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Journal articles on the topic 'Mitogenomics'

Author: Grafiati
Published: 4 June 2021
Last updated: 18 June 2025

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1

Osca, David, José Templado, and Rafael Zardoya. "Caenogastropod mitogenomics." Molecular Phylogenetics and Evolution 93 (December 2015): 118–28. http://dx.doi.org/10.1016/j.ympev.2015.07.011.

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2

Ho, Simon Y. W., and M. Thomas P. Gilbert. "Ancient mitogenomics." Mitochondrion 10, no. 1 (2010): 1–11. http://dx.doi.org/10.1016/j.mito.2009.09.005.

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3

Halasan, Lorenzo C., and Hsiu-Chin Lin. "Diagnostic applicability of mitogenomics in uncovering intraspecific carangid diversifications: insights into phylogeny, divergence time, and characterization of two cryptic Selaroides leptolepis mitogenomes." Organisms Diversity & Evolution 24, no. 3 (2024): 417–34. https://doi.org/10.1007/s13127-024-00648-9.

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Halasan, Lorenzo C., Lin, Hsiu-Chin (2024): Diagnostic applicability of mitogenomics in uncovering intraspecific carangid diversifications: insights into phylogeny, divergence time, and characterization of two cryptic Selaroides leptolepis mitogenomes. Organisms Diversity & Evolution 24 (3): 417-434, DOI: 10.1007/s13127-024-00648-9, URL: https://doi.org/10.1007/s13127-024-00648-9
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4

Horreo, Jose L. "Revisiting the mitogenomic phylogeny of Salmoninae: new insights thanks to recent sequencing advances." PeerJ 5 (September 18, 2017): e3828. http://dx.doi.org/10.7717/peerj.3828.

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The phylogeny of the Salmonidae family, the only living one of the Order Salmoniformes, remains still unclear because of several reasons. Such reasons include insufficient taxon sampling and/or DNA information. The use of complete mitochondrial genomes (mitogenomics) could provide some light on it, but despite the high number of mitogenomes of species belonging to this family published during last years, an integrative work containing all this information has not been done. In this work, the phylogeny of 46 Salmonidae species was inferred from their mitogenomic sequences. Results include a Bayesian molecular-dated phylogenetic tree with very high statistical support showing Coregoninae and Salmoninae as sister subfamilies, as well as several new phylogenetic relationships among species and genus of the family. All these findings contribute to improve our understanding of the Salmonidae systematics and could have consequences on related evolutionary studies, as well as highlight the importance of revisiting phylogenies with integrative studies.
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5

Bellini, Bruno Cavalcante, Feng Zhang, Paolla Gabryelle Cavalcante de Souza, Renata Clicia dos Santos-Costa, Gleyce da Silva Medeiros, and Nerivânia Nunes Godeiro. "The Evolution of Collembola Higher Taxa (Arthropoda, Hexapoda) Based on Mitogenome Data." Diversity 15, no. 1 (2022): 7. http://dx.doi.org/10.3390/d15010007.

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Mitogenomes represent useful tools for investigating the phylogeny of many metazoan clades. Regarding Collembola, the use of mitogenomics has already shown promising results, but few published works include sufficient taxon sampling to study its evolution and systematics on a broader scale. Here, we present a phylogenetic study based on the mitogenomes of 124 species from 24 subfamilies, 16 families, and four orders—one of the most comprehensive datasets used in a molecular study of Collembola evolution to date—and compare our results with the trees from recently published papers and traditional systematic hypotheses. Our main analysis supported the validity of the four orders and the clustering of Poduromorpha with Entomobryomorpha (the traditional Arthropleona). Our data also supported the split of Symphypleona s. str. into the Appendiciphora and Sminthuridida suborders, and the division of the Neelipleona into two subfamilies: Neelinae and Neelidinae subfam. nov. On the other hand, the traditional Symphypleona s. lat., Isotomoidea, and all the Isotomidae subfamilies were refuted by our analyses, indicating a need for a systematic revision of the latter family. Though our results are endorsed by many traditional and recent systematic findings, we highlight a need for additional mitogenomic data for some key taxa and the inclusion of nuclear markers to resolve some residual problematic relationships.
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6

Botero-Castro, Fidel, Marie-ka Tilak, Fabienne Justy, François Catzeflis, Frédéric Delsuc, and Emmanuel J.P. Douzery. "Next-generation sequencing and phylogenetic signal of complete mitochondrial genomes for resolving the evolutionary history of leaf-nosed bats (Phyllostomidae)." Molecular Phylogenetics and Evolution 69, no. 3 (2013): 728–39. https://doi.org/10.5281/zenodo.13421392.

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(Uploaded by Plazi for the Bat Literature Project) Leaf-nosed bats (Phyllostomidae) are one of the most studied groups within the order Chiroptera mainly because of their outstanding species richness and diversity in morphological and ecological traits. Rapid diversification and multiple homoplasies have made the phylogeny of the family difficult to solve using morphological characters. Molecular data have contributed to shed light on the evolutionary history of phyllostomid bats, yet several relationships remain unresolved at the intra-familial level. Complete mitochondrial genomes have proven useful to deal with this kind of situation in other groups of mammals by providing access to a large number of molecular characters. At present, there are only two mitogenomes available for phyllostomid bats hinting at the need for further exploration of the mitogenomic approach in this group. We used both standard Sanger sequencing of PCR products and next-generation sequencing (NGS) of shotgun genomic DNA to obtain new complete mitochondrial genomes from 10 species of phyllostomid bats, including representatives of major subfamilies, plus one outgroup belonging to the closely-related mormoopids. We then evaluated the contribution of mitogenomics to the resolution of the phylogeny of leaf-nosed bats and compared the results to those based on mitochondrial genes and the RAG2 and VWF nuclear makers. Our results demonstrate the advantages of the Illumina NGS approach to efficiently obtain mitogenomes of phyllostomid bats. The phylogenetic signal provided by entire mitogenomes is highly comparable to the one of a concatenation of individual mitochondrial and nuclear markers, and allows increasing both resolution and statistical support for several clades. This enhanced phylogenetic signal is the result of combining markers with heterogeneous evolutionary rates representing a large number of nucleotide sites. Our results illustrate the potential of the NGS mitogenomic approach for resolving the evolutionary history of phyllostomid bats based on a denser species sampling.
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7

Botero-Castro, Fidel, Marie-ka Tilak, Fabienne Justy, François Catzeflis, Frédéric Delsuc, and Emmanuel J.P. Douzery. "Next-generation sequencing and phylogenetic signal of complete mitochondrial genomes for resolving the evolutionary history of leaf-nosed bats (Phyllostomidae)." Molecular Phylogenetics and Evolution 69, no. 3 (2013): 728–39. https://doi.org/10.5281/zenodo.13421392.

