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Bolner M, Bovo S, Ballan M, Schiavo G, Taurisano V, Ribani A, Bertolini F, Fontanesi L. A comprehensive atlas of nuclear sequences of mitochondrial origin (NUMT) inserted into the pig genome. Genet Sel Evol 2024; 56:64. [PMID: 39285356 PMCID: PMC11403998 DOI: 10.1186/s12711-024-00930-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 08/26/2024] [Indexed: 09/20/2024] Open
Abstract
BACKGROUND The integration of nuclear mitochondrial DNA (mtDNA) into the mammalian genomes is an ongoing, yet rare evolutionary process that produces nuclear sequences of mitochondrial origin (NUMT). In this study, we identified and analysed NUMT inserted into the pig (Sus scrofa) genome and in the genomes of a few other Suinae species. First, we constructed a comparative distribution map of NUMT in the Sscrofa11.1 reference genome and in 22 other assembled S. scrofa genomes (from Asian and European pig breeds and populations), as well as the assembled genomes of the Visayan warty pig (Sus cebifrons) and warthog (Phacochoerus africanus). We then analysed a total of 485 whole genome sequencing datasets, from different breeds, populations, or Sus species, to discover polymorphic NUMT (inserted/deleted in the pig genome). The insertion age was inferred based on the presence or absence of orthologous NUMT in the genomes of different species, taking into account their evolutionary divergence. Additionally, the age of the NUMT was calculated based on sequence degradation compared to the authentic mtDNA sequence. We also validated a selected set of representative NUMT via PCR amplification. RESULTS We have constructed an atlas of 418 NUMT regions, 70 of which were not present in any assembled genomes. We identified ancient NUMT regions (older than 55 million years ago, Mya) and NUMT that appeared at different time points along the Suinae evolutionary lineage. We identified very recent polymorphic NUMT (private to S. scrofa, with < 1 Mya), and more ancient polymorphic NUMT (3.5-10 Mya) present in various Sus species. These latest polymorphic NUMT regions, which segregate in European and Asian pig breeds and populations, are likely the results of interspecies admixture within the Sus genus. CONCLUSIONS This study provided a first comprehensive analysis of NUMT present in the Sus scrofa genome, comparing them to NUMT found in other species within the order Cetartiodactyla. The NUMT-based evolutionary window that we reconstructed from NUMT integration ages could be useful to better understand the micro-evolutionary events that shaped the modern pig genome and enriched the genetic diversity of this species.
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Affiliation(s)
- Matteo Bolner
- Animal and Food Genomics Group, Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127, Bologna, Italy
| | - Samuele Bovo
- Animal and Food Genomics Group, Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127, Bologna, Italy
| | - Mohamad Ballan
- Animal and Food Genomics Group, Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127, Bologna, Italy
| | - Giuseppina Schiavo
- Animal and Food Genomics Group, Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127, Bologna, Italy
| | - Valeria Taurisano
- Animal and Food Genomics Group, Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127, Bologna, Italy
| | - Anisa Ribani
- Animal and Food Genomics Group, Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127, Bologna, Italy
| | - Francesca Bertolini
- Animal and Food Genomics Group, Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127, Bologna, Italy
| | - Luca Fontanesi
- Animal and Food Genomics Group, Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127, Bologna, Italy.
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Rugman-Jones PF, Dodge CE, Stouthamer R. Pervasive heteroplasmy in an invasive ambrosia beetle (Scolytinae) in southern California. Heredity (Edinb) 2024:10.1038/s41437-024-00722-0. [PMID: 39266674 DOI: 10.1038/s41437-024-00722-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 08/21/2024] [Accepted: 08/21/2024] [Indexed: 09/14/2024] Open
Abstract
Heteroplasmy, the presence of multiple mitochondrial genotypes (mitotypes) within an individual, has long been thought to be a rare aberrance that is quickly removed by selection or drift. However, heteroplasmy is being reported in natural populations of eukaryotes with increasing frequency, in part due to improved diagnostic methods. Here, we report a seemingly stable heteroplasmic state in California populations of the polyphagous shothole borer (PSHB), Euwallacea fornicatus; an invasive ambrosia beetle that is causing significant tree dieback. We develop and validate a qPCR assay utilizing locked nucleic acid probes to detect different mitotypes, and qualitatively assess heteroplasmy in individual PSHB. We prove the utility of this assay by: (1) mitotyping field-collected PSHB, documenting the prevalence of heteroplasmy across its range in California; and, (2) measuring relative titers of each mitotype across multiple generations of heteroplasmic laboratory colonies to assess the stability of transmission through the maternal germline. We show that our findings are unlikely to be explained by the existence of NUMTs by next generation sequencing of contiguous sections of mitochondrial DNA, where each of the observed heteroplasmic sites are found within fully functional coding regions of mtDNA. Subsequently, we find heteroplasmic individuals are common in Californian field populations, and that heteroplasmy persists for at least 10 generations in experimental colonies. We also looked for evidence of the common occurrence of paternal leakage, but found none. In light of our results, we discuss competing hypotheses as to how heteroplasmy may have arisen, and continues to perpetuate, in Californian PSHB populations.
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Affiliation(s)
- Paul F Rugman-Jones
- Department of Entomology, University of California, Riverside, CA, 92521, USA.
| | - Christine E Dodge
- Department of Entomology, University of California, Riverside, CA, 92521, USA
- Forest Pest Methods Laboratory, USDA-APHIS-PPQ-S&T, 1398 W. Truck Rd, Buzzards Bay, MA, 02542, USA
| | - Richard Stouthamer
- Department of Entomology, University of California, Riverside, CA, 92521, USA
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Marturano G, Carli D, Cucini C, Carapelli A, Plazzi F, Frati F, Passamonti M, Nardi F. SmithHunter: a workflow for the identification of candidate smithRNAs and their targets. BMC Bioinformatics 2024; 25:286. [PMID: 39223476 PMCID: PMC11370224 DOI: 10.1186/s12859-024-05909-0] [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: 02/20/2024] [Accepted: 08/21/2024] [Indexed: 09/04/2024] Open
Abstract
BACKGROUND SmithRNAs (Small MITochondrial Highly-transcribed RNAs) are a novel class of small RNA molecules that are encoded in the mitochondrial genome and regulate the expression of nuclear transcripts. Initial evidence for their existence came from the Manila clam Ruditapes philippinarum, where they have been described and whose activity has been biologically validated through RNA injection experiments. Current evidence on the existence of these RNAs in other species is based only on small RNA sequencing. As a preliminary step to characterize smithRNAs across different metazoan lineages, a dedicated, unified, analytical workflow is needed. RESULTS We propose a novel workflow specifically designed for smithRNAs. Sequence data (from small RNA sequencing) uniquely mapping to the mitochondrial genome are clustered into putative smithRNAs and prefiltered based on their abundance, presence in replicate libraries and 5' and 3' transcription boundary conservation. The surviving sequences are subsequently compared to the untranslated regions of nuclear transcripts based on seed pairing, overall match and thermodynamic stability to identify possible targets. Ample collateral information and graphics are produced to help characterize these molecules in the species of choice and guide the operator through the analysis. The workflow was tested on the original Manila clam data. Under basic settings, the results of the original study are largely replicated. The effect of additional parameter customization (clustering threshold, stringency, minimum number of replicates, seed matching) was further evaluated. CONCLUSIONS The study of smithRNAs is still in its infancy and no dedicated analytical workflow is currently available. At its core, the SmithHunter workflow builds over the bioinformatic procedure originally applied to identify candidate smithRNAs in the Manila clam. In fact, this is currently the only evidence for smithRNAs that has been biologically validated and, therefore, the elective starting point for characterizing smithRNAs in other species. The original analysis was readapted using current software implementations and some minor issues were solved. Moreover, the workflow was improved by allowing the customization of different analytical parameters, mostly focusing on stringency and the possibility of accounting for a minimal level of genetic differentiation among samples.
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Affiliation(s)
| | - Diego Carli
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Via Selmi 3, 40126, Bologna, Italy
| | - Claudio Cucini
- Department of Life Sciences, University of Siena, 53100, Siena, Italy
| | - Antonio Carapelli
- Department of Life Sciences, University of Siena, 53100, Siena, Italy
- National Biodiversity Future Center (NBFC), 90133, Palermo, Italy
| | - Federico Plazzi
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Via Selmi 3, 40126, Bologna, Italy
| | - Francesco Frati
- Department of Life Sciences, University of Siena, 53100, Siena, Italy
- National Biodiversity Future Center (NBFC), 90133, Palermo, Italy
| | - Marco Passamonti
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Via Selmi 3, 40126, Bologna, Italy.
| | - Francesco Nardi
- Department of Life Sciences, University of Siena, 53100, Siena, Italy
- National Biodiversity Future Center (NBFC), 90133, Palermo, Italy
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4
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Helwick K, Ross J. Reciprocal restriction fragment length polymorphism (RFLP) analysis reveals mitochondrial heteroplasmy in Caenorhabditis briggsae hybrids. MICROPUBLICATION BIOLOGY 2024; 2024:10.17912/micropub.biology.001306. [PMID: 39185015 PMCID: PMC11344225 DOI: 10.17912/micropub.biology.001306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2024] [Revised: 08/06/2024] [Accepted: 08/07/2024] [Indexed: 08/27/2024]
Abstract
Although mitochondria are typically inherited maternally, exceptions exist. We previously demonstrated that within-species crosses of Caenorhabditis briggsae result in paternal mitochondrial transmission, and it would be useful to know whether hybrids have only paternal mitochondria (homoplasmy) or paternal and maternal mitochondria (heteroplasmy). We developed a reciprocal restriction fragment length polymorphism analysis to separately detect paternal and maternal mitochondrial DNA. Using new hybrid lines, this approach revealed that some hybrids are heteroplasmous and others have become homoplasmous for the paternal mitotype. These results motivate additional investigation of how paternal mitochondrial transmission is apparently facile in C. briggsae .
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Affiliation(s)
- Kevin Helwick
- Department of Biology, California State University, Fresno
| | - Joseph Ross
- Department of Biology, California State University, Fresno
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Allison PF, Pickich ET, Barnett ZC, Garrick RC. DNA barcoding is currently unreliable for species identification in most crayfishes. Ecol Evol 2024; 14:e70050. [PMID: 39041008 PMCID: PMC11260883 DOI: 10.1002/ece3.70050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 07/06/2024] [Accepted: 07/08/2024] [Indexed: 07/24/2024] Open
Abstract
DNA barcoding is commonly used for species identification. Despite this, there has not been a comprehensive assessment of the utility of DNA barcoding in crayfishes (Decapoda: Astacidea). Here we examined the extent to which local barcoding gaps (used for species identification) and global barcoding gaps (used for species discovery) exist among crayfishes, and whether global gaps met a previously suggested 10× threshold (mean interspecific difference being 10× larger than mean intra specific difference). We examined barcoding gaps using publicly available mitochondrial COI sequence data from the National Center for Biotechnology Information's nucleotide database. We created two versions of the COI datasets used for downstream analyses: one focused on the number of unique haplotypes (N H) per species, and another that focused on total number of sequences (N S; i.e., including redundant haplotypes) per species. A total of 81 species were included, with 58 species and five genera from the family Cambaridae and 23 species from three genera from the family Parastacidae. Local barcoding gaps were present in only 30 species (20 Cambaridae and 10 Parastacidae species). We detected global barcoding gaps in only four genera (Cambarus, Cherax, Euastacus, and Tenuibranchiurus), which were all below (4.2× to 5.2×) the previously suggested 10× threshold. We propose that a ~5× threshold would be a more appropriate working hypothesis for species discovery. While the N H and N S datasets yielded largely similar results, there were some discrepant inferences. To understand why some species lacked a local barcoding gap, we performed species delimitation analyses for each genus using the N H dataset. These results suggest that current taxonomy in crayfishes may be inadequate for the majority of examined species, and that even species with local barcoding gaps present may be in need of taxonomic revisions. Currently, the utility of DNA barcoding for species identification and discovery in crayfish is quite limited, and caution should be exercised when mitochondrial-based approaches are used in place of taxonomic expertise. Assessment of the evidence for local and global barcoding gaps is important for understanding the reliability of molecular species identification and discovery, but outcomes are dependent on the current state of taxonomy. As this improves (e.g., via resolving species complexes, possibly elevating some subspecies to the species-level status, and redressing specimen misidentifications in natural history and other collections), so too will the utility of DNA barcoding.
