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Najer T, Doña J, Buček A, Sweet AD, Sychra O, Johnson KP. Mitochondrial genome fragmentation is correlated with increased rates of molecular evolution. PLoS Genet 2024; 20:e1011266. [PMID: 38701107 PMCID: PMC11095710 DOI: 10.1371/journal.pgen.1011266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 05/15/2024] [Accepted: 04/20/2024] [Indexed: 05/05/2024] Open
Abstract
While mitochondrial genome content and organization is quite diverse across all Eukaryotes, most bilaterian animal mitochondrial genomes (mitogenomes) exhibit highly conserved gene content and organisation, with genes typically encoded on a single circular chromosome. However, many species of parasitic lice (Insecta: Phthiraptera) are among the notable exceptions, having mitogenomes fragmented into multiple circular chromosomes. To better understand the process of mitogenome fragmentation, we conducted a large-scale genomic study of a major group of lice, Amblycera, with extensive taxon sampling. Analyses of the evolution of mitogenome structure across a phylogenomic tree of 90 samples from 53 genera revealed evidence for multiple independent origins of mitogenome fragmentation, some inferred to have occurred less than five million years ago. We leveraged these many independent origins of fragmentation to compare the rates of DNA substitution and gene rearrangement, specifically contrasting branches with fragmented and non-fragmented mitogenomes. We found that lineages with fragmented mitochondrial genomes had significantly higher rates of mitochondrial sequence evolution. In addition, lineages with fragmented mitochondrial genomes were more likely to have mitogenome gene rearrangements than those with single-chromosome mitochondrial genomes. By combining phylogenomics and mitochondrial genomics we provide a detailed portrait of mitogenome evolution across this group of insects with a remarkably unstable mitogenome structure, identifying processes of molecular evolution that are correlated with mitogenome fragmentation.
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Affiliation(s)
- Tomáš Najer
- Department of Veterinary Sciences, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life Sciences Prague, Prague, Czechia
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, Champaign, Illinois, United States of America
| | - Jorge Doña
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, Champaign, Illinois, United States of America
- Departamento de Biología Animal, Universidad de Granada, Granada, Spain
| | - Aleš Buček
- Biology Centre, Czech Academy of Sciences, České Budějovice, Czechia
- Okinawa Institute of Science & Technology Graduate University, Onna-son, Okinawa, Japan
| | - Andrew D. Sweet
- Department of Biological Sciences, Arkansas State University, Jonesboro, Arkansas, United States of America
| | - Oldřich Sychra
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, Brno, Czechia
| | - Kevin P. Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, Champaign, Illinois, United States of America
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Breton S. Comparative mitogenomics of Brachiopods reveals conservatism in articulate species and unusualness in inarticulate species. Mol Biol Rep 2024; 51:298. [PMID: 38341808 DOI: 10.1007/s11033-024-09270-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 01/18/2024] [Indexed: 02/13/2024]
Abstract
BACKGROUND Brachiopods are a phylum of marine invertebrates with over 10,000 fossil species. Today, there are fewer than 500 extant species assigned to the class Articulata or Inarticulata and for which knowledge of evolutionary genetics and genomics is still poor. Until now, complete mitogenome sequences of two inarticulate species and four articulate species were available. METHODS AND RESULTS The complete mitogenome of the inarticulate brachiopod species Lingula reevii (20,778 bp) was obtained by using next generation sequencing. It contains 12 protein-coding genes (the annotation of atp8 is unsure), two ribosomal RNA genes, 26 transfer RNA genes, and one supernumerary ORF that is also conserved in the inarticulate species Lingula anatina. It is hypothesized that this ORF could represent a Lingula-specific mtORFan gene (without obvious homology to other genes). Comparative mitogenomics indicate the mitochondrial gene order of L. reevii is unique among brachiopods, and that compared to articulate species, inarticulate species exhibit massive mitogenome rearrangements, deviant ATP8 protein sequences and supernumerary ORFs, possibly representing species- or lineage-specific mtORFan genes. CONCLUSION The results of this study enrich genetics knowledge of extant brachiopods, which may eventually help to test hypotheses about their decline.
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Affiliation(s)
- Sophie Breton
- Department of Biological Sciences, University of Montreal, Montreal, Canada.