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(Uploaded by Plazi for the Bat Literature Project) Leaf-nosed bats (Phyllostomidae) are one of the most studied groups within the order Chiroptera mainly because of their outstanding species richness and diversity in morphological and ecological traits. Rapid diversification and multiple homoplasies have made the phylogeny of the family difficult to solve using morphological characters. Molecular data have contributed to shed light on the evolutionary history of phyllostomid bats, yet several relationships remain unresolved at the intra-familial level. Complete mitochondrial genomes have proven useful to deal with this kind of situation in other groups of mammals by providing access to a large number of molecular characters. At present, there are only two mitogenomes available for phyllostomid bats hinting at the need for further exploration of the mitogenomic approach in this group. We used both standard Sanger sequencing of PCR products and next-generation sequencing (NGS) of shotgun genomic DNA to obtain new complete mitochondrial genomes from 10 species of phyllostomid bats, including representatives of major subfamilies, plus one outgroup belonging to the closely-related mormoopids. We then evaluated the contribution of mitogenomics to the resolution of the phylogeny of leaf-nosed bats and compared the results to those based on mitochondrial genes and the RAG2 and VWF nuclear makers. Our results demonstrate the advantages of the Illumina NGS approach to efficiently obtain mitogenomes of phyllostomid bats. The phylogenetic signal provided by entire mitogenomes is highly comparable to the one of a concatenation of individual mitochondrial and nuclear markers, and allows increasing both resolution and statistical support for several clades. This enhanced phylogenetic signal is the result of combining markers with heterogeneous evolutionary rates representing a large number of nucleotide sites. Our results illustrate the potential of the NGS mitogenomic approach for resolving the evolutionary history of phyllostomid bats based on a denser species sampling.
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8

Schierwater, Bernd, Peter Stadler, Robert DeSalle, and Lars Podsiadlowski. "Mitogenomics and metazoan evolution." Molecular Phylogenetics and Evolution 69, no. 2 (2013): 311–12. http://dx.doi.org/10.1016/j.ympev.2013.08.009.

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9

Vieira, Gabriel A., and Francisco Prosdocimi. "Accessible molecular phylogenomics at no cost: obtaining 14 new mitogenomes for the ant subfamily Pseudomyrmecinae from public data." PeerJ 7 (January 24, 2019): e6271. http://dx.doi.org/10.7717/peerj.6271.

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The advent of Next Generation Sequencing has reduced sequencing costs and increased genomic projects from a huge amount of organismal taxa, generating an unprecedented amount of genomic datasets publicly available. Often, only a tiny fraction of outstanding relevance of the genomic data produced by researchers is used in their works. This fact allows the data generated to be recycled in further projects worldwide. The assembly of complete mitogenomes is frequently overlooked though it is useful to understand evolutionary relationships among taxa, especially those presenting poor mtDNA sampling at the level of genera and families. This is exactly the case for ants (Hymenoptera:Formicidae) and more specifically for the subfamily Pseudomyrmecinae, a group of arboreal ants with several cases of convergent coevolution without any complete mitochondrial sequence available. In this work, we assembled, annotated and performed comparative genomics analyses of 14 new complete mitochondria from Pseudomyrmecinae species relying solely on public datasets available from the Sequence Read Archive (SRA). We used all complete mitogenomes available for ants to study the gene order conservation and also to generate two phylogenetic trees using both (i) concatenated set of 13 mitochondrial genes and (ii) the whole mitochondrial sequences. Even though the tree topologies diverged subtly from each other (and from previous studies), our results confirm several known relationships and generate new evidences for sister clade classification inside Pseudomyrmecinae clade. We also performed a synteny analysis for Formicidae and identified possible sites in which nucleotidic insertions happened in mitogenomes of pseudomyrmecine ants. Using a data mining/bioinformatics approach, the current work increased the number of complete mitochondrial genomes available for ants from 15 to 29, demonstrating the unique potential of public databases for mitogenomics studies. The wide applications of mitogenomes in research and presence of mitochondrial data in different public dataset types makes the “no budget mitogenomics” approach ideal for comprehensive molecular studies, especially for subsampled taxa.
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10

Xu, Shiwen, Yunfei Wu, Yingqi Liu, et al. "Comparative Mitogenomics and Phylogenetic Analyses of Pentatomoidea (Hemiptera: Heteroptera)." Genes 12, no. 9 (2021): 1306. http://dx.doi.org/10.3390/genes12091306.

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Pentatomoidea is the largest superfamily of Pentatomomorpha; however, the phylogenetic relationships among pentatomoid families have been debated for a long time. In the present study, we gathered the mitogenomes of 55 species from eight common families (Acanthosomatidae, Cydnidae, Dinidoridae, Scutelleridae, Tessaratomidae, Plataspidae, Urostylididae and Pentatomidae), including 20 newly sequenced mitogenomes, and conducted comparative mitogenomic studies with an emphasis on the structures of non-coding regions. Heterogeneity in the base composition, and contrasting evolutionary rates were encountered among the mitogenomes in Pentatomoidea, especially in Urostylididae, which may lead to unstable phylogenetic topologies. When the family Urostylididae is excluded in taxa sampling or the third codon positions of protein coding genes are removed, phylogenetic analyses under site-homogenous models could provide more stable tree topologies. However, the relationships between families remained the same in all PhyloBayes analyses under the site-heterogeneous mixture model CAT + GTR with different datasets and were recovered as (Cydnidae + (((Tessaratomidae + Dinidoridae) + (Plataspidae + Scutelleridae)) + ((Acanthosomatidae + Urostylididae) + Pentatomidae)))). Our study showed that data optimizing strategies after heterogeneity assessments based on denser sampling and the use of site-heterogeneous mixture models are essential for further analysis of the phylogenetic relationships of Pentatomoidea.
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11

Powell, Chanté, Virgilio Caleca, Clint Rhode, Luis Teixeira da Costa, and Barbara van Asch. "New Mitochondrial Gene Rearrangement in Psyttalia concolor, P. humilis and P. lounsburyi (Hymenoptera: Braconidae), Three Parasitoid Species of Economic Interest." Insects 11, no. 12 (2020): 854. http://dx.doi.org/10.3390/insects11120854.