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Affiliation(s)
| | - Emily T. Pickich
- Department of BiologyUniversity of MississippiUniversityMississippiUSA
| | - Zanethia C. Barnett
- Southern Research StationUSDA Forest Service, Center for Bottomland Hardwoods ResearchClemsonSouth CarolinaUSA
| | - Ryan C. Garrick
- Department of BiologyUniversity of MississippiUniversityMississippiUSA
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Laifi-Necibi N, Amor N, Merella P, Mohammed OB, Medini L. DNA barcoding reveals cryptic species in the sea slater Ligia italica (Crustacea, Isopoda) from Tunisia. Mitochondrial DNA A DNA Mapp Seq Anal 2024:1-11. [PMID: 38899428 DOI: 10.1080/24701394.2024.2363350] [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: 03/06/2023] [Accepted: 03/14/2024] [Indexed: 06/21/2024]
Abstract
Barcoding studies have provided significant insights into phylogenetic relationships among species belonging to the genus Ligia (Crustacea, Isopoda). Herein the diversity of the Italian sea slater Ligia italica from Tunisia is studied for the first time. Samples were collected from 18 localities in Tunisia, and the analysis included previously published sequences from Italy and Greece available in GenBank. Bayesian and Maximum Likelihood phylogenetic analyses were carried out using a fragment of the mitochondrial COI gene. Putative cryptic species were explored using the 'barcode gap' approach in the software ASAP. A genetic landscape shape analysis was carried out using the program Alleles in Space. The analyses revealed highly divergent and well-supported clades of L. italica dispersed across Tunisia (Clades A1 and A2), Greece (Clade B) and Italy (Clades C1 and C2). High genetic dissimilarity among clades suggested that L. italica constitute a cryptic species complex. Divergence among different L. italica lineages (Clades A, B and C) occurred around 7-4.5 Ma. The detected high genetic distances among clades did not result from atypical mitochondrial DNAs or intracellular infection by Wolbachia bacteria. The complex history of the Mediterranean Sea appears to have played a significant role in shaping the phylogeographic pattern of Ligia italica. Additional morphological and molecular studies are needed to confirm the existence of cryptic species in Ligia italica in Mediterranean.
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Affiliation(s)
- Nermine Laifi-Necibi
- Faculté des Sciences de Tunis, Laboratoire Diversité, Gestion et Conservation des Systèmes Biologiques, Université de Tunis El Manar, Tunis, Tunisia
| | - Nabil Amor
- Higher Institute of Applied Biological Sciences of Tunis, University Tunis EL Manar, Tunis, Tunisia
| | - Paolo Merella
- Parassitologia e Malattie Parassitarie, Dipartimento di Medicina Veterinaria, Università di Sassari, Sassari, Italy
| | | | - Lamia Medini
- Faculté des Sciences de Tunis, Laboratoire Diversité, Gestion et Conservation des Systèmes Biologiques, Université de Tunis El Manar, Tunis, Tunisia
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Uvizl M, Puechmaille SJ, Power S, Pippel M, Carthy S, Haerty W, Myers EW, Teeling EC, Huang Z. Comparative Genome Microsynteny Illuminates the Fast Evolution of Nuclear Mitochondrial Segments (NUMTs) in Mammals. Mol Biol Evol 2024; 41:msad278. [PMID: 38124445 PMCID: PMC10764098 DOI: 10.1093/molbev/msad278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 11/16/2023] [Accepted: 12/12/2023] [Indexed: 12/23/2023] Open
Abstract
The escape of DNA from mitochondria into the nuclear genome (nuclear mitochondrial DNA, NUMT) is an ongoing process. Although pervasively observed in eukaryotic genomes, their evolutionary trajectories in a mammal-wide context are poorly understood. The main challenge lies in the orthology assignment of NUMTs across species due to their fast evolution and chromosomal rearrangements over the past 200 million years. To address this issue, we systematically investigated the characteristics of NUMT insertions in 45 mammalian genomes and established a novel, synteny-based method to accurately predict orthologous NUMTs and ascertain their evolution across mammals. With a series of comparative analyses across taxa, we revealed that NUMTs may originate from nonrandom regions in mtDNA, are likely found in transposon-rich and intergenic regions, and unlikely code for functional proteins. Using our synteny-based approach, we leveraged 630 pairwise comparisons of genome-wide microsynteny and predicted the NUMT orthology relationships across 36 mammals. With the phylogenetic patterns of NUMT presence-and-absence across taxa, we constructed the ancestral state of NUMTs given the mammal tree using a coalescent method. We found support on the ancestral node of Fereuungulata within Laurasiatheria, whose subordinal relationships are still controversial. This study broadens our knowledge on NUMT insertion and evolution in mammalian genomes and highlights the merit of NUMTs as alternative genetic markers in phylogenetic inference.
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Affiliation(s)
- Marek Uvizl
- Department of Zoology, National Museum, 19300 Prague, Czech Republic
- Department of Zoology, Faculty of Science, Charles University, 12844 Prague, Czech Republic
| | - Sebastien J Puechmaille
- Institut des Sciences de l’Evolution de Montpellier (ISEM), University of Montpellier, 34095 Montpellier, France
- Institut Universitaire de France, Paris, France
| | - Sarahjane Power
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Martin Pippel
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
- National Bioinformatics Infrastructure Sweden, Uppsala, Sweden
| | - Samuel Carthy
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Wilfried Haerty
- Earlham Institute, Norwich Research Park, Colney Ln, NR4 7UZ Norwich, UK
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Eugene W Myers
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Emma C Teeling
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Zixia Huang
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
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8
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Kuprina K, Smorkatcheva A, Rudyk A, Galkina S. Numerous insertions of mitochondrial DNA in the genome of the northern mole vole, Ellobius talpinus. Mol Biol Rep 2023; 51:36. [PMID: 38157080 PMCID: PMC10756869 DOI: 10.1007/s11033-023-08913-4] [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: 09/04/2023] [Accepted: 10/23/2023] [Indexed: 01/03/2024]
Abstract
BACKGROUND Ellobius talpinus is a subterranean rodent representing an attractive model in population ecology studies due to its highly special lifestyle and sociality. In such studies, mitochondrial DNA (mtDNA) is widely used. However, if nuclear copies of mtDNA, aka NUMTs, are present, they may co-amplify with the target mtDNA fragment, generating misleading results. The aim of this study was to determine whether NUMTs are present in E. talpinus. METHODS AND RESULTS PCR amplification of the putative mtDNA CytB-D-loop fragment using 'universal' primers from 56 E. talpinus samples produced multiple double peaks in 90% of the sequencing chromatograms. To reveal NUMTs, molecular cloning and sequencing of PCR products of three specimens was conducted, followed by phylogenetic analysis. The pseudogene nature of three out of the seven detected haplotypes was confirmed by their basal positions in relation to other Ellobius haplotypes in the phylogenetic tree. Additionally, 'haplotype B' was basal in relation to other E. talpinus haplotypes and found present in very distant sampling sites. BLASTN search revealed 195 NUMTs in the E. talpinus nuclear genome, including fragments of all four PCR amplified pseudogenes. Although the majority of the NUMTs studied were short, the entire mtDNA had copies in the nuclear genome. The most numerous NUMTs were found for rrnL, COXI, and D-loop. CONCLUSIONS Numerous NUMTs are present in E. talpinus and can be difficult to discriminate against mtDNA sequences. Thus, in future population or phylogenetic studies in E. talpinus, the possibility of cryptic NUMTs amplification should always be taken into account.
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Affiliation(s)
- Kristina Kuprina
- Institute of Botany and Landscape Ecology, University of Greifswald, Soldmannstr. 15, Greifswald, 17489, Germany.
- Department of Vertebrate Zoology, Saint Petersburg State University, Universitetskaya nab. 7/9, Saint Petersburg, 199034, Russia.
| | - Antonina Smorkatcheva
- Department of Vertebrate Zoology, Saint Petersburg State University, Universitetskaya nab. 7/9, Saint Petersburg, 199034, Russia
| | - Anna Rudyk
- Department of Vertebrate Zoology, Saint Petersburg State University, Universitetskaya nab. 7/9, Saint Petersburg, 199034, Russia
| | - Svetlana Galkina
- Department of Genetics and Biotechnology, Saint Petersburg State University, Universitetskaya nab. 7/9, Saint Petersburg, 199034, Russia
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9
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Piwczyński M, Granjon L, Trzeciak P, Carlos Brito J, Oana Popa M, Daba Dinka M, Johnston NP, Boratyński Z. Unraveling phylogenetic relationships and species boundaries in the arid adapted Gerbillus rodents (Muridae: Gerbillinae) by RAD-seq data. Mol Phylogenet Evol 2023; 189:107913. [PMID: 37659480 DOI: 10.1016/j.ympev.2023.107913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 08/25/2023] [Accepted: 08/28/2023] [Indexed: 09/04/2023]
Abstract
Gerbillus is one of the most speciose genera among rodents, with ca. 51 recognized species. Previous attempts to reconstruct the evolutionary history of Gerbillus mainly relied on the mitochondrial cyt-b marker as a source of phylogenetic information. In this study, we utilize RAD-seq genomic data from 37 specimens representing 11 species to reconstruct the phylogenetic tree for Gerbillus, applying concatenation and coalescence methods. We identified four highly supported clades corresponding to the traditionally recognized subgenera: Dipodillus, Gerbillus, Hendecapleura and Monodia. Only two uncertain branches were detected in the resulting trees, with one leading to diversification of the main lineages in the genus, recognized by quartet sampling analysis as uncertain due to possible introgression. We also examined species boundaries for four pairs of sister taxa, including potentially new species from Morocco, using SNAPP. The results strongly supported a speciation model in which all taxa are treated as separate species. The dating analyses confirmed the Plio-Pleistocene diversification of the genus, with the uncertain branch coinciding with the beginning of aridification of the Sahara at the the Plio-Pleistocene boundary. This study aligns well with the earlier analyses based on the cyt-b marker, reaffirming its suitability as an adequate marker for estimating genetic diversity in Gerbillus.
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Affiliation(s)
- Marcin Piwczyński
- Department of Ecology and Biogeography, Nicolaus Copernicus University in Toruń, Lwowska 1, PL-87-100 Toruń, Poland.
| | - Laurent Granjon
- CBGP, IRD, CIRAD, INRAE, Institut Agro, Université de Montpellier, Montpellier, France
| | - Paulina Trzeciak
- Department of Ecology and Biogeography, Nicolaus Copernicus University in Toruń, Lwowska 1, PL-87-100 Toruń, Poland
| | - José Carlos Brito
- CIBIO-InBio, Research Center in Biodiversity and Genetic Resources, University of Porto, Campus de Vairão, Rua Padre Armando Quintas 7, 4485-661 Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Madalina Oana Popa
- Department of Ecology and Biogeography, Nicolaus Copernicus University in Toruń, Lwowska 1, PL-87-100 Toruń, Poland; "Stejarul" Research Centre for Biological Sciences, National Institute of Research and Development for Biological Sciences, Alexandru cel Bun 6, RO-610004, Piatra Neamţ, Romania
| | - Mergi Daba Dinka
- Department of Ecology and Biogeography, Nicolaus Copernicus University in Toruń, Lwowska 1, PL-87-100 Toruń, Poland
| | - Nikolas P Johnston
- School of Life Sciences, University of Technology Sydney, 15 Broadway, Ultimo, NSW 2007, Australia; Centre for Sustainable Ecosystem Solutions, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Northfields Ave, Wollongong, NSW 2500, Australia
| | - Zbyszek Boratyński
- CIBIO-InBio, Research Center in Biodiversity and Genetic Resources, University of Porto, Campus de Vairão, Rua Padre Armando Quintas 7, 4485-661 Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
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10
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Naarmann-de Vries IS, Gjerga E, Gandor CLA, Dieterich C. Adaptive sampling for nanopore direct RNA-sequencing. RNA (NEW YORK, N.Y.) 2023; 29:1939-1949. [PMID: 37673469 PMCID: PMC10653383 DOI: 10.1261/rna.079727.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 08/14/2023] [Indexed: 09/08/2023]
Abstract
Nanopore long-read sequencing enables real-time monitoring and controlling of individual nanopores. This allows us to enrich or deplete specific sequences in DNA sequencing in a process called "adaptive sampling." So far, adaptive sampling (AS) was not applicable to the direct sequencing of RNA. Here, we show that AS is feasible and useful for direct RNA sequencing (DRS), which has its specific technical and biological challenges. Using a well-controlled in vitro transcript-based model system, we identify essential characteristics and parameter settings for AS in DRS, as the superior performance of depletion over enrichment. Here, the efficiency of depletion is close to the theoretical maximum. Additionally, we demonstrate that AS efficiently depletes specific transcripts in transcriptome-wide sequencing applications. Specifically, we applied our AS approach to poly(A)-enriched RNA samples from human-induced pluripotent stem cell-derived cardiomyocytes and mouse whole heart tissue and show efficient 2.5- to 2.8-fold depletion of highly abundant mitochondrial-encoded transcripts. Finally, we characterize depletion and enrichment performance for complex transcriptome subsets, that is, at the level of the entire Chromosome 11, proving the general applicability of direct RNA AS. Our analyses provide evidence that AS is especially useful to enable the detection of lowly expressed transcripts and reduce the sequencing of highly abundant disturbing transcripts.
