D. setosa. Interestingly, both genomes also had the lowest GC content (D. setosa – 15.9%; B. ansifera – 17.0%) of any available Hippoboscoidea mitochondrial genome (18.8–23.9%). These mitogenomes represent the first sequences from species within the bat fly family Nycteribiidae. The sequence data here will provide a foundation for continued studies of genome evolution more generally within obligate blood-feeding ectoparasites, and specifically for the bat flies as vectors of significant ‘bat-associated’ viruses and microorganisms.

The complete mitochondrial genome sequence of Sinomicrurus peinani (Serpentes: Elapidae)

Sinomicrurus peinani is a new species of the genus Sinomicrurus (Serpentes: Elapidae) from China and Vietnam in 2020. In this study, we successfully sequenced mitochondrial genome of an individual S. peinani. The complete mitochondrial genome of S. peinani is a circular molecule with the entire length of 19,477 bp. The base composition is T (28.1%), G (11.9%), and GC (38.5%), which contains two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, 13 protein-coding genes, one origin of replication gene (D-loop), and two non-coding control regions, an origin of light-strand replication, and a 2346 bp non-coding region between tRNA-N and tRNA-Y. A maximum-likelihood (ML) tree of S. peinani and 13 other related species was constructed. The DNA data presented here will be useful to study the evolutionary relationships and genetic diversity of S. peinani.

Advanced age increases frequencies of de novo mitochondrial mutations in macaque oocytes and somatic tissues

Mutations in mitochondrial DNA (mtDNA) contribute to multiple diseases. However, how new mtDNA mutations arise and accumulate with age remains understudied because of the high error rates of current sequencing technologies. Duplex sequencing reduces error rates by several orders of magnitude via independently tagging and analyzing each of the two template DNA strands. Here, using duplex sequencing, we obtained high-quality mtDNA sequences for somatic tissues (liver and skeletal muscle) and single oocytes of 30 unrelated rhesus macaques, from 1 to 23 y of age. Sequencing single oocytes minimized effects of natural selection on germline mutations. In total, we identified 17,637 tissue-specific de novo mutations. Their frequency increased ∼3.5-fold in liver and ∼2.8-fold in muscle over the ∼20 y assessed. Mutation frequency in oocytes increased ∼2.5-fold until the age of 9 y, but did not increase after that, suggesting that oocytes of older animals maintain the quality of their mtDNA. We found the light-strand origin of replication (OriL) to be a hotspot for mutation accumulation with aging in liver. Indeed, the 33-nucleotide-long OriL harbored 12 variant hotspots, 10 of which likely disrupt its hairpin structure and affect replication efficiency. Moreover, in somatic tissues, protein-coding variants were subject to positive selection (potentially mitigating toxic effects of mitochondrial activity), the strength of which increased with the number of macaques harboring variants. Our work illuminates the origins and accumulation of somatic and germline mtDNA mutations with aging in primates and has implications for delayed reproduction in modern human societies.

Characterization of the complete mitochondrial genome of Garra motuoensis (Cypriniformes: Cyprinidae) and its phylogenetic position within genus Garra

Garra motuoensis, an endemic labeonine fish, was reported distributed in the lower Yarlung Tsangpo River drainage with little published biological information. Herein, we sequenced and characterized the complete mitochondrial genome of G. motuoensis, which was 16,806 bp in length, containing 13 PCGs, 22 tRNA genes, two rRNA genes, one light strand replication origin (OL ), one control region (D-loop), and one replication region. Phylogenetic analysis based on 13 PCGs sequences revealed that G. motuoensis had a closest relationship with G. qiaojiensis. Then, both species clustered with other species of Garra, and next grouped with other genera of subfamily Labeoninae.

The complete mitochondrial genome of Formosania galericula (Cypriniformes: Gastromyzontidae)

This study determined the complete mitochondrial genome of Formosania galericula (Cypriniformes: Gastromyzontidae) from Zhejiang, China, for the first time. The complete mitochondrial genome of F. galericula was sequenced to be 16,555 bp in length. The genome contained 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs, two central non-coding regions (the control region and the origin of light strand replication), identical to most other vertebrates. Phylogenetic analysis highly supported that F. galericula was close to Crossostoma lacustre and the genus Vanmanenia fish. However, F. galericula was not firstly clustered with Formosania chenyiyui but after the genus Vanmanenia fish. These data would explain the evolutionary mechanisms and biogeography of the family Gastromyzontidae and is helpful for the conservation of genetics and stock evaluation for F. galericula.