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The family Braconidae consists mostly of specialized parasitoids, some of which hold potential in biocontrol of agricultural pests. Psyttalia concolor, Psyttalia humilis and Psyttalia lounsburyi are parasitoids associated with Bactrocera oleae, a major pest of cultivated olives. The native range of Psyttalia concolor is the Mediterranean, and P. humilis and P. lounsburyi are native to sub-Saharan Africa. This study reports the mitochondrial genomes of the three species, thus laying the foundation for mitogenomic analyses in the genus Psyttalia. Comparative mitogenomics within Braconidae showed a novel gene arrangement in Psyttalia in involving translocation and inversion of transfer RNA genes. The placement of Psyttalia in the subfamily Opiinae was well-supported, and the divergence between Psyttalia and its closest relative (Diachasmimorpha longicaudata) was at ~55 MYA [95% highest posterior density (HPD): 34–83 MYA]. Psyttalia lounsburyi occupied the most basal position among the three Psyttalia, having diverged from the other two species ~11 MYA (95% HPD: 6–17 MYA). Psyttalia concolor and P. humilis were recovered as sister species diverged at ~2 MYA (95% HPD: 1.1–3.6 MYA). This phylogeny combining new sequences and a set of 31 other cyclostomes and non-cyclostomes highlights the importance of a comprehensive taxonomic coverage of Braconidae mitogenomes to overcome the lack of robustness in the placement of several subfamilies.
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12

Yang, Chao, Xiaojuan Du, Yuxin Liu, et al. "Comparative mitogenomics of the genus Motacilla (Aves, Passeriformes) and its phylogenetic implications." ZooKeys 1109 (July 1, 2022): 49–65. http://dx.doi.org/10.3897/zookeys.1109.81125.

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The genus Motacilla belongs to Motacillidae (Passeriformes), where mitochondrial features are poorly understood and phylogeny is controversial. Whole mitochondrial genome (mitogenome) data and large taxon sampling are considered to be ideal strategies to obtain this information. We generated four complete mitogenomes of M. flava, M. cinerea, M. alba and Dendronanthus indicus, and made comparative analyses of Motacilla species combined with mitogenome data from GenBank, and then reconstructed phylogenetic trees based on 37 mitochondrial genes. The mitogenomes of four mitogenome sequences exhibited the same gene order observed in most Passeriformes species. Comparative analyses were performed among all six sampled Motacilla mitogenomes. The complete mitogenomes showed A-skew and C-skew. Most protein-coding genes (PCGs) start with an ATG codon and terminate with a TAA codon. The secondary structures of RNAs were similar among Motacilla and Dendronanthus. All tRNAs except for trnS(agy) could be folded into classic clover-leaf structures. Three domains and several conserved boxes were detected. Phylogenetic analysis of 90 mitogenomes of Passeriformes using maximum likelihood (ML) and Bayesian inference (BI) revealed that Motacilla was a monophyletic group. Among Motacilla species, M. flava and M. tschutschensis showed closer relationships, and M. cinerea was located in a basal position within Motacilla. These data provide important information for better understanding the mitogenomic characteristics and phylogeny of Motacilla.
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13

Yang, Chao, Xiaojuan Du, Yuxin Liu, et al. "Comparative mitogenomics of the genus Motacilla (Aves, Passeriformes) and its phylogenetic implications." ZooKeys 1109 (July 1, 2022): 49–65. https://doi.org/10.3897/zookeys.1109.81125.

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The genus Motacilla belongs to Motacillidae (Passeriformes), where mitochondrial features are poorly understood and phylogeny is controversial. Whole mitochondrial genome (mitogenome) data and large taxon sampling are considered to be ideal strategies to obtain this information. We generated four complete mitogenomes of M. flava, M. cinerea, M. alba and Dendronanthus indicus, and made comparative analyses of Motacilla species combined with mitogenome data from GenBank, and then reconstructed phylogenetic trees based on 37 mitochondrial genes. The mitogenomes of four mitogenome sequences exhibited the same gene order observed in most Passeriformes species. Comparative analyses were performed among all six sampled Motacilla mitogenomes. The complete mitogenomes showed A-skew and C-skew. Most protein-coding genes (PCGs) start with an ATG codon and terminate with a TAA codon. The secondary structures of RNAs were similar among Motacilla and Dendronanthus. All tRNAs except for trnS(agy) could be folded into classic clover-leaf structures. Three domains and several conserved boxes were detected. Phylogenetic analysis of 90 mitogenomes of Passeriformes using maximum likelihood (ML) and Bayesian inference (BI) revealed that Motacilla was a monophyletic group. Among Motacilla species, M. flava and M. tschutschensis showed closer relationships, and M. cinerea was located in a basal position within Motacilla. These data provide important information for better understanding the mitogenomic characteristics and phylogeny of Motacilla.
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14

Xing, Guoqing, Shunpei Xie, Zhanxiang Qiao, et al. "Characterization and Phylogenetic Analysis of the Complete Mitogenomes of Valsa mali and Valsa pyri." Journal of Fungi 11, no. 5 (2025): 348. https://doi.org/10.3390/jof11050348.

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Apple Valsa canker, caused by Valsa mali and Valsa pyri, is a devastating disease of apple trees and poses a severe threat to the sustainable development of apple production. Although the two species’ whole genomes have been sequenced, their mitochondrial genomes are still uncharacterized. In this study, the complete mitochondrial genomes of V. mali and V. pyri were assembled, annotated, and compared by bioinformatic methods. The results indicate that the mitogenomes are both circular DNA molecules with sizes of 213,406 bp and 128,022 bp, respectively. The AT skew values of the two Valsa species’ mitogenomes were positive, while the GC skew values were negative. Comparative mitogenome analysis revealed that the length and base composition of protein-coding genes (PCGs), rRNA genes, and tRNA genes differed between the two Valsa species. It was found that the expansion of V. mali was primarily attributable to the intronic regions. There are large numbers of interspersed repetitive sequences (IRS) in both Valsa mitogenomes; however, the proportion of IRS in V. mali (43.56%) was much higher than that in V. pyri (2.41%). The alignment of large fragments between the mitochondrial and nuclear genomes of both V. mali (1.73 kb) and V. pyri (5.17 kb) indicates that gene transfer between mitochondrial and nuclear genomes occurred during evolution. The ka/ks ratios for 15 core PCGs were below one, suggesting that these genes were subjected to purifying selection pressure. Comparative mitogenomics revealed that the two fungi had significant mitogenomic collinearity and large-scale gene rearrangements. The results of phylogenetic analysis based on Bayesian inference (BI) and maximum likelihood (ML) using a combined mitochondrial gene set confirmed that V. mali and V. pyri were fully independent taxa with a high bootstrap value of 100 (ML) and a high posterior probability of 1.0 (BI). This is the first report on the mitogenomes within the genus Valsa. These results will pave the way to understanding the evolution and differentiation of mitogenomes in the genus Valsa.
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15

Kim, J.Y., and Y.C. Park. "Gene organization and characterization of the complete mitogenome of Hypsugo alaschanicus (Chiroptera: Vespertilionidae)." Genetics and Molecular Research 14, no. 4 (2015): 16325–31. https://doi.org/10.5281/zenodo.13451280.