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Affiliation(s)
- Isabel S Naarmann-de Vries
- Klaus Tschira Institute for Integrative Computational Cardiology, University Hospital Heidelberg, 69120 Heidelberg, Germany
- German Center for Cardiovascular Research (DZHK), Partner site Heidelberg/Mannheim, 69120 Heidelberg, Germany
| | - Enio Gjerga
- Klaus Tschira Institute for Integrative Computational Cardiology, University Hospital Heidelberg, 69120 Heidelberg, Germany
- German Center for Cardiovascular Research (DZHK), Partner site Heidelberg/Mannheim, 69120 Heidelberg, Germany
| | - Catharina L A Gandor
- Klaus Tschira Institute for Integrative Computational Cardiology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Christoph Dieterich
- Klaus Tschira Institute for Integrative Computational Cardiology, University Hospital Heidelberg, 69120 Heidelberg, Germany
- German Center for Cardiovascular Research (DZHK), Partner site Heidelberg/Mannheim, 69120 Heidelberg, Germany
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11
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Namasivayam S, Sun C, Bah AB, Oberstaller J, Pierre-Louis E, Etheridge RD, Feschotte C, Pritham EJ, Kissinger JC. Massive invasion of organellar DNA drives nuclear genome evolution in Toxoplasma. Proc Natl Acad Sci U S A 2023; 120:e2308569120. [PMID: 37917792 PMCID: PMC10636329 DOI: 10.1073/pnas.2308569120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 09/26/2023] [Indexed: 11/04/2023] Open
Abstract
Toxoplasma gondii is a zoonotic protist pathogen that infects up to one third of the human population. This apicomplexan parasite contains three genome sequences: nuclear (65 Mb); plastid organellar, ptDNA (35 kb); and mitochondrial organellar, mtDNA (5.9 kb of non-repetitive sequence). We find that the nuclear genome contains a significant amount of NUMTs (nuclear integrants of mitochondrial DNA) and NUPTs (nuclear integrants of plastid DNA) that are continuously acquired and represent a significant source of intraspecific genetic variation. NUOT (nuclear DNA of organellar origin) accretion has generated 1.6% of the extant T. gondii ME49 nuclear genome-the highest fraction ever reported in any organism. NUOTs are primarily found in organisms that retain the non-homologous end-joining repair pathway. Significant movement of organellar DNA was experimentally captured via amplicon sequencing of a CRISPR-induced double-strand break in non-homologous end-joining repair competent, but not ku80 mutant, Toxoplasma parasites. Comparisons with Neospora caninum, a species that diverged from Toxoplasma ~28 mya, revealed that the movement and fixation of five NUMTs predates the split of the two genera. This unexpected level of NUMT conservation suggests evolutionary constraint for cellular function. Most NUMT insertions reside within (60%) or nearby genes (23% within 1.5 kb), and reporter assays indicate that some NUMTs have the ability to function as cis-regulatory elements modulating gene expression. Together, these findings portray a role for organellar sequence insertion in dynamically shaping the genomic architecture and likely contributing to adaptation and phenotypic changes in this important human pathogen.
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Affiliation(s)
| | - Cheng Sun
- Department of Biology, University of Texas at Arlington, Arlington, TX76019
| | - Assiatu B. Bah
- Department of Biology, University of Texas at Arlington, Arlington, TX76019
| | | | - Edwin Pierre-Louis
- Department of Cellular Biology, Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA30602
| | - Ronald Drew Etheridge
- Department of Cellular Biology, Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA30602
| | - Cedric Feschotte
- Department of Biology, University of Texas at Arlington, Arlington, TX76019
| | - Ellen J. Pritham
- Department of Biology, University of Texas at Arlington, Arlington, TX76019
| | - Jessica C. Kissinger
- Department of Genetics, Institute of Bioinformatics, Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA30602
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12
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Nieto-Panqueva F, Rubalcava-Gracia D, Hamel PP, González-Halphen D. The constraints of allotopic expression. Mitochondrion 2023; 73:30-50. [PMID: 37739243 DOI: 10.1016/j.mito.2023.09.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 08/28/2023] [Accepted: 09/18/2023] [Indexed: 09/24/2023]
Abstract
Allotopic expression is the functional transfer of an organellar gene to the nucleus, followed by synthesis of the gene product in the cytosol and import into the appropriate organellar sub compartment. Here, we focus on mitochondrial genes encoding OXPHOS subunits that were naturally transferred to the nucleus, and critically review experimental evidence that claim their allotopic expression. We emphasize aspects that may have been overlooked before, i.e., when modifying a mitochondrial gene for allotopic expression━besides adapting the codon usage and including sequences encoding mitochondrial targeting signals━three additional constraints should be considered: (i) the average apparent free energy of membrane insertion (μΔGapp) of the transmembrane stretches (TMS) in proteins earmarked for the inner mitochondrial membrane, (ii) the final, functional topology attained by each membrane-bound OXPHOS subunit; and (iii) the defined mechanism by which the protein translocator TIM23 sorts cytosol-synthesized precursors. The mechanistic constraints imposed by TIM23 dictate the operation of two pathways through which alpha-helices in TMS are sorted, that eventually determine the final topology of membrane proteins. We used the biological hydrophobicity scale to assign an average apparent free energy of membrane insertion (μΔGapp) and a "traffic light" color code to all TMS of OXPHOS membrane proteins, thereby predicting which are more likely to be internalized into mitochondria if allotopically produced. We propose that the design of proteins for allotopic expression must make allowance for μΔGapp maximization of highly hydrophobic TMS in polypeptides whose corresponding genes have not been transferred to the nucleus in some organisms.
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Affiliation(s)
- Felipe Nieto-Panqueva
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Diana Rubalcava-Gracia
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico; Division of Molecular Metabolism, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Patrice P Hamel
- Department of Molecular Genetics and Department of Biological Chemistry and Pharmacology, Ohio State University, Columbus, OH, USA; Vellore Institute of Technology (VIT), School of BioScience and Technology, Vellore, Tamil Nadu, India
| | - Diego González-Halphen
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico.
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13
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Martínez-Ríos M, Martín-Torrijos L, Casabella-Herrero G, Tedesco P, Machordom A, Diéguez-Uribeondo J. On the conservation of white-clawed crayfish in the Iberian Peninsula: Unraveling its genetic diversity and structure, and origin. PLoS One 2023; 18:e0292679. [PMID: 37831691 PMCID: PMC10575519 DOI: 10.1371/journal.pone.0292679] [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: 06/29/2023] [Accepted: 09/26/2023] [Indexed: 10/15/2023] Open
Abstract
European crayfish species are a clear example of the drastic decline that freshwater species are experiencing. In particular, the native species of the Iberian Peninsula, the white clawed-crayfish (WCC) Austropotamobius pallipes, is listed as "endangered" by the IUCN and included in Annex II of the EU Habitat Directive and requires especially attention. Currently, implemented conservation management strategies require a better understanding of the genetic diversity and phylogeographic patterns, as well as of its evolutionary history. For this purpose, we have generated the largest datasets of two informative ribosomal mitochondrial DNA regions, i.e., cytochrome oxidase subunit I and 16S, from selected populations of the WCC covering its geographical distribution. These datasets allowed us to analyze in detail the (i) genetic diversity and structure of WCC populations, and (ii) divergence times for Iberian populations by testing three evolutionary scenarios with different mtDNA substitution rates (low, intermediate, and high rates). The results indicate high levels of haplotype diversity and a complex geographical structure for WCC in the Iberian Peninsula. The diversity found includes new unique haplotypes from the Iberian Peninsula and reveals that most of the WCC genetic variability is concentrated in the northern and central-eastern regions. Despite the fact that molecular dating analyses provided divergence times that were not statistically supported, the proposed scenarios were congruent with previous studies, which related the origin of these populations with paleogeographic events during the Pleistocene, which suggests an Iberian origin for these WCC. All results generated in this study, indicate that the alternative hypothesis of an introduced origin of the Iberian WCC is highly improbable. The result of this study, therefore, has allowed us to better understand of the genetic diversity, structure patterns, and evolutionary history of the WCC in the Iberian Peninsula, which is crucial for the management and conservation needs of this endangered species.
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Affiliation(s)
| | | | | | - Perla Tedesco
- Department of Veterinary Medical Sciences Alma Mater Studiorum, University of Bologna, Ozzano dell’Emilia, Italy
| | - Annie Machordom
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales (MNCN-CSIC), Madrid, Spain
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14
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Zhong Y, Zeng K, Adnan A, Li YZ, Hou XK, Pan Y, Li A, Zhu XM, Lv P, Du Z, Yang Y, Yao J. Discrimination of monozygotic twins using mtDNA heteroplasmy through probe capture enrichment and massively parallel sequencing. Int J Legal Med 2023; 137:1337-1345. [PMID: 37270462 DOI: 10.1007/s00414-023-03033-x] [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: 04/05/2023] [Accepted: 05/30/2023] [Indexed: 06/05/2023]
Abstract
Differentiating between monozygotic (MZ) twins remains difficult because they have the same genetic makeup. Applying the traditional STR genotyping approach cannot differentiate one from the other. Heteroplasmy refers to the presence of two or more different mtDNA copies within a single cell and this phenomenon is common in humans. The levels of heteroplasmy cannot change dramatically during transmission in the female germ line but increase or decrease during germ-line transmission and in somatic tissues during life. As massively parallel sequencing (MPS) technology has advanced, it has shown the extraordinary quantity of mtDNA heteroplasmy in humans. In this study, a probe hybridization technique was used to obtain mtDNA and then MPS was performed with an average sequencing depth of above 4000. The results showed us that all ten pairs of MZ twins were clearly differentiated with the minor heteroplasmy threshold at 1.0%, 0.5%, and 0.1%, respectively. Finally, we used a probe that targeted mtDNA to boost sequencing depth without interfering with nuclear DNA and this technique can be used in forensic genetics to differentiate the MZ twins.