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Françoso E, Zuntini AR, Ricardo PC, Santos PKF, de Souza Araujo N, Silva JPN, Gonçalves LT, Brito R, Gloag R, Taylor BA, Harpur B, Oldroyd BP, Brown MJF, Arias MC. Rapid evolution, rearrangements and whole mitogenome duplication in the Australian stingless bees Tetragonula (Hymenoptera: Apidae): A steppingstone towards understanding mitochondrial function and evolution. Int J Biol Macromol 2023; 242:124568. [PMID: 37100315 DOI: 10.1016/j.ijbiomac.2023.124568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 03/16/2023] [Accepted: 04/10/2023] [Indexed: 04/28/2023]
Abstract
The extreme conservation of mitochondrial genomes in metazoans poses a significant challenge to understanding mitogenome evolution. However, the presence of variation in gene order or genome structure, found in a small number of taxa, can provide unique insights into this evolution. Previous work on two stingless bees in the genus Tetragonula (T. carbonaria and T. hockingsi) revealed highly divergent CO1 regions between them and when compared to the bees from the same tribe (Meliponini), indicating rapid evolution. Using mtDNA isolation and Illumina sequencing, we elucidated the mitogenomes of both species. In both species, there has been a duplication of the whole mitogenome to give a total genome size of 30,666 bp in T. carbonaria; and 30,662 bp in T. hockingsi. These duplicated genomes present a circular structure with two identical and mirrored copies of all 13 protein coding genes and 22 tRNAs, with the exception of a few tRNAs that are present as single copies. In addition, the mitogenomes are characterized by rearrangements of two block of genes. We believe that rapid evolution is present in the whole Indo-Malay/Australasian group of Meliponini but is extraordinarily elevated in T. carbonaria and T. hockingsi, probably due to founder effect, low effective population size and the mitogenome duplication. All these features - rapid evolution, rearrangements, and duplication - deviate significantly from the vast majority of the mitogenomes described so far, making the mitogenomes of Tetragonula unique opportunities to address fundamental questions of mitogenome function and evolution.
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Affiliation(s)
- Elaine Françoso
- Centre for Ecology, Evolution and Behaviour, Department of Biological Sciences, School of Life Sciences and the Environment, Royal Holloway University of London, Egham TW20 0EX, UK; Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP 05508-090, Brazil.
| | | | - Paulo Cseri Ricardo
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP 05508-090, Brazil
| | | | - Natalia de Souza Araujo
- Unit of Evolutionary Biology & Ecology, Université libre de Bruxelles (ULB), Brussels, Belgium
| | - João Paulo Naldi Silva
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP 05508-090, Brazil
| | | | | | - Rosalyn Gloag
- School of Life and Environmental Sciences, The University of Sydney, NSW, 2006, Australia
| | - Benjamin A Taylor
- Department of Entomology, Purdue University, West Lafayette, Indiana, USA
| | - Brock Harpur
- Department of Entomology, Purdue University, West Lafayette, Indiana, USA
| | - Benjamin P Oldroyd
- School of Life and Environmental Sciences, The University of Sydney, NSW, 2006, Australia
| | - Mark J F Brown
- Centre for Ecology, Evolution and Behaviour, Department of Biological Sciences, School of Life Sciences and the Environment, Royal Holloway University of London, Egham TW20 0EX, UK
| | - Maria Cristina Arias
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP 05508-090, Brazil
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Shtolz N, Mishmar D. The metazoan landscape of mitochondrial DNA gene order and content is shaped by selection and affects mitochondrial transcription. Commun Biol 2023; 6:93. [PMID: 36690686 PMCID: PMC9871016 DOI: 10.1038/s42003-023-04471-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 01/12/2023] [Indexed: 01/25/2023] Open
Abstract
Mitochondrial DNA (mtDNA) harbors essential genes in most metazoans, yet the regulatory impact of the multiple evolutionary mtDNA rearrangements has been overlooked. Here, by analyzing mtDNAs from ~8000 metazoans we found high gene content conservation (especially of protein and rRNA genes), and codon preferences for mtDNA-encoded tRNAs across most metazoans. In contrast, mtDNA gene order (MGO) was selectively constrained within but not between phyla, yet certain gene stretches (ATP8-ATP6, ND4-ND4L) were highly conserved across metazoans. Since certain metazoans with different MGOs diverge in mtDNA transcription, we hypothesized that evolutionary mtDNA rearrangements affected mtDNA transcriptional patterns. As a first step to test this hypothesis, we analyzed available RNA-seq data from 53 metazoans. Since polycistron mtDNA transcripts constitute a small fraction of the steady-state RNA, we enriched for polycistronic boundaries by calculating RNA-seq read densities across junctions between gene couples encoded either by the same strand (SSJ) or by different strands (DSJ). We found that organisms whose mtDNA is organized in alternating reverse-strand/forward-strand gene blocks (mostly arthropods), displayed significantly reduced DSJ read counts, in contrast to organisms whose mtDNA genes are preferentially encoded by one strand (all chordates). Our findings suggest that mtDNA rearrangements are selectively constrained and likely impact mtDNA regulation.
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Affiliation(s)
- Noam Shtolz
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Dan Mishmar
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel.