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(Uploaded by Plazi for the Bat Literature Project) We sequenced and characterized the complete mitogenome of Hypsugo alaschanicus (Vespertilionidae) to provide more data for comparative mitogenomics of the genus Hypsugo. The mitogenome of H. alaschanicus is a circular molecule of 17,300 bp, consisting of a control region and a typically conserved set of 37 vertebrate genes containing 13 protein-coding genes (PCGs), 22 tRNA genes, and two rRNA genes (12S rRNA and 16S rRNA). The mitogenome of H. alaschanicus is AT-biased, with a nucleotide composition of 34.1 A, 30.9 T, 22.4 C, and 12.6% G. In the 13 mitochondrial PCGs of H. alaschanicus, the start codon ATG is used in all PCGs, except Nd2 and Nd3 (which use ATT), and Nd5 (which uses ATA). Eight PCGs (Nd1, Cox1, Cox2, Atp8, Atp6, Nd4L, Nd5, and Nd6) use TAA as the stop codon, while the stop codon AGA occurs only in Cytb. Incomplete stop codons (T--) are used in the other four PCGs (Cox3, Nd2, Nd3, and Nd4). These findings contribute to our understanding of the nucleotide composition and molecular evolution of the mitogenomes of the genus Hypsugo, and provide more data for comparative mitogenomics and higher phylogeny in the family Vespertilionidae.
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Kim, J.Y., and Y.C. Park. "Gene organization and characterization of the complete mitogenome of Hypsugo alaschanicus (Chiroptera: Vespertilionidae)." Genetics and Molecular Research 14, no. 4 (2015): 16325–31. https://doi.org/10.5281/zenodo.13451280.

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(Uploaded by Plazi for the Bat Literature Project) We sequenced and characterized the complete mitogenome of Hypsugo alaschanicus (Vespertilionidae) to provide more data for comparative mitogenomics of the genus Hypsugo. The mitogenome of H. alaschanicus is a circular molecule of 17,300 bp, consisting of a control region and a typically conserved set of 37 vertebrate genes containing 13 protein-coding genes (PCGs), 22 tRNA genes, and two rRNA genes (12S rRNA and 16S rRNA). The mitogenome of H. alaschanicus is AT-biased, with a nucleotide composition of 34.1 A, 30.9 T, 22.4 C, and 12.6% G. In the 13 mitochondrial PCGs of H. alaschanicus, the start codon ATG is used in all PCGs, except Nd2 and Nd3 (which use ATT), and Nd5 (which uses ATA). Eight PCGs (Nd1, Cox1, Cox2, Atp8, Atp6, Nd4L, Nd5, and Nd6) use TAA as the stop codon, while the stop codon AGA occurs only in Cytb. Incomplete stop codons (T--) are used in the other four PCGs (Cox3, Nd2, Nd3, and Nd4). These findings contribute to our understanding of the nucleotide composition and molecular evolution of the mitogenomes of the genus Hypsugo, and provide more data for comparative mitogenomics and higher phylogeny in the family Vespertilionidae.
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17

Zapelloni, Francesco, José A. Jurado-Rivera, Damià Jaume, Carlos Juan, and Joan Pons. "Comparative Mitogenomics in Hyalella (Amphipoda: Crustacea)." Genes 12, no. 2 (2021): 292. http://dx.doi.org/10.3390/genes12020292.

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We present the sequencing and comparative analysis of 17 mitochondrial genomes of Nearctic and Neotropical amphipods of the genus Hyalella, most from the Andean Altiplano. The mitogenomes obtained comprised the usual 37 gene-set of the metazoan mitochondrial genome showing a gene rearrangement (a reverse transposition and a reversal) between the North and South American Hyalella mitogenomes. Hyalella mitochondrial genomes show the typical AT-richness and strong nucleotide bias among codon sites and strands of pancrustaceans. Protein-coding sequences are biased towards AT-rich codons, with a preference for leucine and serine amino acids. Numerous base changes (539) were found in tRNA stems, with 103 classified as fully compensatory, 253 hemi-compensatory and the remaining base mismatches and indels. Most compensatory Watson–Crick switches were AU -> GC linked in the same haplotype, whereas most hemi-compensatory changes resulted in wobble GU and a few AC pairs. These results suggest a pairing fitness increase in tRNAs after crossing low fitness valleys. Branch-site level models detected positive selection for several amino acid positions in up to eight mitochondrial genes, with atp6 and nad5 as the genes displaying more sites under selection.
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18

Derenko, Miroslava, Galina Denisova, Irina Dambueva, Boris Malyarchuk, and Boris Bazarov. "Mitogenomics of modern Mongolic-speaking populations." Molecular Genetics and Genomics 297, no. 1 (2021): 47–62. http://dx.doi.org/10.1007/s00438-021-01830-w.

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19

Osigus, Hans-Jürgen, Michael Eitel, Matthias Bernt, Alexander Donath, and Bernd Schierwater. "Mitogenomics at the base of Metazoa." Molecular Phylogenetics and Evolution 69, no. 2 (2013): 339–51. http://dx.doi.org/10.1016/j.ympev.2013.07.016.

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20

Ramsden, Samuel D., Henner Brinkmann, Craig W. Hawryshyn, and John S. Taylor. "Mitogenomics and the sister of Salmonidae." Trends in Ecology & Evolution 18, no. 12 (2003): 607–10. http://dx.doi.org/10.1016/j.tree.2003.09.020.

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21

Gong, Zheng, Wanxiang Jiang, Huizhe Feng, Yanchao Liu, and Tianshun Zhu. "Comparative Mitogenomics of Two Sympatric Catfishes of Exostoma (Siluriformes: Sisoridae) from the Lower Yarlung Tsangpo River and Its Application for Phylogenetic Consideration." Genes 13, no. 9 (2022): 1615. http://dx.doi.org/10.3390/genes13091615.

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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
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22

Han, Shiyun, Hengwu Ding, Hui Peng, et al. "Sturnidae sensu lato Mitogenomics: Novel Insights into Codon Aversion, Selection, and Phylogeny." Animals 14, no. 19 (2024): 2777. http://dx.doi.org/10.3390/ani14192777.