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Affiliation(s)
- Yang Zhong
- School of Forensic Medicine, China Medical University, No.77, Puhe Road, Shenbei New District, Shenyang, 110122, People's Republic of China
- Key Laboratory of Forensic Bio-evidence Sciences, Shenyang, Liaoning Province, China
- China Medical University Center of Forensic Investigation, Chengdu, China
| | - Kuo Zeng
- Institute of Evidence Law and Forensic Science, China University of Political Science and Law, Beijing, China
| | - Atif Adnan
- Department of Forensic Sciences, College of Criminal Justice, Naif University of Security Sciences, Riyadh, 11452, Kingdom of Saudi Arabia
| | - Yu-Zhang Li
- School of Forensic Medicine, China Medical University, No.77, Puhe Road, Shenbei New District, Shenyang, 110122, People's Republic of China
- Key Laboratory of Forensic Bio-evidence Sciences, Shenyang, Liaoning Province, China
- China Medical University Center of Forensic Investigation, Chengdu, China
| | - Xi-Kai Hou
- School of Forensic Medicine, China Medical University, No.77, Puhe Road, Shenbei New District, Shenyang, 110122, People's Republic of China
- Key Laboratory of Forensic Bio-evidence Sciences, Shenyang, Liaoning Province, China
- China Medical University Center of Forensic Investigation, Chengdu, China
| | - Ying Pan
- School of Forensic Medicine, China Medical University, No.77, Puhe Road, Shenbei New District, Shenyang, 110122, People's Republic of China
- Key Laboratory of Forensic Bio-evidence Sciences, Shenyang, Liaoning Province, China
- China Medical University Center of Forensic Investigation, Chengdu, China
| | - Ang Li
- School of Forensic Medicine, China Medical University, No.77, Puhe Road, Shenbei New District, Shenyang, 110122, People's Republic of China
- Key Laboratory of Forensic Bio-evidence Sciences, Shenyang, Liaoning Province, China
- China Medical University Center of Forensic Investigation, Chengdu, China
| | - Xiu-Mei Zhu
- School of Forensic Medicine, China Medical University, No.77, Puhe Road, Shenbei New District, Shenyang, 110122, People's Republic of China
- Key Laboratory of Forensic Bio-evidence Sciences, Shenyang, Liaoning Province, China
- China Medical University Center of Forensic Investigation, Chengdu, China
| | - Peng Lv
- School of Forensic Medicine, China Medical University, No.77, Puhe Road, Shenbei New District, Shenyang, 110122, People's Republic of China
- Key Laboratory of Forensic Bio-evidence Sciences, Shenyang, Liaoning Province, China
- China Medical University Center of Forensic Investigation, Chengdu, China
| | - Zhe Du
- School of Forensic Medicine, China Medical University, No.77, Puhe Road, Shenbei New District, Shenyang, 110122, People's Republic of China
- Key Laboratory of Forensic Bio-evidence Sciences, Shenyang, Liaoning Province, China
- China Medical University Center of Forensic Investigation, Chengdu, China
| | - Ying Yang
- Department of Gastroenterology, Shengjing Hospital of China Medical University, Shenyang, China.
| | - Jun Yao
- School of Forensic Medicine, China Medical University, No.77, Puhe Road, Shenbei New District, Shenyang, 110122, People's Republic of China.
- Key Laboratory of Forensic Bio-evidence Sciences, Shenyang, Liaoning Province, China.
- China Medical University Center of Forensic Investigation, Chengdu, China.
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15
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Doimo M, Chaudhari N, Abrahamsson S, L’Hôte V, Nguyen TH, Berner A, Ndi M, Abrahamsson A, Das R, Aasumets K, Goffart S, Pohjoismäki JLO, López MD, Chorell E, Wanrooij S. Enhanced mitochondrial G-quadruplex formation impedes replication fork progression leading to mtDNA loss in human cells. Nucleic Acids Res 2023; 51:7392-7408. [PMID: 37351621 PMCID: PMC10415151 DOI: 10.1093/nar/gkad535] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 06/09/2023] [Indexed: 06/24/2023] Open
Abstract
Mitochondrial DNA (mtDNA) replication stalling is considered an initial step in the formation of mtDNA deletions that associate with genetic inherited disorders and aging. However, the molecular details of how stalled replication forks lead to mtDNA deletions accumulation are still unclear. Mitochondrial DNA deletion breakpoints preferentially occur at sequence motifs predicted to form G-quadruplexes (G4s), four-stranded nucleic acid structures that can fold in guanine-rich regions. Whether mtDNA G4s form in vivo and their potential implication for mtDNA instability is still under debate. In here, we developed new tools to map G4s in the mtDNA of living cells. We engineered a G4-binding protein targeted to the mitochondrial matrix of a human cell line and established the mtG4-ChIP method, enabling the determination of mtDNA G4s under different cellular conditions. Our results are indicative of transient mtDNA G4 formation in human cells. We demonstrate that mtDNA-specific replication stalling increases formation of G4s, particularly in the major arc. Moreover, elevated levels of G4 block the progression of the mtDNA replication fork and cause mtDNA loss. We conclude that stalling of the mtDNA replisome enhances mtDNA G4 occurrence, and that G4s not resolved in a timely manner can have a negative impact on mtDNA integrity.
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Affiliation(s)
- Mara Doimo
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden
- Department of Women and Children Health, University of Padova, 35128 Padova, Italy
| | - Namrata Chaudhari
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden
| | - Sanna Abrahamsson
- Bioinformatics and Data Centre, Sahlgrenska Academy, University of Gothenburg, 41390 Gothenburg, Sweden
| | - Valentin L’Hôte
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden
| | - Tran V H Nguyen
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden
| | - Andreas Berner
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden
| | - Mama Ndi
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden
| | | | | | - Koit Aasumets
- Department of Environmental and Biological Sciences, University of Eastern Finland, FI-80101 Joensuu, Finland
| | - Steffi Goffart
- Department of Environmental and Biological Sciences, University of Eastern Finland, FI-80101 Joensuu, Finland
| | - Jaakko L O Pohjoismäki
- Department of Environmental and Biological Sciences, University of Eastern Finland, FI-80101 Joensuu, Finland
| | - Marcela Dávila López
- Bioinformatics and Data Centre, Sahlgrenska Academy, University of Gothenburg, 41390 Gothenburg, Sweden
| | - Erik Chorell
- Department of Chemistry, Umeå University, 90187 Umeå, Sweden
| | - Sjoerd Wanrooij
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden
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16
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Hebert PDN, Bock DG, Prosser SWJ. Interrogating 1000 insect genomes for NUMTs: A risk assessment for estimates of species richness. PLoS One 2023; 18:e0286620. [PMID: 37289794 PMCID: PMC10249859 DOI: 10.1371/journal.pone.0286620] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 05/22/2023] [Indexed: 06/10/2023] Open
Abstract
The nuclear genomes of most animal species include NUMTs, segments of the mitogenome incorporated into their chromosomes. Although NUMT counts are known to vary greatly among species, there has been no comprehensive study of their frequency/attributes in the most diverse group of terrestrial organisms, insects. This study examines NUMTs derived from a 658 bp 5' segment of the cytochrome c oxidase I (COI) gene, the barcode region for the animal kingdom. This assessment is important because unrecognized NUMTs can elevate estimates of species richness obtained through DNA barcoding and derived approaches (eDNA, metabarcoding). This investigation detected nearly 10,000 COI NUMTs ≥ 100 bp in the genomes of 1,002 insect species (range = 0-443). Variation in nuclear genome size explained 56% of the mitogenome-wide variation in NUMT counts. Although insect orders with the largest genome sizes possessed the highest NUMT counts, there was considerable variation among their component lineages. Two thirds of COI NUMTs possessed an IPSC (indel and/or premature stop codon) allowing their recognition and exclusion from downstream analyses. The remainder can elevate species richness as they showed 10.1% mean divergence from their mitochondrial homologue. The extent of exposure to "ghost species" is strongly impacted by the target amplicon's length. NUMTs can raise apparent species richness by up to 22% when a 658 bp COI amplicon is examined versus a doubling of apparent richness when 150 bp amplicons are targeted. Given these impacts, metabarcoding and eDNA studies should target the longest possible amplicons while also avoiding use of 12S/16S rDNA as they triple NUMT exposure because IPSC screens cannot be employed.
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Affiliation(s)
- Paul D. N. Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Dan G. Bock
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Sean W. J. Prosser
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
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17
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Namasivayam S, Sun C, Bah AB, Oberstaller J, Pierre-Louis E, Etheridge RD, Feschotte C, Pritham EJ, Kissinger JC. Massive invasion of organellar DNA drives nuclear genome evolution in Toxoplasma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.22.539837. [PMID: 37293002 PMCID: PMC10245829 DOI: 10.1101/2023.05.22.539837] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Toxoplasma gondii is a zoonotic protist pathogen that infects up to 1/3 of the human population. This apicomplexan parasite contains three genome sequences: nuclear (63 Mb); plastid organellar, ptDNA (35 kb); and mitochondrial organellar, mtDNA (5.9 kb of non-repetitive sequence). We find that the nuclear genome contains a significant amount of NUMTs (nuclear DNA of mitochondrial origin) and NUPTs (nuclear DNA of plastid origin) that are continuously acquired and represent a significant source of intraspecific genetic variation. NUOT (nuclear DNA of organellar origin) accretion has generated 1.6% of the extant T. gondii ME49 nuclear genome; the highest fraction ever reported in any organism. NUOTs are primarily found in organisms that retain the non-homologous end-joining repair pathway. Significant movement of organellar DNA was experimentally captured via amplicon sequencing of a CRISPR-induced double-strand break in non-homologous end-joining repair competent, but not ku80 mutant, Toxoplasma parasites. Comparisons with Neospora caninum, a species that diverged from Toxoplasma ~28 MY ago, revealed that the movement and fixation of 5 NUMTs predates the split of the two genera. This unexpected level of NUMT conservation suggests evolutionary constraint for cellular function. Most NUMT insertions reside within (60%) or nearby genes (23% within 1.5 kb) and reporter assays indicate that some NUMTs have the ability to function as cis-regulatory elements modulating gene expression. Together these findings portray a role for organellar sequence insertion in dynamically shaping the genomic architecture and likely contributing to adaptation and phenotypic changes in this important human pathogen.
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Affiliation(s)
- Sivaranjani Namasivayam
- Department of Genetics, University of Georgia, Athens, GA 30602, USA; Present address: Clinical Microbiome Unit, Laboratory of Host Immunity and Microbiome, NIAID, NIH, Bethesda, MD 20892, USA
| | - Cheng Sun
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA; Present address: College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Assiatu B Bah
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019
| | - Jenna Oberstaller
- Department of Genetics, University of Georgia, Athens, GA 30602, USA; Present address: Department of Global Health, University of South Florida, Tampa, FL 33620, USA
| | - Edwin Pierre-Louis
- Department of Cellular Biology, Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA
| | - Ronald Drew Etheridge
- Department of Cellular Biology, Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA
| | - Cedric Feschotte
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019; Present address: Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853-2703, USA
| | - Ellen J. Pritham
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019
| | - Jessica C. Kissinger
- Department of Genetics, Institute of Bioinformatics, and Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA
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18
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Liu H, Wang D, Zhang C, Pu T, Xiong L, Wei F, Hu Y. Development of short-target primers for species identification in biological studies of Carnivora. Ecol Evol 2023; 13:e10135. [PMID: 37250442 PMCID: PMC10212699 DOI: 10.1002/ece3.10135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/27/2023] [Accepted: 05/12/2023] [Indexed: 05/31/2023] Open
Abstract
Noninvasive genetic sampling greatly facilitates studies on the genetics, ecology, and conservation of threatened species. Species identification is often a prerequisite for noninvasive sampling-based biological studies. Due to the low quantity and quality of genomic DNA from noninvasive samples, high-performance short-target PCR primers are necessary for DNA barcoding applications. The order Carnivora is characterized by an elusive habit and threatened status. In this study, we developed three pairs of short-target primers for identifying Carnivora species. The COI279 primer pair was suitable for samples with better DNA quality. The COI157a and COI157b primer pairs performed well for noninvasive samples and reduced the interference of nuclear mitochondrial pseudogenes (numts). COI157a could effectively identify samples from Felidae, Canidae, Viverridae, and Hyaenidae, while COI157b could be applied to samples from Ursidae, Ailuridae, Mustelidae, Procyonidae, and Herpestidae. These short-target primers will facilitate noninvasive biological studies and efforts to conserve Carnivora species.
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Affiliation(s)
- Huiwen Liu
- CAS Key Laboratory of Animal Ecology and Conservation BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Dan Wang
- CAS Key Laboratory of Animal Ecology and Conservation BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | | | | | - Lijuan Xiong
- School of Life SciencesGuizhou Normal UniversityGuiyangChina
| | - Fuwen Wei
- CAS Key Laboratory of Animal Ecology and Conservation BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yibo Hu
- CAS Key Laboratory of Animal Ecology and Conservation BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
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19
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Baltazar-Soares M, Karell P, Wright D, Nilsson JÅ, Brommer JE. Bringing to light nuclear-mitochondrial insertions in the genomes of nocturnal predatory birds. Mol Phylogenet Evol 2023; 181:107722. [PMID: 36720422 DOI: 10.1016/j.ympev.2023.107722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 01/24/2023] [Accepted: 01/24/2023] [Indexed: 01/31/2023]
Abstract
Mito-nuclear insertions, or NUMTs, relate to genetic material of mitochondrial origin that have been transferred to the nuclear DNA molecule. The increasing amounts of genomic data currently being produced presents an opportunity to investigate this type of patterns in genome evolution of non-model organisms. Identifying NUMTs across a range of closely related taxa allows one to generalize patterns of insertion and maintenance in autosomes, which is ultimately relevant to the understanding of genome biology and evolution. Here we collected existing pairwise genome-mitogenome data of the order Strigiformes, a group that includes all the nocturnal bird predators. We identified NUMTs by applying percent similarity thresholds after blasting mitochondrial genomes against nuclear genome assemblies. We identified NUMTsin all genomes with numbers ranging from 4 in Bubo bubo to 24 in Ciccaba nigrolineata. Statistical analyses revealed NUMT size to negatively correlate with NUMT's sequence similarity to with original mtDNA region. Lastly, characterizing these nuclear insertions of mitochondrial origin in a comparative genomics framework produced variable phylogenetic patterns, suggesting in some cases that insertions might pre-date speciation events within Strigiformes.