The complete mitochondrial genome of Japanese sea lion, Zalophus japonicus (Carnivora: Otariidae) analyzed using the excavated skeletal remains from Ulleungdo, South Korea

The Japanese sea lion, Zalophus japonicus, is an extinct pinniped species, which had inhabited along the coast of the Japanese archipelago and Korean peninsula. Its mitochondrial genome was determined by the assembly of PCR amplicons from the skeletal remains excavated from the Ulleungdo, South Korea. The whole mitogenome was 16,698 bp in length, which encoded 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNA), 2 ribosomal RNAs (rRNA), an origin of light-strand replication (OL), and a control region (D-loop). Unusual start codons were identified in ND2 (ATA), ND3 (ATA), and ND5 (ATC), while COIII, ND3, and ND4 were terminated with an incomplete stop codon (T–/TA-). Phylogenetic analysis showed that Z. japonicus was a sister species to Z. californianus with 98.61% nucleotide sequence identity among 11 pinniped species in the infraorder Pinnipedia, which supported the previous results. The complete mitochondrial genome sequence of Z. japonicus would be valuable information for its restoration and the evolutional understandings of pinniped species in the Pacific Ocean.

The determination and analysis of the complete mitochondrial genome of Dario dario (Anabantiformes: Badidae)

The classification of Badidae family based on morphology has been revised several times, but data on complete mitogenome are scarce, the complete mitochondrial genome of the Badidae fish Dario dario was characterized for the first time in the present study. The whole mitogenome was 16,830 bp in size and consisted of 13 protein-coding genes, 22 tRNAs, two rRNAs genes, a control region and origin of light-strand replication. The proportion of coding sequences with a total length of 11,431 bp was 67.92%, which encoded 3800 amino acids. The genome composition was highly A + T biased (58.12%), and exhibited a negative AT-skew (–0.0045) and GC-skew (–0.2347). All protein-coding genes started with ATG except for GTG in CO1, while stopped with the standard TAN codons or a single T. The control region (D-loop) ranging from 15,658 bp to 16,830 bp was 1173 bp in size. Phylogenetic analysis showed that D. dario was most closely related to Badis badis. The complete mitochondrial genome sequence provided new insight into taxonomic classification, and a more complex picture of species diversity within the Anabantiformes.

The mitochondrial genome of Sinobdella sinensis (Synbranchiformes: Mastacembelidae) from China's Qiantang River

This study determined the mitochondrial genome of Sinobdella sinensis (Synbranchiformes: Mastacembelidae) from China's Qiantang River for the first time. The mitochondrial genome of S. sinensis was sequenced to be 16,543 bp in length, larger than S. sinensis from China's Yangtze River. The genome contains 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs, two central non-coding regions (the control region and the origin of light strand replication), identical to most other vertebrates. Phylogenetic analysis highly supported that S. sinensis from China's Qiantang River was different from other Mastacembelus fish. However, it showed a close relationship with Macrognathus aculeatus. These data would explain the evolutionary mechanisms and biogeography of the family Mastacembelidae and is helpful for the conservation of genetics and stock evaluation for S. sinensis.

Complete mitochondrial genome of the Caribbean reef shark, Carcharhinus perezi (Carcharhinformes: Carcharhinidae)

The Caribbean reef shark (Carcharhinus perezi; Poey, 1876) is a medium to large-bodied coastal and reef-associated predator found throughout the subtropical and tropical waters of the Atlantic Ocean and Caribbean Sea, although its populations are increasingly threatened by overfishing. We describe the first mitochondrial genome sequence for this species, using Illumina MiSeq sequencing of an individual from The Bahamas. We report the mitogenome sequence of the Caribbean reef shark to be 16,709 bp and composed two rRNA genes, 22 tRNA genes, 13 protein-coding genes, 2 non-coding regions; the D-loop control region and the origin of light-strand replication. We discuss the implications of this new information on future monitoring efforts and conservation measures such as marine protected areas, and urge for greater application of mitochondrial studies of sharks in the Atlantic Ocean.

The complete mitochondrial genome of Hemitripterus villosus (Pallas, 1814) from Zhoushan archipelago

In this study, we used whole genome sequencing to obtain the complete mitochondrial genome of Hemitripterus villosus. This mitochondrial genome, consisting of 17,449 base pairs (bp), contains 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs and 2 noncoding control regions (control region and origin of light-strand replication) as those found in other vertebrates. Control region, of 1799 bp in length, is located between tRNAPro and tRNAPhe. We identified short tandem repeat sequences in the control region, which contributed largely to the relatively long mitogenome. The complete mitogenome data provides useful genetic markers for the studies on the molecular identification, phylogenetic analysis and conservation genetics.