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The Sturnidae family comprises 123 recognized species in 35 genera. The taxa Mimidae and Buphagidae were formerly treated as subfamilies within Sturnidae. The phylogenetic relationships among the Sturnidae and related taxa (Sturnidae sensu lato) remain unresolved due to high rates of morphological change and concomitant morphological homoplasy. This study presents five new mitogenomes of Sturnidae sensu lato and comprehensive mitogenomic analyses. The investigated mitogenomes exhibit an identical gene composition of 37 genes—including 13 protein-coding genes (PCGs), 2 rRNA genes, and 22 tRNA genes—and one control region (CR). The most important finding of this study is drawn from CAM analyses. The surprisingly unique motifs for each species provide a new direction for the molecular species identification of avian. Furthermore, the pervasiveness of the natural selection of PCGs is found in all examined species when analyzing their nucleotide composition and codon usage. We also determine the structures of mt-tRNA, mt-rRNA, and CR structures of Sturnidae sensu lato. Lastly, our phylogenetic analyses not only well support the monophyly of Sturnidae, Mimidae, and Buphagidae, but also define nine stable subclades. Taken together, our findings will enable the further elucidation of the evolutionary relationships within Sturnidae sensu lato.
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Śmietanka, Beata, Marek Lubośny, Aleksandra Przyłucka, Karin Gérard, and Artur Burzyński. "Mitogenomics of Perumytilus purpuratus (Bivalvia: Mytilidae) and its implications for doubly uniparental inheritance of mitochondria." PeerJ 6 (September 18, 2018): e5593. http://dx.doi.org/10.7717/peerj.5593.

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Animal mitochondria are usually inherited through the maternal lineage. The exceptional system allowing fathers to transmit their mitochondria to the offspring exists in some bivalves. Its taxonomic spread is poorly understood and new mitogenomic data are needed to fill the gap. Here, we present for the first time the two divergent mitogenomes from Chilean mussel Perumytilus purpuratus. The existence of these sex-specific mitogenomes confirms that this species has the doubly uniparental inheritance (DUI) of mitochondria. The genetic distance between the two mitochondrial lineages in P. purpuratus is not only much bigger than in the Mytilus edulis species complex but also greater than the distance observed in Musculista senhousia, the only other DUI-positive member of the Mytilidae family for which both complete mitochondrial genomes were published to date. One additional, long ORF (open reading frame) is present exclusively in the maternal mitogenome of P. purpuratus. This ORF evolves under purifying selection, and will likely be a target for future DUI research.
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Curole, Jason P., and Thomas D. Kocher. "Mitogenomics: digging deeper with complete mitochondrial genomes." Trends in Ecology & Evolution 14, no. 10 (1999): 394–98. http://dx.doi.org/10.1016/s0169-5347(99)01660-2.

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Kayal, Ehsan, Béatrice Roure, Hervé Philippe, Allen G. Collins, and Dennis V. Lavrov. "Cnidarian phylogenetic relationships as revealed by mitogenomics." BMC Evolutionary Biology 13, no. 1 (2013): 5. http://dx.doi.org/10.1186/1471-2148-13-5.

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Aguilar, Celestino, Matthew J. Miller, Jose R. Loaiza, Rüdiger Krahe, and Luis F. De León. "Mitogenomics of Central American weakly-electric fishes." Gene 686 (February 2019): 164–70. http://dx.doi.org/10.1016/j.gene.2018.11.045.

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Zhou, Shengyang, Xibao Wang, Lidong Wang, et al. "Different Evolutionary Trends of Galloanseres: Mitogenomics Analysis." Animals 14, no. 10 (2024): 1437. http://dx.doi.org/10.3390/ani14101437.

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The two existing clades of Galloanseres, orders Galliformes (landfowl) and Anseriformes (waterfowl), exhibit dramatically different evolutionary trends. Mitochondria serve as primary sites for energy production in organisms, and numerous studies have revealed their role in biological evolution and ecological adaptation. We assembled the complete mitogenome sequences of two species of the genus Aythya within Anseriformes: Aythya baeri and Aythya marila. A phylogenetic tree was constructed for 142 species within Galloanseres, and their divergence times were inferred. The divergence between Galliformes and Anseriformes occurred ~79.62 million years ago (Mya), followed by rapid evolution and diversification after the Middle Miocene (~13.82 Mya). The analysis of selective pressure indicated that the mitochondrial protein-coding genes (PCGs) of Galloanseres species have predominantly undergone purifying selection. The free-ratio model revealed that the evolutionary rates of COX1 and COX3 were lower than those of the other PCGs, whereas ND2 and ND6 had faster evolutionary rates. The CmC model also indicated that most PCGs in Anseriformes exhibited stronger selective constraints. Our study suggests that the distinct evolutionary trends and energy requirements of Galliformes and Anseriformes drive different evolutionary patterns in the mitogenome.
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Lait, Linda A., and Steven M. Carr. "Intraspecific mitogenomics of three marine species-at-risk: Atlantic, spotted, and northern wolffish (Anarhichas spp.)." Genome 61, no. 9 (2018): 625–34. http://dx.doi.org/10.1139/gen-2018-0043.

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High-resolution mitogenomics of within-species relationships can answer such phylogeographic questions as how species survived the most recent glaciation, as well as identify contemporary factors such as physical barriers, isolation, and gene flow. We examined the mitogenomic population structure of three at-risk species of wolffish: Atlantic (Anarhichas lupus), spotted (A. minor), and northern (A. denticulatus). These species are extensively sympatric across the North Atlantic but exhibit very different life history strategies, a combination that results in concordant and discordant patterns of genetic variation and structure. Wolffish haplogroups were not structured geographically: Atlantic and spotted wolffish each comprised three shallow clades, whereas northern wolffish comprised two deeper but unstructured lineages. We suggest that wolffish species survived in isolation in multiple glacial refugia, either refugia within refugia (Atlantic and spotted wolffish) or more distant refugia (northern wolffish), followed by secondary admixture upon post-glacial recolonisation of the North Atlantic.
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Chen, Wan, Keer Miao, Junqi Wang, et al. "Five new mitogenomes sequences of Calidridine sandpipers (Aves: Charadriiformes) and comparative mitogenomics of genus Calidris." PeerJ 10 (April 18, 2022): e13268. http://dx.doi.org/10.7717/peerj.13268.