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Affiliation(s)
| | - Patrik Karell
- Bioeconomy Research Team, Novia University of Applied Sciences, Raseborgsvägen 9, FI-10600 Raseborg, Finland; Evolutionary Ecology Unit, Department of Biology, Lund University, Sölvegatan 39 (Ecology Building), SE-223 62 Lund, Sweden
| | - Dominic Wright
- IFM Biology, Linköping University, Linköping 58183, Sweden
| | - Jan-Åke Nilsson
- Department of Biology, Section of Evolutionary Ecology, Lund University, Ecology Building, 223 62 Lund, Sweden
| | - Jon E Brommer
- Department of Biology, University of Turku, Turku 20500, Finland
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20
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Hoffman JR, Karol KG, Ohmura Y, Pogoda CS, Keepers KG, McMullin RT, Lendemer JC. Mitochondrial genomes in the iconic reindeer lichens: Architecture, variation, and synteny across multiple evolutionary scales. Mycologia 2023; 115:187-205. [PMID: 36736327 DOI: 10.1080/00275514.2022.2157665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Variation in mitochondrial genome composition across intraspecific, interspecific, and higher taxonomic scales has been little studied in lichen obligate symbioses. Cladonia is one of the most diverse and ecologically important lichen genera, with over 500 species representing an array of unique morphologies and chemical profiles. Here, we assess mitochondrial genome diversity and variation in this flagship genus, with focused sampling of two clades of the "true" reindeer lichens, Cladonia subgenus Cladina, and additional genomes from nine outgroup taxa. We describe composition and architecture at the gene and the genome scale, examining patterns in organellar genome size in larger taxonomic groups in Ascomycota. Mitochondrial genomes of Cladonia, Pilophorus, and Stereocaulon were consistently larger than those of Lepraria and contained more introns, suggesting a selective pressure in asexual morphology in Lepraria driving it toward genomic simplification. Collectively, lichen mitochondrial genomes were larger than most other fungal life strategies, reaffirming the notion that coevolutionary streamlining does not correlate to genome size reductions. Genomes from Cladonia ravenelii and Stereocaulon pileatum exhibited ATP9 duplication, bearing paralogs that may still be functional. Homing endonuclease genes (HEGs), though scarce in Lepraria, were diverse and abundant in Cladonia, exhibiting variable evolutionary histories that were sometimes independent of the mitochondrial evolutionary history. Intraspecific HEG diversity was also high, with C. rangiferina especially bearing a range of HEGs with one unique to the species. This study reveals a rich history of events that have transformed mitochondrial genomes of Cladonia and related genera, allowing future study alongside a wealth of assembled genomes.
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Affiliation(s)
- Jordan R Hoffman
- Department of Biology, The City University of New York Graduate Center, 365 5th Avenue, New York, New York 10016
- Institute of Systemic Botany, The New York Botanical Garden, Bronx, New York 10458-5126
| | - Kenneth G Karol
- Institute of Systemic Botany, The New York Botanical Garden, Bronx, New York 10458-5126
| | - Yoshihito Ohmura
- Department of Botany, National Museum of Nature and Science, 4-1-1 Amakubo, Tsukuba 305-0005, Japan
| | - Cloe S Pogoda
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado 80309
| | - Kyle G Keepers
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado 80309
| | - Richard T McMullin
- Research and Collections, Canadian Museum of Nature, PO Box 3443, Station D, Ottawa, Ontario K1P 6P4, Canada
| | - James C Lendemer
- Institute of Systemic Botany, The New York Botanical Garden, Bronx, New York 10458-5126
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21
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Identification of Fish Species and Targeted Genetic Modifications Based on DNA Analysis: State of the Art. Foods 2023; 12:foods12010228. [PMID: 36613444 PMCID: PMC9818732 DOI: 10.3390/foods12010228] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/22/2022] [Accepted: 12/30/2022] [Indexed: 01/05/2023] Open
Abstract
Food adulteration is one of the most serious problems regarding food safety and quality worldwide. Besides misleading consumers, it poses a considerable health risk associated with the potential non-labeled allergen content. Fish and fish products are one of the most expensive and widely traded commodities, which predisposes them to being adulterated. Among all fraud types, replacing high-quality or rare fish with a less valuable species predominates. Because fish differ in their allergen content, specifically the main one, parvalbumin, their replacement can endanger consumers. This underlines the need for reliable, robust control systems for fish species identification. Various methods may be used for the aforementioned purpose. DNA-based methods are favored due to the characteristics of the target molecule, DNA, which is heat resistant, and the fact that through its sequencing, several other traits, including the recognition of genetic modifications, can be determined. Thus, they are considered to be powerful tools for identifying cases of food fraud. In this review, the major DNA-based methods applicable for fish meat and product authentication and their commercial applications are discussed, the possibilities of detecting genetic modifications in fish are evaluated, and future trends are highlighted, emphasizing the need for comprehensive and regularly updated online database resources.
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22
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Special Issue "Feature Papers in Population and Evolutionary Genetics and Genomics". Genes (Basel) 2022; 14:genes14010038. [PMID: 36672779 PMCID: PMC9858693 DOI: 10.3390/genes14010038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 12/19/2022] [Indexed: 12/25/2022] Open
Abstract
Theodosius Dobzhansky famously wrote in 1973 that "nothing in biology makes sense except in the light of evolution" [...].
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23
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Triant DA, Pearson WR. Comparison of detection methods and genome quality when quantifying nuclear mitochondrial insertions in vertebrate genomes. Front Genet 2022; 13:984513. [PMID: 36482890 PMCID: PMC9723244 DOI: 10.3389/fgene.2022.984513] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 11/03/2022] [Indexed: 01/27/2024] Open
Abstract
The integration of mitochondrial genome fragments into the nuclear genome is well documented, and the transfer of these mitochondrial nuclear pseudogenes (numts) is thought to be an ongoing evolutionary process. With the increasing number of eukaryotic genomes available, genome-wide distributions of numts are often surveyed. However, inconsistencies in genome quality can reduce the accuracy of numt estimates, and methods used for identification can be complicated by the diverse sizes and ages of numts. Numts have been previously characterized in rodent genomes and it was postulated that they might be more prevalent in a group of voles with rapidly evolving karyotypes. Here, we examine 37 rodent genomes, and an additional 26 vertebrate genomes, while also considering numt detection methods. We identify numts using DNA:DNA and protein:translated-DNA similarity searches and compare numt distributions among rodent and vertebrate taxa to assess whether some groups are more susceptible to transfer. A combination of protein sequence comparisons (protein:translated-DNA) and BLASTN genomic DNA searches detect 50% more numts than genomic DNA:DNA searches alone. In addition, higher-quality RefSeq genomes produce lower estimates of numts than GenBank genomes, suggesting that lower quality genome assemblies can overestimate numts abundance. Phylogenetic analysis shows that mitochondrial transfers are not associated with karyotypic diversity among rodents. Surprisingly, we did not find a strong correlation between numt counts and genome size. Estimates using DNA: DNA analyses can underestimate the amount of mitochondrial DNA that is transferred to the nucleus.
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Affiliation(s)
- Deborah A. Triant
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, United States
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24
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Mitochondrial DNA variation of the caracal (Caracal caracal) in Iran and range-wide phylogeographic comparisons. Mamm Biol 2022. [DOI: 10.1007/s42991-022-00328-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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25
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Johnson SB, Winnikoff JR, Schultz DT, Christianson LM, Patry WL, Mills CE, Haddock SHD. Speciation of pelagic zooplankton: Invisible boundaries can drive isolation of oceanic ctenophores. Front Genet 2022; 13:970314. [PMID: 36276958 PMCID: PMC9585324 DOI: 10.3389/fgene.2022.970314] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 09/12/2022] [Indexed: 11/13/2022] Open
Abstract
The study of evolution and speciation in non-model systems provides us with an opportunity to expand our understanding of biodiversity in nature. Connectivity studies generally focus on species with obvious boundaries to gene flow, but in open-ocean environments, such boundaries are difficult to identify. Due to the lack of obvious boundaries, speciation and population subdivision in the pelagic environment remain largely unexplained. Comb jellies (Phylum Ctenophora) are mostly planktonic gelatinous invertebrates, many of which are considered to have freely interbreeding distributions worldwide. It is thought that the lobate ctenophore Bolinopsis infundibulum is distributed throughout cooler northern latitudes and B. vitrea warmer. Here, we examined the global population structure for species of Bolinopsis with genetic and morphological data. We found distinct evolutionary patterns within the genus, where B. infundibulum had a broad distribution from northern Pacific to Atlantic waters despite many physical barriers, while other species were geographically segregated despite few barriers. Divergent patterns of speciation within the genus suggest that oceanic currents, sea-level, and geological changes over time can act as either barriers or aids to dispersal in the pelagic environment. Further, we used population genomic data to examine evolution in the open ocean of a distinct lineage of Bolinopsis ctenophores from the North Eastern Pacific. Genetic information and morphological observations validated this as a separate species, Bolinopsis microptera, which was previously described but has recently been called B. infundibulum. We found that populations of B. microptera from California were in cytonuclear discordance, which indicates a secondary contact zone for previously isolated populations. Discordance at this scale is rare, especially in a continuous setting.
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Affiliation(s)
- Shannon B. Johnson
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, United States
- *Correspondence: Shannon B. Johnson, ; Steven H. D. Haddock,
| | - Jacob R. Winnikoff
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, United States
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Darrin T. Schultz
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, United States
- Department of Neurosciences and Developmental Biology, University of Vienna, Vienna, Austria
- Department of Biomolecular Engineering and Bioinformatics, University of California, Santa Cruz, Santa Cruz, CA, United States
| | | | - Wyatt L. Patry
- Animal Care Division, Monterey Bay Aquarium, Monterey, CA, United States
| | - Claudia E. Mills
- Friday Harbor Laboratories and the Department of Biology, University of Washington, Friday Harbor, WA, United States
| | - Steven H. D. Haddock
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, United States
- *Correspondence: Shannon B. Johnson, ; Steven H. D. Haddock,
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26
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Vendrami DLJ, Gossmann TI, Chakarov N, Paijmans AJ, Eyre-Walker A, Forcada J, Hoffman JI. Signatures of selection on mitonuclear integrated genes uncover hidden mitogenomic variation in fur seals. Genome Biol Evol 2022; 14:6637498. [PMID: 35809042 PMCID: PMC9338431 DOI: 10.1093/gbe/evac104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/02/2022] [Indexed: 11/13/2022] Open
Abstract
Nuclear copies of mitochondrial genes (numts) are commonplace in vertebrate genomes and have been characterized in many species. However, relatively little attention has been paid to understanding their evolutionary origins and to disentangling alternative sources of insertions. Numts containing genes with intact mitochondrial reading frames represent good candidates for this purpose. The sequences of the genes they contain can be compared to their mitochondrial homologs to characterize synonymous to non-synonymous substitution rates, which can shed light on the selection pressures these genes have been subjected to. Here, we characterise 25 numts in the Antarctic fur seal (Arctocephalus gazella) genome. Among those containing genes with intact mitochondrial reading frames, three carry multiple substitutions in comparison to their mitochondrial homologs. Our analyses reveal that one represents a historic insertion subjected to strong purifying selection since it colonized the Otarioidea in a genomic region enriched in retrotransposons. By contrast, the other two numts appear to be more recent and their large number of substitutions can be attributed to non-canonical insertions, either the integration of heteroplasmic mtDNA or hybridization. Our study sheds new light on the evolutionary history of pinniped numts and uncovers the presence of hidden sources of mitonuclear variation.