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Fu YT, Suleman, Yao C, Wang HM, Wang W, Liu GH. A Novel Mitochondrial Genome Fragmentation Pattern in the Buffalo Louse Haematopinus tuberculatus (Psocodea: Haematopinidae). Int J Mol Sci 2022; 23:13092. [PMID: 36361879 PMCID: PMC9658350 DOI: 10.3390/ijms232113092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/08/2022] [Accepted: 10/25/2022] [Indexed: 08/01/2023] Open
Abstract
Sucking lice are obligate ectoparasites of mammalian hosts, causing serious public health problems and economic losses worldwide. It is well known that sucking lice have fragmented mitochondrial (mt) genomes, but many remain undetermined. To better understand patterns of mt genome fragmentation in the sucking lice, we sequenced the mt genome of the buffalo louse Haematopinus tuberculatus using next-generation sequencing (NGS). The mt genome of H. tuberculatus has ten circular minichromosomes containing a total of 37 genes. Each minichromosome is 2.9-5.0 kb long and carries one to eight genes plus one large non-coding region. The number of mt minichromosomes of H. tuberculatus (ten) is different from those of congeneric species (horse louse H. asini, domestic pig louse H. suis and wild pig louse H. apri) and other sucking lice. Two events (gene translocation and merger of mt minichromosome) are observed in Haematopinus. Compared to other studies, our phylogeny generated from mt genome datasets showed a different topology, suggesting that inclusion of data other than mt genomes would be required to resolve phylogeny of sucking lice. To our knowledge, this is the first report of a ten mt minichromosomes genome in sucking lice, which opens a new outlook into unexplored mt genome fragmentation patterns in sucking lice.
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Affiliation(s)
- Yi-Tian Fu
- Research Center for Parasites & Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China
| | - Suleman
- Department of Zoology, University of Swabi, Swabi 23561, Pakistan
| | - Chaoqun Yao
- Department of Biomedical Sciences and One Health Center for Zoonoses and Tropical Veterinary Medicine, Ross University School of Veterinary Medicine, Basseterre P.O. Box 334, Saint Kitts and Nevis
| | - Hui-Mei Wang
- Research Center for Parasites & Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China
| | - Wei Wang
- The Centre for Bioinnovation, School of Science and Engineering, University of the Sunshine Coast, Sippy Downs, QLD 4556, Australia
| | - Guo-Hua Liu
- Research Center for Parasites & Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China
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Fu YT, Yao C, Deng YP, Elsheikha HM, Shao R, Zhu XQ, Liu GH. Human pediculosis, a global public health problem. Infect Dis Poverty 2022; 11:58. [PMID: 35619191 PMCID: PMC9134731 DOI: 10.1186/s40249-022-00986-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 05/11/2022] [Indexed: 12/04/2022] Open
Abstract
Background Human pediculosis is caused by hematophagous lice, which are transmitted between individuals via direct and/or indirect contact. Despite the public health importance of louse infestation, information concerning the global burden of pediculosis and the epidemiological landscape of louse-borne diseases is limited. The aim of this review was to summarize the biology, epidemiology, diagnosis, and control of lice infestation in humans. We also discussed the latest advances in molecular taxonomy and molecular genetics of lice. Methods We searched five electronic bibliographic databases (PubMed, ScienceDirect, CNKI, VIP Chinese Journal Database, and Wanfang Data) and followed a standard approach for conducting scoping reviews to identify studies on various aspects of human lice. Relevant information reported in the identified studies were collated, categorized, and summarized. Results A total of 282 studies were eligible for the final review. Human pediculosis remains a public health issue affecting millions of people worldwide. Emerging evidence suggests that head lice and body lice should be considered conspecific, with different genotypes and ecotypes. Phylogenetic analysis based on mitochondrial (mt) cytb gene sequences identified six distinct clades of lice worldwide. In addition to the direct effect on human health, lice can serve as vectors of disease-causing pathogens. The use of insecticides plays a crucial role in the treatment and prevention of louse infestation. Genome sequencing has advanced our knowledge of the genetic structure and evolutionary biology of human lice. Conclusions Human pediculosis is a public health problem affecting millions of people worldwide, particularly in developing countries. More progress can be made if emphasis is placed on the use of emerging omics technologies to elucidate the mechanisms that underpin the physiological, ecological, and evolutionary aspects of lice. Graphic Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s40249-022-00986-w.
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Affiliation(s)
- Yi-Tian Fu
- Research Center for Parasites and Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan, China
| | - Chaoqun Yao
- Department of Biomedical Sciences and One Health Center for Zoonoses and Tropical Veterinary Medicine, Ross University School of Veterinary Medicine, Basseterre, Saint Kitts and Nevis.
| | - Yuan-Ping Deng
- Research Center for Parasites and Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan, China
| | - Hany M Elsheikha
- Faculty of Medicine and Health Sciences, School of Veterinary Medicine and Science, University of Nottingham, Loughborough, LE12 5RD, UK
| | - Renfu Shao
- Centre for Bioinnovation, School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, 4556, Australia
| | - Xing-Quan Zhu
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu, 030801, Shanxi, China. .,Key Laboratory of Veterinary Public Health of Higher Education of Yunnan Province, College of Veterinary Medicine, Yunnan Agricultural University, Kunming, Yunnan, 650201, People's Republic of China.
| | - Guo-Hua Liu
- Research Center for Parasites and Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan, China.
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