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Background The genus Calidris (Charadriiformes, Scolopacidae) includes shorebirds known as dunlin, knots, and sanderlings. The relationships between species nested within Calidris, including Eurynorynchus, Limicola and Aphriza, are not well-resolved. Methods Samples were collected from Xiaoyangkou, Rudong County, Jiangsu Province, China. Mitogenomes were sequenced using the Illumina Novaseq 6000 platform for PE 2 × 150 bp sequencing, and then checked for PCR products. Protein-coding genes were determined using an Open Reading Frame Finder. tRNAscan-SE, MITOS, and ARWEN were used to confirm tRNA and rRNA annotations. Bioinformatic analyses were conducted using DnaSP 5.1 and MEGA X. Phylogenic trees were constructed using maximum likelihood and Bayesian analyses. Results We sequenced and annotated the mitogenome of five species and obtained four complete mitogenomes and one nearly complete mitogenome. Circular mitogenomes displayed moderate size variation, with a mean length of 16,747 bp, ranging from 16,642 to 16,791 bp. The mitogenome encoded a control region and a typical set of 37 genes containing two rRNA genes, 13 protein-coding genes, and 22 tRNA genes. There were four start codons, four stop codons, and one incomplete stop codon (T–). The nucleotide composition was consistently AT-biased. The average uncorrected pairwise distances revealed heterogeneity in the evolutionary rate for each gene; the COIII had a slow evolutionary rate, whereas the ATP8 gene had a fast rate. dN/dS analysis indicated that the protein-coding genes were under purifying selection. The genetic distances between species showed that the greatest genetic distance was between Eurynorhynchus pygmeus and Limicola falcinellus (22.5%), and the shortest was between E. pygmeus and Calidris ruficollis (12.8%). Phylogenetic trees revealed that Calidris is not a monophyletic genus, as species from the genera Eurynorynchus and Limicola were nested within Calidris. The molecular data obtained in this study are valuable for research on the taxonomy, population genetics, and evolution of birds in the genus Calidris.
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Nethavhani, Zwannda, Rieze Straeuli, Kayleigh Hiscock, et al. "Mitogenomics and phylogenetics of twelve species of African Saturniidae (Lepidoptera)." PeerJ 10 (April 18, 2022): e13275. http://dx.doi.org/10.7717/peerj.13275.

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African Saturniidae (Lepidoptera) include numerous species consumed at the caterpillar stage throughout the continent, and their importance to local communities as a source of nutrition and seasonal income cannot be overestimated. However, baseline genetic data with utility for the characterization of their diversity, phylogeography and phylogenetic relationships have remained scarce compared to their Asian counterparts. To bridge this gap, we sequenced the mitochondrial genomes of 12 species found in southern Africa for comparative mitogenomics and phylogenetic reconstruction of the family, including the first representatives of the tribes Eochroini and Micragonini. Mitochondrial gene content and organization were conserved across all Saturniidae included in the analyses. The phylogenetic positions of the 12 species were assessed in the context of publicly available mitogenomes using Bayesian inference and maximum likelihood (ML) methods. The monophyly of the tribes Saturniini, Attacini, Bunaeini and Micragonini, the sister relationship between Saturniini and Attacini, and the placement of Eochroa trimenii and Rhodinia fugax in the tribes Eochroini and Attacini, respectively, were strongly supported. These results contribute to significantly expanding genetic data available for African Saturniidae and allow for the development of new mitochondrial markers in future studies.
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Márquez, Edna Judith, Daniel Alfredo Gómez-Chavarría, and Juan Fernando Alzate. "Exploring the mitochondrial genomes and phylogenetic relationships of trans-Andean Bryconidae species (Actinopterygii: Ostariophysi: Characiformes)." PLOS ONE 19, no. 8 (2024): e0300830. http://dx.doi.org/10.1371/journal.pone.0300830.

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Comparative mitogenomics and its evolutionary relationships within Bryconidae remains largely unexplored. To bridge this gap, this study assembled 15 mitogenomes from 11 Bryconidae species, including five newly sequenced. Salminus mitogenomes, exceeding 17,700 bp, exhibited the largest size, contrasting with a median size of 16,848 bp in the remaining species (Brycon and Chilobrycon). These mitogenomes encode 37 typical mitochondrial genes, including 13 protein-coding, 2 ribosomal RNA, and 22 transfer RNA genes, and exhibit the conserved gene arrangement found in most fish species. Phylogenetic relationships, based on the maximum-likelihood method, revealed that the trans-Andean species (found in northwestern South America) clustered into two main sister clades. One clade comprised the trans-Andean species from the Pacific slope, Brycon chagrensis and Chilobrycon deuterodon. The other clade grouped the trans-Andean species from the Magdalena-Cauca Basin Brycon moorei and Salminus affinis, with their respective cis-Andean congeners (found in eastern South America), with Brycon rubricauda as its sister clade. Since the current members of Brycon are split in three separated lineages, the systematic classification of Bryconidae requires further examination. This study provides novel insights into mitogenome characteristics and evolutionary pathways within Bryconidae, standing as crucial information for prospective phylogenetic and taxonomic studies, molecular ecology, and provides a valuable resource for environmental DNA applications.
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Shang, Jin, Wentian Xu, Xiaofang Huang, Dong Zhang, Liping Yan, and Thomas Pape. "Comparative Mitogenomics of Flesh Flies: Implications for Phylogeny." Insects 13, no. 8 (2022): 718. http://dx.doi.org/10.3390/insects13080718.

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Flesh flies (Diptera: Sarcophagidae) represent a rapid radiation belonging to the Calyptratae. With more than 3000 known species, they are extraordinarily diverse in terms of their breeding habits and are therefore of particular importance in human and veterinary medicine, forensics, and ecology. To better comprehend the phylogenetic relationships and evolutionary characteristics of the Sarcophagidae, we sequenced the complete mitochondrial genomes of five species of flesh flies and performed mitogenomic comparisons amongst the three subfamilies. The mitochondrial genomes match the hypothetical condition of the insect ancestor in terms of gene content and gene arrangement. The evolutionary rates of the subfamilies of Sarcophagidae differ significantly, with Miltogramminae exhibiting a higher rate than the other two subfamilies. The monophyly of the Sarcophagidae and each subfamily is strongly supported by phylogenetic analysis, with the subfamily-level relationship inferred as (Sarcophaginae, (Miltogramminae, Paramacronychiinae)). This study suggests that phylogenetic analysis based on mitochondrial genomes may not be appropriate for rapidly evolving groups such as Miltogramminae and that the third-codon positions could play a considerable role in reconstructing the phylogeny of Sarcophagidae. The protein-coding genes ND2 and ND6 have the potential to be employed as DNA markers for species identification and delimitation in flesh flies.
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Stöger, I., and M. Schrödl. "Mitogenomics does not resolve deep molluscan relationships (yet?)." Molecular Phylogenetics and Evolution 69, no. 2 (2013): 376–92. http://dx.doi.org/10.1016/j.ympev.2012.11.017.

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Mikkelsen, Nina T., Kevin M. Kocot, and Kenneth M. Halanych. "Mitogenomics reveals phylogenetic relationships of caudofoveate aplacophoran molluscs." Molecular Phylogenetics and Evolution 127 (October 2018): 429–36. http://dx.doi.org/10.1016/j.ympev.2018.04.031.

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Meng, Xueping, Xin Shen, Nana Zhao, et al. "Mitogenomics reveals two subspecies inCoelomactra antiquata(Mollusca: Bivalvia)." Mitochondrial DNA 24, no. 2 (2012): 102–4. http://dx.doi.org/10.3109/19401736.2012.726620.