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Affiliation(s)
- David L J Vendrami
- Department of Animal Behaviour, Bielefeld University, 33501 Bielefeld, Germany
| | - Toni I Gossmann
- Department of Animal Behaviour, Bielefeld University, 33501 Bielefeld, Germany
| | - Nayden Chakarov
- Department of Animal Behaviour, Bielefeld University, 33501 Bielefeld, Germany
| | - Anneke J Paijmans
- Department of Animal Behaviour, Bielefeld University, 33501 Bielefeld, Germany
| | - Adam Eyre-Walker
- School of Life Science, University of Sussex, Brighton, BN1 9QG, UK
| | - Jaume Forcada
- British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK
| | - Joseph I Hoffman
- Department of Animal Behaviour, Bielefeld University, 33501 Bielefeld, Germany.,British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK
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27
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Camus MF, Alexander-Lawrie B, Sharbrough J, Hurst GDD. Inheritance through the cytoplasm. Heredity (Edinb) 2022; 129:31-43. [PMID: 35525886 PMCID: PMC9273588 DOI: 10.1038/s41437-022-00540-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 12/11/2022] Open
Abstract
Most heritable information in eukaryotic cells is encoded in the nuclear genome, with inheritance patterns following classic Mendelian segregation. Genomes residing in the cytoplasm, however, prove to be a peculiar exception to this rule. Cytoplasmic genetic elements are generally maternally inherited, although there are several exceptions where these are paternally, biparentally or doubly-uniparentally inherited. In this review, we examine the diversity and peculiarities of cytoplasmically inherited genomes, and the broad evolutionary consequences that non-Mendelian inheritance brings. We first explore the origins of vertical transmission and uniparental inheritance, before detailing the vast diversity of cytoplasmic inheritance systems across Eukaryota. We then describe the evolution of genomic organisation across lineages, how this process has been shaped by interactions with the nuclear genome and population genetics dynamics. Finally, we discuss how both nuclear and cytoplasmic genomes have evolved to co-inhabit the same host cell via one of the longest symbiotic processes, and all the opportunities for intergenomic conflict that arise due to divergence in inheritance patterns. In sum, we cannot understand the evolution of eukaryotes without understanding hereditary symbiosis.
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Affiliation(s)
- M Florencia Camus
- Department of Genetics, Evolution and Environment, University College London, London, UK.
| | | | - Joel Sharbrough
- Biology Department, New Mexico Institute of Mining and Technology, Socorro, NM, USA
| | - Gregory D D Hurst
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, England
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28
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Solovyev VI, Dubatolov VV, Vavilova VY, Kosterin OE. Estimating range disjunction time of the Palearctic Admirals (Limenitis L.) with COI and histone H1 genes. ORG DIVERS EVOL 2022. [DOI: 10.1007/s13127-022-00565-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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29
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Owen CL, Marshall DC, Wade EJ, Meister R, Goemans G, Kunte K, Moulds M, Hill K, Villet M, Pham TH, Kortyna M, Lemmon EM, Lemmon AR, Simon C. Detecting and removing sample contamination in phylogenomic data: an example and its implications for Cicadidae phylogeny (Insecta: Hemiptera). Syst Biol 2022; 71:1504-1523. [PMID: 35708660 DOI: 10.1093/sysbio/syac043] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 05/23/2022] [Accepted: 06/07/2022] [Indexed: 11/13/2022] Open
Abstract
Contamination of a genetic sample with DNA from one or more non-target species is a continuing concern of molecular phylogenetic studies, both Sanger sequencing studies and Next-Generation Sequencing (NGS) studies. We developed an automated pipeline for identifying and excluding likely cross-contaminated loci based on detection of bimodal distributions of patristic distances across gene trees. When the contamination occurs between samples within a dataset, comparisons between a contaminated sample and its contaminant taxon will yield bimodal distributions with one peak close to zero patristic distance. This new method does not rely on a priori knowledge of taxon relatedness nor does it determine the causes(s) of the contamination. Exclusion of putatively contaminated loci from a dataset generated for the insect family Cicadidae showed that these sequences were affecting some topological patterns and branch supports, although the effects were sometimes subtle, with some contamination-influenced relationships exhibiting strong bootstrap support. Long tip branches and outlier values for one anchored phylogenomic pipeline statistic (AvgNHomologs) were correlated with the presence of contamination. While the AHE markers used here, which target hemipteroid taxa, proved effective in resolving deep and shallow level Cicadidae relationships in aggregate, individual markers contained inadequate phylogenetic signal, in part probably due to short length. The cleaned dataset, consisting of 429 loci, from 90 genera representing 44 of 56 current Cicadidae tribes, supported three of the four sampled Cicadidae subfamilies in concatenated-matrix maximum likelihood (ML) and multispecies coalescent-based species tree analyses, with the fourth subfamily weakly supported in the ML trees. No well-supported patterns from previous family-level Sanger sequencing studies of Cicadidae phylogeny were contradicted. One taxon (Aragualna plenalinea) did not fall with its current subfamily in the genetic tree, and this genus and its tribe Aragualnini is reclassified to Tibicininae following morphological re-examination. Only subtle differences were observed in trees after removal of loci for which divergent base frequencies were detected. Greater success may be achieved by increased taxon sampling and developing a probe set targeting a more recent common ancestor and longer loci. Searches for contamination are an essential step in phylogenomic analyses of all kinds and our pipeline is an effective solution.
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Affiliation(s)
- Christopher L Owen
- Systematic Entomology Laboratory, USDA-ARS, c/o National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - David C Marshall
- Dept. of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Elizabeth J Wade
- Dept. of Natural Science and Mathematics, Curry College, Milton, MA 02186, USA
| | - Russ Meister
- Dept. of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Geert Goemans
- Dept. of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Krushnamegh Kunte
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bellary Road, Bangalore 560 065, India
| | - Max Moulds
- Australian Museum Research Institute, 1 William Street, Sydney N.S.W, Australia. 2010
| | - Kathy Hill
- Dept. of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | - M Villet
- Dept. of Biology, Rhodes University, Grahamstown 6140, South Africa
| | - Thai-Hong Pham
- Mientrung Institute for Scientific Research, Vietnam Academy of Science and Technology, Hue, Vietnam.,Vietnam National Museum of Nature and Graduate School of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Michelle Kortyna
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, USA
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University 400 Dirac Science Library, Tallahassee, FL 32306, USA
| | - Chris Simon
- Dept. of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
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30
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Parakatselaki ME, Zhu CT, Rand D, Ladoukakis ED. NUMTs Can Imitate Biparental Transmission of mtDNA-A Case in Drosophila melanogaster. Genes (Basel) 2022; 13:genes13061023. [PMID: 35741785 PMCID: PMC9222939 DOI: 10.3390/genes13061023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/27/2022] [Accepted: 06/02/2022] [Indexed: 11/16/2022] Open
Abstract
mtDNA sequences can be incorporated into the nuclear genome and produce nuclear mitochondrial fragments (NUMTs), which resemble mtDNA in their sequence but are transmitted biparentally, like the nuclear genome. NUMTs can be mistaken as real mtDNA and may lead to the erroneous impression that mtDNA is biparentally transmitted. Here, we report a case of mtDNA heteroplasmy in a Drosophila melanogaster DGRP line, in which the one haplotype was biparentally transmitted in an autosomal manner. Given the sequence identity of this haplotype with the mtDNA, the crossing experiments led to uncertainty about whether heteroplasmy was real or an artifact due to a NUMT. More specific experiments revealed that there is a large NUMT insertion in the X chromosome of a specific DGRP line, imitating biparental inheritance of mtDNA. Our result suggests that studies on mtDNA heteroplasmy and on mtDNA inheritance should first exclude the possibility of NUMT interference in their data.
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Affiliation(s)
| | - Chen-Tseh Zhu
- Department of Ecology, Evolutionary and Organismal Biology, Brown University, Providence, RI 02912, USA; (C.-T.Z.); (D.R.)
| | - David Rand
- Department of Ecology, Evolutionary and Organismal Biology, Brown University, Providence, RI 02912, USA; (C.-T.Z.); (D.R.)
| | - Emmanuel D. Ladoukakis
- Department of Biology, University of Crete, Voutes University Campus, 70013 Iraklio, Greece;
- Correspondence: ; Tel.: +30-281-039-4067
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31
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Lucas T, Vincent B, Eric P. Translocation of mitochondrial DNA into the nuclear genome blurs phylogeographic and conservation genetic studies in seabirds. ROYAL SOCIETY OPEN SCIENCE 2022; 9:211888. [PMID: 35719890 PMCID: PMC9198517 DOI: 10.1098/rsos.211888] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 04/19/2022] [Indexed: 05/03/2023]
Abstract
Mitochondrial DNA (mtDNA) translocated into the nuclear genome (numt), when co-analysed with genuine mtDNA, could plague phylogeographic studies. To evaluate numt-related biases in population genetics parameters in birds, which are prone to accumulating numts, we targeted the mitochondrial mt-cytb gene. We looked at 13 populations of Audubon's shearwater (Puffinus lherminieri), including five mitochondrial lineages. mt-cytb homologue and paralogue (numt) sequences were determined by Sanger sequencing with and without prior exonuclease digestion of nuclear DNA. Numts formed monophyletic clades corresponding to three of the five mitochondrial lineages tested (the remaining two forming a paraphyletic group). Nineteen percent of numt alleles fell outside of their expected mitochondrial clade, a pattern consistent with multiple translocation events, incomplete lineage sorting (ILS), and/or introgression. When co-analysing mt-cytb paralogues and homologues, excluding individuals with ambiguities underestimates genetic diversity (4%) and differentiation (11%) among least-sampled populations. Removing ambiguous sites drops the proportion of inter-lineage genetic variance by 63%. While co-analysing numts with mitochondrial sequences can lead to severe bias and information loss in bird phylogeographic studies, the separate analysis of genuine mitochondrial loci and their nuclear paralogues can shed light on numt molecular evolution, as well as evolutionary processes such as ILS and introgression.
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Affiliation(s)
- Torres Lucas
- Centre d'Etudes Biologiques de Chizé, UMR 7372, CNRS - La Rochelle Universite, Villiers en Bois, France
- Littoral, Environnement et Sociétés, UMR 7266 CNRS - La Rochelle Université, La Rochelle, France
| | - Bretagnolle Vincent
- Centre d'Etudes Biologiques de Chizé, UMR 7372, CNRS - La Rochelle Universite, Villiers en Bois, France
| | - Pante Eric
- Littoral, Environnement et Sociétés, UMR 7266 CNRS - La Rochelle Université, La Rochelle, France
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32
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Lee J, Willett CS. Frequent Paternal Mitochondrial Inheritance and Rapid Haplotype Frequency Shifts in Copepod Hybrids. J Hered 2022; 113:171-183. [PMID: 35575078 DOI: 10.1093/jhered/esab068] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 10/29/2021] [Indexed: 11/13/2022] Open
Abstract
Mitochondria are assumed to be maternally inherited in most animal species, and this foundational concept has fostered advances in phylogenetics, conservation, and population genetics. Like other animals, mitochondria were thought to be solely maternally inherited in the marine copepod Tigriopus californicus, which has served as a useful model for studying mitonuclear interactions, hybrid breakdown, and environmental tolerance. However, we present PCR, Sanger sequencing, and Illumina Nextera sequencing evidence that extensive paternal mitochondrial DNA (mtDNA) transmission is occurring in inter-population hybrids of T. californicus. PCR on four types of crosses between three populations (total sample size of 376 F1 individuals) with 20% genome-wide mitochondrial divergence showed 2% to 59% of F1 hybrids with both paternal and maternal mtDNA, where low and high paternal leakage values were found in different cross directions of the same population pairs. Sequencing methods further verified nucleotide similarities between F1 mtDNA and paternal mtDNA sequences. Interestingly, the paternal mtDNA in F1s from some crosses inherited haplotypes that were uncommon in the paternal population. Compared to some previous research on paternal leakage, we employed more rigorous methods to rule out contamination and false detection of paternal mtDNA due to non-functional nuclear mitochondrial DNA fragments. Our results raise the potential that other animal systems thought to only inherit maternal mitochondria may also have paternal leakage, which would then affect the interpretation of past and future population genetics or phylogenetic studies that rely on mitochondria as uniparental markers.