Comparative mitochondrial genome analysis of the Mongolian redfin, Chanodichthys mongolicus (Xenocyprididae) from China reveals heteroplasmy

This study determined the mitochondrial genome (mitogenome) of Chanodichthys mongolicus from China's Qiantang River and analyzed its phylogenetic history in the Subfamily Cultrinae. Next-generation sequencing was used to obtain the mitogenome of C. mongolicus, GenBank Accession Number MZ032228. The mitochondrial genome length of C. mongolicus from China's Qiantang River is 16,622 bp. The genome contains 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs, and two central noncoding regions (the control region and the origin of light strand replication). Based on BLAST comparisons, the sequence identity of C. mongolicus MZ032228 from China's Qiantang River was 99.84% to that of Ancherythroculter wangi MG783573 from China's Nei River, 99.75% to C. mongolicus AP009060 from Russia's Black River. The phylogenetic analysis is consistent with BLAST comparisons in confirming that A. wangi MG783573 and C. mongolicus MZ032228 show a high genetic similarity. This study also confirms mitochondrial DNA heteroplasmy in C. mongolicus for the first time and documents 35 heterogeneous loci that were detected.

The complete mitochondrial genome of the barcheek trevally, Carangoides plagiotaenia Bleeker, 1857 from Beqa Lagoon in Fiji

The complete mitochondrial genome of the Barcheek trevally, Carangoides plagiotaenia Bleeker, 1857 from Beqa lagoon, Fiji Islands, was determined by high-throughput sequencing (HTS). Its mitogenome (16,551 bp) contained the typical 37 genes, including 13 protein-coding genes (PCGs), 2 ribosomal RNAs, 22 tRNAs, along with two non-coding regions: control region (D-loop) and the origin of light-strand replication (OL). In its mitogenome, one unusual start codon (GTG) was identified in COI and incomplete stop codons (TA-/T–) were predicted in seven PCGs including ND2, COII, ATP6, COIII, ND3, ND4 and CytB. The phylogenetic tree revealed that C. plagiotaenia is sister to C. bajad with 88.75% nucleotide identity in 13 PCGs and 90.49% in the complete mitogenomes.

The complete mitochondrial genome of Platycephalus sp.1 (Teleostei, Platycephalidae) obtained by whole genome sequencing

In this study, we used next-generation sequencing to obtain the complete mitochondrial genome of Platycephalus sp.1. This mitochondrial genome, consisting of 16,552 base pairs (bp), contains 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNAs, and two non-coding control regions (control region and origin of light-strand replication) as those found in other vertebrates. Control region, of 877 bp in length, is located between tRNAPro and tRNAPhe. Within the control region, typical conserved domains, such as the termination-associated sequence, central and conserved sequence blocks domains were identified. The overall base composition shows 25.83% of T, 29.98% of C, 27.01% of A, and 17.18% of G, with a slight A + T rich feature (52.84%). The complete mitogenome data provides useful genetic markers for the studies on the molecular identification, population genetics, phylogenetic analysis and conservation genetics.

The first determination and analysis of the complete mitochondrial genome of Ancistrus temmincki (Siluriformes: Loricariidae)

In order to fully comprehend the evolution and kinship of fishes in the family of Loricariidae, the complete mitochondrial genome of the Loricariidae fish Ancistrus temmincki was firstly characterized in the present study. The whole mitogenome was 16,657 bp in size and consisted of 13 protein-coding genes, 22 tRNAs, 2 rRNAs genes, a control region and origin of light-strand replication. The proportion of coding sequences with a total length of 11,473 bp was 68.88%, which encoded 3,813 amino acids. The genome composition was highly A + T biased (56.29%), and exhibited AT-skew (0.0661) and a negative GC-skew (–0.2740). All protein-coding genes were started with ATG except for GTG in CO1, while stopped with the standard TAN codons or a single T. The control region (D-loop) ranging from 15,635 bp to 16,657 bp was 1023 bp in size. Until now, there is hardly any studies on the complete mitochondrial sequence in the genus of Ancistrus, phylogenetic analysis showed that A. temmincki was most closely related to Ancistrus cryptophthalmus in the genus of Ancistrus. The complete mitochondrial genome sequence has provided a new insight into the taxonomic classification, and a more complex picture of the species diversity within the family of Loricariidae.