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Li, Yuanning, Kevin M. Kocot, Michael G. Tassia, Johanna T. Cannon, Matthias Bernt, and Kenneth M. Halanych. "Mitogenomics Reveals a Novel Genetic Code in Hemichordata." Genome Biology and Evolution 11, no. 1 (2018): 29–40. http://dx.doi.org/10.1093/gbe/evy254.

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Iannelli, Fabio, Graziano Pesole, Paolo Sordino, and Carmela Gissi. "Mitogenomics reveals two cryptic species in Ciona intestinalis." Trends in Genetics 23, no. 9 (2007): 419–22. http://dx.doi.org/10.1016/j.tig.2007.07.001.

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Van de Paer, Céline, Cynthia Hong-Wa, Céline Jeziorski, and Guillaume Besnard. "Mitogenomics of Hesperelaea, an extinct genus of Oleaceae." Gene 594, no. 2 (2016): 197–202. http://dx.doi.org/10.1016/j.gene.2016.09.007.

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Wang, Xibao, Yongquan Shang, Xiaoyang Wu, et al. "Divergent evolution of mitogenomics in Cetartiodactyla niche adaptation." Organisms Diversity & Evolution 23, no. 1 (2022): 243–59. https://doi.org/10.1007/s13127-022-00574-8.

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Wang, Xibao, Shang, Yongquan, Wu, Xiaoyang, Wei, Qinguo, Zhou, Shengyang, Sun, Guolei, Mei, Xuesong, Dong, Yuehuan, Sha, Weilai, Zhang, Honghai (2023): Divergent evolution of mitogenomics in Cetartiodactyla niche adaptation. Organisms Diversity & Evolution (New York, N.Y.) 23 (1): 243-259, DOI: 10.1007/s13127-022-00574-8, URL: http://dx.doi.org/10.1007/s13127-022-00574-8
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Li, Hu, John M. Leavengood, Eric G. Chapman, et al. "Mitochondrial phylogenomics of Hemiptera reveals adaptive innovations driving the diversification of true bugs." Proceedings of the Royal Society B: Biological Sciences 284, no. 1862 (2017): 20171223. http://dx.doi.org/10.1098/rspb.2017.1223.

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Hemiptera, the largest non-holometabolous order of insects, represents approximately 7% of metazoan diversity. With extraordinary life histories and highly specialized morphological adaptations, hemipterans have exploited diverse habitats and food sources through approximately 300 Myr of evolution. To elucidate the phylogeny and evolutionary history of Hemiptera, we carried out the most comprehensive mitogenomics analysis on the richest taxon sampling to date covering all the suborders and infraorders, including 34 newly sequenced and 94 published mitogenomes. With optimized branch length and sequence heterogeneity, Bayesian analyses using a site-heterogeneous mixture model resolved the higher-level hemipteran phylogeny as (Sternorrhyncha, (Auchenorrhyncha, (Coleorrhyncha, Heteroptera))). Ancestral character state reconstruction and divergence time estimation suggest that the success of true bugs (Heteroptera) is probably due to angiosperm coevolution, but key adaptive innovations (e.g. prognathous mouthpart, predatory behaviour, and haemelytron) facilitated multiple independent shifts among diverse feeding habits and multiple independent colonizations of aquatic habitats.
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Shen-Gunther, Jane, Rutger S. Gunther, Hong Cai, and Yufeng Wang. "A Customized Human Mitochondrial DNA Database (hMITO DB v1.0) for Rapid Sequence Analysis, Haplotyping and Geo-Mapping." International Journal of Molecular Sciences 24, no. 17 (2023): 13505. http://dx.doi.org/10.3390/ijms241713505.

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The field of mitochondrial genomics has advanced rapidly and has revolutionized disciplines such as molecular anthropology, population genetics, and medical genetics/oncogenetics. However, mtDNA next-generation sequencing (NGS) analysis for matrilineal haplotyping and phylogeographic inference remains hindered by the lack of a consolidated mitogenome database and an efficient bioinformatics pipeline. To address this, we developed a customized human mitogenome database (hMITO DB) embedded in a CLC Genomics workflow for read mapping, variant analysis, haplotyping, and geo-mapping. The database was constructed from 4286 mitogenomes. The macro-haplogroup (A to Z) distribution and representative phylogenetic tree were found to be consistent with published literature. The hMITO DB automated workflow was tested using mtDNA-NGS sequences derived from Pap smears and cervical cancer cell lines. The auto-generated read mapping, variants track, and table of haplotypes and geo-origins were completed in 15 min for 47 samples. The mtDNA workflow proved to be a rapid, efficient, and accurate means of sequence analysis for translational mitogenomics.
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Wang, Chengxin, Site Luo, Na Yao, Xinyue Wang, Yong Song, and Shengao Chen. "A Comprehensive Analysis of Triplophysa labiata (Kessler, 1874) Mitogenome and Its Phylogenetic Implications within the Triplophysa Genus." Genes 14, no. 7 (2023): 1356. http://dx.doi.org/10.3390/genes14071356.

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In order to resolve the long-standing controversy surrounding the relationships within the Triplophysa genus, we conducted an extensive analysis of the complete mitogenome of Triplophysa labiata using DNBSEQ short reads. Additionally, we reconstructed the phylogeny of the Nemacheilidae family using mitogenome data. By comparing all available mitogenomes within the Triplophysa genus, we gained valuable insights into its evolutionary history. Our findings revealed that the mitogenome sequence of T. labiata is circular, spanning a length of 16,573 bp. It encompasses 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), 2 ribosomal RNAs (rRNAs), and a control region (D-loop). Among the PCGs, the start codon ATG was commonly observed, except in cox1, while the stop codons TAA/TAG/T were found in all PCGs. Furthermore, purifying selection was evident across all PCGs. Utilizing maximum likelihood (ML) methods, we employed the 13 PCGs and the concatenated nucleotide sequences of 30 Triplophysa mitogenomes to infer the phylogeny. Our results strongly supported the division of the Triplophysa genus into four primary clades. Notably, our study provides the first evidence of the close relationship between T. labiata and T. dorsalis. These findings serve as a significant foundation for future investigations into the mitogenomics and phylogeny of Nemacheilidae fishes, paving the way for further advancements in this field of research.
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Koga, Cassandra, and Greg W. Rouse. "Mitogenomics and the Phylogeny of Mantis Shrimps (Crustacea: Stomatopoda)." Diversity 13, no. 12 (2021): 647. http://dx.doi.org/10.3390/d13120647.