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Affiliation(s)
- Jeeyun Lee
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Christopher S Willett
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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33
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Fields PD, Waneka G, Naish M, Schatz MC, Henderson IR, Sloan DB. Complete Sequence of a 641-kb Insertion of Mitochondrial DNA in the Arabidopsis thaliana Nuclear Genome. Genome Biol Evol 2022; 14:evac059. [PMID: 35446419 PMCID: PMC9071559 DOI: 10.1093/gbe/evac059] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/20/2022] [Indexed: 11/14/2022] Open
Abstract
Intracellular transfers of mitochondrial DNA continue to shape nuclear genomes. Chromosome 2 of the model plant Arabidopsis thaliana contains one of the largest known nuclear insertions of mitochondrial DNA (numts). Estimated at over 600 kb in size, this numt is larger than the entire Arabidopsis mitochondrial genome. The primary Arabidopsis nuclear reference genome contains less than half of the numt because of its structural complexity and repetitiveness. Recent data sets generated with improved long-read sequencing technologies (PacBio HiFi) provide an opportunity to finally determine the accurate sequence and structure of this numt. We performed a de novo assembly using sequencing data from recent initiatives to span the Arabidopsis centromeres, producing a gap-free sequence of the Chromosome 2 numt, which is 641 kb in length and has 99.933% nucleotide sequence identity with the actual mitochondrial genome. The numt assembly is consistent with the repetitive structure previously predicted from fiber-based fluorescent in situ hybridization. Nanopore sequencing data indicate that the numt has high levels of cytosine methylation, helping to explain its biased spectrum of nucleotide sequence divergence and supporting previous inferences that it is transcriptionally inactive. The original numt insertion appears to have involved multiple mitochondrial DNA copies with alternative structures that subsequently underwent an additional duplication event within the nuclear genome. This work provides insights into numt evolution, addresses one of the last unresolved regions of the Arabidopsis reference genome, and represents a resource for distinguishing between highly similar numt and mitochondrial sequences in studies of transcription, epigenetic modifications, and de novo mutations.
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Affiliation(s)
- Peter D. Fields
- Department of Biology, Colorado State University, Fort Collins, Colorado, USA
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland
| | - Gus Waneka
- Department of Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Matthew Naish
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Michael C. Schatz
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, USA
| | - Ian R. Henderson
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Daniel B. Sloan
- Department of Biology, Colorado State University, Fort Collins, Colorado, USA
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Popadin K, Gunbin K, Peshkin L, Annis S, Fleischmann Z, Franco M, Kraytsberg Y, Markuzon N, Ackermann RR, Khrapko K. Mitochondrial Pseudogenes Suggest Repeated Inter-Species Hybridization among Direct Human Ancestors. Genes (Basel) 2022; 13:810. [PMID: 35627195 PMCID: PMC9140377 DOI: 10.3390/genes13050810] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 04/12/2022] [Accepted: 04/16/2022] [Indexed: 12/02/2022] Open
Abstract
The hypothesis that the evolution of humans involves hybridization between diverged species has been actively debated in recent years. We present the following novel evidence in support of this hypothesis: the analysis of nuclear pseudogenes of mtDNA ("NUMTs"). NUMTs are considered "mtDNA fossils" as they preserve sequences of ancient mtDNA and thus carry unique information about ancestral populations. Our comparison of a NUMT sequence shared by humans, chimpanzees, and gorillas with their mtDNAs implies that, around the time of divergence between humans and chimpanzees, our evolutionary history involved the interbreeding of individuals whose mtDNA had diverged as much as ~4.5 Myr prior. This large divergence suggests a distant interspecies hybridization. Additionally, analysis of two other NUMTs suggests that such events occur repeatedly. Our findings suggest a complex pattern of speciation in primate/human ancestors and provide one potential explanation for the mosaic nature of fossil morphology found at the emergence of the hominin lineage. A preliminary version of this manuscript was uploaded to the preprint server BioRxiv in 2017 (10.1101/134502).
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Affiliation(s)
- Konstantin Popadin
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland;
- Center for Mitochondrial Functional Genomics, Institute of Living Systems, Immanuel Kant Baltic Federal University, 236040 Kaliningrad, Russia
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | | | - Leonid Peshkin
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA;
| | - Sofia Annis
- Department of Biology, Northeastern University, Boston, MA 02115, USA; (S.A.); (Z.F.); (M.F.)
| | - Zoe Fleischmann
- Department of Biology, Northeastern University, Boston, MA 02115, USA; (S.A.); (Z.F.); (M.F.)
| | - Melissa Franco
- Department of Biology, Northeastern University, Boston, MA 02115, USA; (S.A.); (Z.F.); (M.F.)
| | | | | | - Rebecca R. Ackermann
- Human Evolution Research Institute, Department of Archaeology, University of Cape Town, Cape Town 7700, South Africa;
| | - Konstantin Khrapko
- Department of Biology, Northeastern University, Boston, MA 02115, USA; (S.A.); (Z.F.); (M.F.)
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Universal Mitochondrial Multi-Locus Sequence Analysis (mtMLSA) to Characterise Populations of Unanticipated Plant Pest Biosecurity Detections. BIOLOGY 2022; 11:biology11050654. [PMID: 35625382 PMCID: PMC9138331 DOI: 10.3390/biology11050654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/11/2022] [Accepted: 04/21/2022] [Indexed: 12/02/2022]
Abstract
Simple Summary Agricultural and environmental sustainability requires effective biosecurity responses that prevent the establishment or spread of exotic insect pests. Understanding where new detections may have come from or if recurrent detections are connected contributes to this. Suitable population genetic markers use relatively rapidly evolving gene regions which render the PCR method species-specific at best. Because resource limitations mean these are pre-emptively developed for the highest risk species, populations of other exotic pests are unable to be characterised at the time. Here we have developed a generic method that is useful across species within the same taxonomic Order, including where there is little or no prior knowledge of their gene sequences. Markers are formed by concomitant sequencing of four gene regions. Sequence concatenation was shown to retrieve higher resolution signatures than standard DNA barcoding. The method is encouragingly universal, as illustrated across species in ten fly and 11 moth superfamilies. Although as-yet untested in a biosecurity situation, this relatively low-tech, off-the-shelf method makes a proactive contribution to the toolbox of quarantine agencies at the time of detection without the need for impromptu species-specific research and development. Abstract Biosecurity responses to post-border exotic pest detections are more effective with knowledge of where the species may have originated from or if recurrent detections are connected. Population genetic markers for this are typically species-specific and not available in advance for any but the highest risk species, leaving other less anticipated species difficult to assess at the time. Here, new degenerate PCR primer sets are designed for within the Lepidoptera and Diptera for the 3′ COI, ND3, ND6, and 3′ plus 5′ 16S gene regions. These are shown to be universal at the ordinal level amongst species of 14 and 15 families across 10 and 11 dipteran and lepidopteran superfamilies, respectively. Sequencing the ND3 amplicons as an example of all the loci confirmed detection of population-level variation. This supported finding multiple population haplotypes from the publicly available sequences. Concatenation of the sequences also confirmed that higher population resolution is achieved than for the individual genes. Although as-yet untested in a biosecurity situation, this method is a relatively simple, off-the-shelf means to characterise populations. This makes a proactive contribution to the toolbox of quarantine agencies at the time of detection without the need for unprepared species-specific research and development.
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Ruiz-García M, Cáceres AM, Luengas-Villamil K, Aliaga-Rossel E, Zeballos H, Singh MD, Shostell JM. Mitogenomic phylogenetics and population genetics of several taxa of agouties (Dasyprocta sp., Dasyproctidae, Rodentia): molecular nonexistence of some claimed endemic taxa. MAMMAL RES 2022. [DOI: 10.1007/s13364-022-00626-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Hazkani-Covo E. A Burst of Numt Insertion in the Dasyuridae Family During Marsupial Evolution. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.844443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Nuclear pseudogenes of mitochondrial origin (numts) are common in all eukaryotes. Our previous scan of numts in sequenced nuclear genomes suggested that the highest numt content currently known in animals is that in the gray short-tailed opossum. The present work sought to determine numt content in marsupials and to compare it to those in placental and monothematic mammals as well as in non-mammalian vertebrates. To achieve this, 70 vertebrate species with available nuclear and mitochondrial genomes were scanned for numt content. An extreme numt content was found in the Dasyuridae, with 3,450 in Sarcophilus harrisii (1,955 kb) and 2,813 in Antechinus flavipes (847 kb). The evolutionarily closest species analyzed, the extinct Thylacinus cynocephalus belonging to the Thylacindae family, had only 435 numts (238 kb). These two Dasyuridae genomes featured the highest numt content identified in animals to date. A phylogenetic analysis of numts longer than 300 bp, using a Diprotodonita mitochondrial tree, indicated a burst of numt insertion that began before the divergence of the Dasyurini and Phascogalini, reaching a peak in the early evolution of the two tribes. No comparable increase was found in the early divergent species T. cynocephalus. Divergence of the Dasyuridae tribes has been previously dated to shortly after the Miocene climate transition, characterized by a rapid temperature decline. Interestingly, deviation from optimal growth temperature is one of the environmental factors reported to increase numt insertions in a laboratory setting.
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Raupach MJ, Rulik B, Spelda J. Surprisingly high genetic divergence of the mitochondrial DNA barcode fragment (COI) within Central European woodlice species (Crustacea, Isopoda, Oniscidea). Zookeys 2022; 1082:103-125. [PMID: 35115867 PMCID: PMC8794987 DOI: 10.3897/zookeys.1082.69851] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 12/20/2021] [Indexed: 11/12/2022] Open
Abstract
DNA barcoding has become the most popular approach for species identification in recent years. As part of the German Barcode of Life project, the first DNA barcode library for terrestrial and freshwater isopods from Germany is presented. The analyzed barcode library included 38 terrestrial (78% of the documented species of Germany) and five freshwater (63%) species. A total of 513 new barcodes was generated and 518 DNA barcodes were analyzed. This analysis revealed surprisingly high intraspecific genetic distances for numerous species, with a maximum of 29.4% for Platyarthrus hoffmannseggii Brandt, 1833. The number of BINs per species ranged from one (32 species, 68%) to a maximum of six for Trachelipus rathkii (Brandt, 1833). In spite of such high intraspecific variability, interspecific distances with values between 12.6% and 29.8% allowed a valid species assignment of all analyzed isopods. The observed high intraspecific distances presumably result from phylogeographic events, Wolbachia infections, atypical mitochondrial DNAs, heteroplasmy, or various combinations of these factors. Our study represents the first step in generating an extensive reference library of DNA barcodes for terrestrial and freshwater isopods for future molecular biodiversity assessment studies.