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Stomatopoda, commonly known as mantis shrimps, are notable for their enlarged second maxillipeds encompassing the raptorial claw. The form of the claw can be used to divide them into two basic groups: smashers and spearers. Previous phylogenetic studies of Stomatopoda have focused on morphology or a few genes, though there have been whole mitochondrial genomes published for 15 members of Stomatopoda. However, the sampling has been somewhat limited with key taxa not included. Here, nine additional stomatopod mitochondrial genomes were generated and combined with the other available mitogenomes for a phylogenetic analysis. We used the 13 protein coding genes, as well as 12S rRNA, 16S rRNA genes, and included nuclear 18S rRNA gene sequences. Different rooting options were used for the analyses: (1) single and multiple outgroups from various eumalocostracan relatives and (2) a stomatopod-only dataset, with Hemisquilla californiensis used to root the topologies, based on the current hypothesis that Hemisquilla is the sister group to the rest of Stomatopoda. The eumalocostracan-rooted analyses all showed H. californiensis nested within Stomatopoda, raising doubts as to previous hypotheses as to its placement. Allowing for the rooting difference, the H. californiensis outgroup datasets had the same tree topology as the eumalocostracan outgroup datasets with slight variation at poorly supported nodes. Of the major taxonomic groupings sampled to date, Squilloidea was generally found to be monophyletic while Gonodactyloidea was not. The position of H. californiensis was found inside its superfamily, Gonodactyloidea, and grouped in a weakly supported clade containing Odontodactylus havanensis and Lysiosquillina maculata for the eumalocostracan-rooted datasets. An ancestral state reconstruction was performed on the raptorial claw form and provides support that spearing is the ancestral state for extant Stomatopoda, with smashing evolving subsequently one or more times.
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Poliseno, Angelo, Christian Feregrino, Stéphane Sartoretto, et al. "Comparative mitogenomics, phylogeny and evolutionary history of Leptogorgia (Gorgoniidae)." Molecular Phylogenetics and Evolution 115 (October 2017): 181–89. http://dx.doi.org/10.1016/j.ympev.2017.08.001.

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Gaitan-Espitia, Juan Diego, Jaiber J. Solano-Iguaran, Daniela Tejada-Martinez, and Julian F. Quintero-Galvis. "Mitogenomics of electric rays: evolutionary considerations within Torpediniformes (Batoidea; Chondrichthyes)." Zoological Journal of the Linnean Society 178, no. 2 (2016): 257–66. https://doi.org/10.1111/zoj.12417.

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Gaitan-Espitia, Juan Diego, Solano-Iguaran, Jaiber J., Tejada-Martinez, Daniela, Quintero-Galvis, Julian F. (2016): Mitogenomics of electric rays: evolutionary considerations within Torpediniformes (Batoidea; Chondrichthyes). Zoological Journal of the Linnean Society 178 (2): 257-266, DOI: 10.1111/zoj.12417, URL: http://dx.doi.org/10.1111/zoj.12417
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Trevisan, Bruna, Daniel M. C. Alcantara, Denis Jacob Machado, Fernando P. L. Marques, and Daniel J. G. Lahr. "Genome skimming is a low-cost and robust strategy to assemble complete mitochondrial genomes from ethanol preserved specimens in biodiversity studies." PeerJ 7 (September 13, 2019): e7543. http://dx.doi.org/10.7717/peerj.7543.

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Global loss of biodiversity is an ongoing process that concerns both local and global authorities. Studies of biodiversity mainly involve traditional methods using morphological characters and molecular protocols. However, conventional methods are a time consuming and resource demanding task. The development of high-throughput sequencing (HTS) techniques has reshaped the way we explore biodiversity and opened a path to new questions and novel empirical approaches. With the emergence of HTS, sequencing the complete mitochondrial genome became more accessible, and the number of genome sequences published has increased exponentially during the last decades. Despite the current state of knowledge about the potential of mitogenomics in phylogenetics, this is still a relatively under-explored area for a multitude of taxonomic groups, especially for those without commercial relevance, non-models organisms and with preserved DNA. Here we take the first step to assemble and annotate the genomes from HTS data using a new protocol of genome skimming which will offer an opportunity to extend the field of mitogenomics to under-studied organisms. We extracted genomic DNA from specimens preserved in ethanol. We used Nextera XT DNA to prepare indexed paired-end libraries since it is a powerful tool for working with diverse samples, requiring a low amount of input DNA. We sequenced the samples in two different Illumina platform (MiSeq or NextSeq 550). We trimmed raw reads, filtered and had their quality tested accordingly. We performed the assembly using a baiting and iterative mapping strategy, and the annotated the putative mitochondrion through a semi-automatic procedure. We applied the contiguity index to access the completeness of each new mitogenome. Our results reveal the efficiency of the proposed method to recover the whole mitogenomes of preserved DNA from non-model organisms even if there are gene rearrangement in the specimens. Our findings suggest the potential of combining the adequate platform and library to the genome skimming as an innovative approach, which opens a new range of possibilities of its use to obtain molecular data from organisms with different levels of preservation.
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Poliseno, Angelo, Alvaro Altuna, Carlo Cerrano, Gert Wörheide, and Sergio Vargas. "Historical biogeography and mitogenomics of two endemic Mediterranean gorgonians (Holaxonia, Plexauridae)." Organisms Diversity & Evolution 17, no. 2 (2017): 365–73. https://doi.org/10.1007/s13127-017-0322-x.

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Poliseno, Angelo, Altuna, Alvaro, Cerrano, Carlo, Wörheide, Gert, Vargas, Sergio (2017): Historical biogeography and mitogenomics of two endemic Mediterranean gorgonians (Holaxonia, Plexauridae). Organisms Diversity & Evolution (New York, N.Y.) 17 (2): 365-373, DOI: 10.1007/s13127-017-0322-x, URL: http://dx.doi.org/10.1007/s13127-017-0322-x
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Zheng, Xiao-Yu, Li-Jun Cao, Peng-Yan Chen, et al. "Comparative mitogenomics and phylogenetics of the stinging wasps (Hymenoptera: Aculeata)." Molecular Phylogenetics and Evolution 159 (June 2021): 107119. http://dx.doi.org/10.1016/j.ympev.2021.107119.

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Uribe, Juan E., Yasunori Kano, José Templado, and Rafael Zardoya. "Mitogenomics of Vetigastropoda: insights into the evolution of pallial symmetry." Zoologica Scripta 45, no. 2 (2015): 145–59. http://dx.doi.org/10.1111/zsc.12146.

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Paijmans, Johanna L. A., Ross Barnett, M. Thomas P. Gilbert, et al. "Evolutionary History of Saber-Toothed Cats Based on Ancient Mitogenomics." Current Biology 27, no. 21 (2017): 3330–36. http://dx.doi.org/10.1016/j.cub.2017.09.033.

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