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Liu A, Wei Q, Lin H, Ding Y, Sun YV, Zhao D, He J, Ma Z, Li F, Zhou S, Chen X, Shen W, Gao M, He N. Baseline Characteristics of Mitochondrial DNA and Mutations Associated With Short-Term Posttreatment CD4+T-Cell Recovery in Chinese People With HIV. Front Immunol 2022; 12:793375. [PMID: 34970271 PMCID: PMC8712318 DOI: 10.3389/fimmu.2021.793375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 11/16/2021] [Indexed: 11/25/2022] Open
Abstract
Background Mitochondrial DNA (mtDNA) profiles and contributions of mtDNA variants to CD4+T-cell recovery in Euramerican people living with HIV (PLWH) may not be transferred to East-Asian PLWH, highlighting the need to consider more regional studies. We aimed to identify mtDNA characteristics and mutations that explain the variability of short-term CD4+T-cell recovery in East-Asian PLWH. Method Eight hundred fifty-six newly reported antiretroviral therapy (ART)-naïve Chinese PLWH from the Comparative HIV and Aging Research in Taizhou (CHART) cohort (Zhejiang Province, Eastern China) were enrolled. MtDNA was extracted from peripheral whole blood of those PLWH at HIV diagnosis, amplified, and sequenced using polymerase chain reaction and gene array. Characterization metrics such as mutational diversity and momentum were developed to delineate baseline mtDNA mutational patterns in ART-naïve PLWH. The associations between mtDNA genome-wide single nucleotide variants and CD4+T-cell recovery after short-term (within ~48 weeks) ART in 724 PLWH were examined using bootstrapping median regressions. Results Of 856 participants, 74.18% and 25.82% were male and female, respectively. The median age was 37 years; 94.51% were of the major Han ethnicity, and 69.04% and 28.62% were of the heterosexual and homosexual transmission, respectively. We identified 2,352 types of mtDNA mutations and mtDNA regions D-loop, ND5, CYB, or RNR1 with highest mutational diversity or volume. Female PLWH rather than male PLWH at the baseline showed remarkable age-related uptrends of momentum and mutational diversity as well as correlations between CD4+T <200 (cells/μl) and age-related uptrends of mutational diversity in many mtDNA regions. After adjustments of important sociodemographic and clinical variables, m.1005T>C, m.1824T>C, m.3394T>C, m.4491G>A, m.7828A>G, m.9814T>C, m.10586G>A, m.12338T>C, m.13708G>A, and m.14308T>C (at the Bonferroni-corrected significance) were negatively associated with short-term CD4+T-cell recovery whereas m.93A>G, m.15218A>G, and m.16399A>G were positively associated with short-term CD4+T-cell recovery. Conclusion Our baseline mtDNA characterization stresses the attention to East-Asian female PLWH at risk of CD4+T-cell loss-related aging and noncommunicable chronic diseases. Furthermore, mtDNA variants identified in regression analyses account for heterogeneity in short-term CD4+T-cell recovery of East-Asian PLWH. These results may help individualize the East-Asian immune recovery strategies under complicated HIV management caused by CD4+T-cell loss.
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Affiliation(s)
- Anni Liu
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China.,Key Laboratory of Public Health Safety of Ministry of Education, Fudan University, Shanghai, China.,Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY, United States
| | - Qian Wei
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China.,Key Laboratory of Public Health Safety of Ministry of Education, Fudan University, Shanghai, China
| | - Haijiang Lin
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China.,Key Laboratory of Public Health Safety of Ministry of Education, Fudan University, Shanghai, China.,Department of AIDS/STD Control and Prevention, Taizhou City Center for Disease Control and Prevention, Taizhou, China
| | - Yingying Ding
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China.,Key Laboratory of Public Health Safety of Ministry of Education, Fudan University, Shanghai, China
| | - Yan V Sun
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, United States.,Department of Biomedical Informatics, School of Medicine, Emory University, Atlanta, GA, United States
| | - Dan Zhao
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China.,Key Laboratory of Public Health Safety of Ministry of Education, Fudan University, Shanghai, China
| | - Jiayu He
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China.,Key Laboratory of Public Health Safety of Ministry of Education, Fudan University, Shanghai, China
| | - Zhonghui Ma
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China.,Key Laboratory of Public Health Safety of Ministry of Education, Fudan University, Shanghai, China
| | - Feihu Li
- School of Mathematical Sciences, Fudan University, Shanghai, China
| | - Sujuan Zhou
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China.,Key Laboratory of Public Health Safety of Ministry of Education, Fudan University, Shanghai, China
| | - Xiaoxiao Chen
- Department of AIDS/STD Control and Prevention, Taizhou City Center for Disease Control and Prevention, Taizhou, China
| | - Weiwei Shen
- Department of AIDS/STD Control and Prevention, Taizhou City Center for Disease Control and Prevention, Taizhou, China
| | - Meiyang Gao
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China.,Key Laboratory of Public Health Safety of Ministry of Education, Fudan University, Shanghai, China
| | - Na He
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China.,Key Laboratory of Public Health Safety of Ministry of Education, Fudan University, Shanghai, China.,Key Laboratory of Health Technology Assessment, National Commission of Health, Fudan University, Shanghai, China
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Honka J, Baini S, Searle JB, Kvist L, Aspi J. Genetic assessment reveals inbreeding, possible hybridization, and low levels of genetic structure in a declining goose population. Ecol Evol 2022; 12:e8547. [PMID: 35127046 PMCID: PMC8796947 DOI: 10.1002/ece3.8547] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 12/18/2021] [Accepted: 12/21/2021] [Indexed: 11/30/2022] Open
Abstract
The population numbers of taiga bean goose (Anser fabalis fabalis) have halved during recent decades. Since this subspecies is hunted throughout most of its range, the decline is of management concern. Knowledge of the genetic population structure and diversity is important for guiding management and conservation efforts. Genetically unique subpopulations might be hunted to extinction if not managed separately, and any inbreeding depression or lack of genetic diversity may affect the ability to adapt to changing environments and increase extinction risk. We used microsatellite and mitochondrial DNA markers to study the genetic population structure and diversity among taiga bean geese breeding within the Central flyway management unit using non-invasively collected feathers. We found some genetic structuring with the maternally inherited mitochondrial DNA between four geographic regions (ɸ ST = 0.11-0.20) but none with the nuclear microsatellite markers (all pairwise F ST-values = 0.002-0.005). These results could be explained by female natal philopatry and male-biased dispersal, which completely homogenizes the nuclear genome. Therefore, the population could be managed as a single unit. Genetic diversity was still at a moderate level (average H E = 0.69) and there were no signs of past population size reductions, although significantly positive inbreeding coefficients in all sampling sites (F IS = 0.05-0.10) and high relatedness values (r = 0.60-0.86) between some individuals could indicate inbreeding. In addition, there was evidence of either incomplete lineage sorting or introgression from the pink-footed goose (Anser brachyrhynchus). The current population is not under threat by genetic impoverishment but monitoring in the future is desirable.
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Affiliation(s)
- Johanna Honka
- Ecology and Genetics Research UnitUniversity of OuluOuluFinland
| | - Serena Baini
- Department of BiologyUniversity of Rome “Tor Vergata”RomeItaly
| | - Jeremy B. Searle
- Department of Ecology and Evolutionary BiologyCornell UniversityIthacaNew YorkUSA
| | - Laura Kvist
- Ecology and Genetics Research UnitUniversity of OuluOuluFinland
| | - Jouni Aspi
- Ecology and Genetics Research UnitUniversity of OuluOuluFinland
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Khater EIM, Baig F, Kamal HA, Powell JR, Saleh AA. Molecular Phylogenetics and Population Genetics of the Dengue Vector Aedes aegypti From the Arabian Peninsula. JOURNAL OF MEDICAL ENTOMOLOGY 2021; 58:2161-2176. [PMID: 34313761 DOI: 10.1093/jme/tjab112] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Indexed: 06/13/2023]
Abstract
Aedes aegypti mosquito is the principal dengue vector in the Kingdom of Saudi Arabia (KSA); however, no study has addressed its ecology and population structure yet. Therefore, we report on Ae. aegypti phylo- and population genetics using three DNA markers: COI, ND4, and rDNA-ITS2. Sampling the immature stages of Ae. aegypti revealed that water storage tanks (34.3% of habitats) were the most productive and contained 33% of immatures stages. Other important habitats included containers for wastewater drainage (including air-conditioning and water cooler trays) and containers associated with ornamentation. Shallow water leakage spots (2.7% of habitats, 8% of immatures) can be considered rare-but-epidemiologically-important containers. Neighbor-joining (NJ) phylogenetic analysis of Ae. aegypti identified 8, 14, and 9 haplotypes of COI, ND4, and ITS2, respectively, and revealed high levels of genetic variation in Ae. aegypti populations of KSA. Global distribution of haplotypes also indicated multiple gene introductions into these populations, with high levels of intra-population genetic variation and continuous gene exchange. The neutrality values indicated a deficiency of alleles and suggested that the KSA Ae. aegypti loci tested did not follow a neutral model of molecular evolution. Fst values and AMOVA indicated that most of the genetic variation in the KSA Ae. aegypti populations is due to intra- rather than inter-population differences. This is the first comprehensive report on the phylo- and population genetics of Ae. aegypti from the Arabian Peninsula. This information expands our understanding of the ecology and population dynamics of this important arboviral vector for informed control efforts.
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Affiliation(s)
- Emad I M Khater
- Plant Protection Department, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
- Department of Entomology, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Farrukh Baig
- Plant Protection Department, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Hany A Kamal
- Department of Pest Control Projects, Dallah Establishment, Jeddah, Saudi Arabia
| | - Jeffery R Powell
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Amgad A Saleh
- Plant Protection Department, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
- Agricultural Genetic Engineering Research Institute, Agriculture Research Center, Giza, Egypt
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Rocha RM, Teixeira JA, Barros RCD. Genetic diversity in the Diplosoma listerianum complex (Ascidiacea: Didemnidae) from the Western Atlantic. SYST BIODIVERS 2021. [DOI: 10.1080/14772000.2021.1988003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Rosana M. Rocha
- Zoology Department, Universidade Federal do Paraná, CP 19020, Curitiba 81531-980, Brazil
| | - Joyce Ana Teixeira
- Zoology Department, Universidade Federal do Paraná, CP 19020, Curitiba 81531-980, Brazil
| | - Rodolfo Corrêa de Barros
- Parasitology Laboratory, Hospital de Clínicas, Universidade Federal do Paraná, Rua Padre Camargo, 280, Curitiba 80060-240, Brazil
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Understanding the convoluted evolutionary history of the capped-golden langur lineage (Cercopithecidae: Colobinae)†. J Genet 2021. [DOI: 10.1007/s12041-021-01329-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Chow S, Yanagimoto T, Takeyama H. Detection of heteroplasmy and nuclear mitochondrial pseudogenes in the Japanese spiny lobster Panulirus japonicus. Sci Rep 2021; 11:21780. [PMID: 34741113 PMCID: PMC8571370 DOI: 10.1038/s41598-021-01346-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 10/26/2021] [Indexed: 11/09/2022] Open
Abstract
Partial mtDNA cytochrome oxidase subunit I (COI) fragments and near entire stretch of 12S rDNA (12S) and control region (Dloop) of the Japanese spiny lobster (Panulirus japonicus) (n = 3) were amplified by PCR and used for direct nucleotide sequencing and for clone library-based nucleotide sequence analysis. Nucleotide sequences of a total of 75 clones in COI, 77 in 12S and 92 in Dloop were determined. Haplotypes of the clones matched with those obtained by direct sequencing were determined to be genuine mtDNA sequence of the individual. Phylogenetic analysis revealed several distinct groups of haplotypes in all three regions. Genuine mtDNA sequences were observed to form a group with their closely related variables, and most of these variables may be due to amplification error but a few to be heteroplasmy. Haplotypes determined as nuclear mitochondrial pseudogenes (NUMTs) formed distinct groups. Nucleotide sequence divergence (K2P distance) between genuine haplotypes and NUMTs were substantial (7.169-23.880% for COI, 1.336-23.434% for 12S, and 7.897-71.862% for Dloop). These values were comparable to or smaller than those between species of the genus Panulirus, indicating that integration of mtDNA into the nuclear genome is a continuous and dynamic process throughout pre- and post-speciation events. Double peaks in electropherograms obtained by direct nucleotide sequencing were attributed to common nucleotides shared by multiple NUMTs. Information on the heteroplasmy and NUMTs would be very important for addressing their impact on direct nucleotide sequencing and for quality control of nucleotide sequences obtained.
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Affiliation(s)
- Seinen Chow
- Research Organization for Nano and Life Innovation, Waseda University, 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo, 162-0041, Japan.
| | - Takashi Yanagimoto
- Fisheries Resources Institute, Japan Fisheries Research and Education Agency, Fukuura 2-12-4, Yokohama, Kanagawa, 236-8648, Japan
| | - Haruko Takeyama
- Research Organization for Nano and Life Innovation, Waseda University, 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo, 162-0041, Japan. .,Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu cho, Shinjuku, Tokyo, 162-8480, Japan. .,Computational Bio Big-Data Open Innovation Laboratory, AIST-Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-0072, Japan.
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Zafeiropoulos H, Gargan L, Hintikka S, Pavloudi C, Carlsson J. The Dark mAtteR iNvestigator (DARN) tool: getting to know the known unknowns in COI amplicon data. METABARCODING AND METAGENOMICS 2021. [DOI: 10.3897/mbmg.5.69657] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The mitochondrial cytochrome C oxidase subunit I gene (COI) is commonly used in environmental DNA (eDNA) metabarcoding studies, especially for assessing metazoan diversity. Yet, a great number of COI operational taxonomic units (OTUs) or/and amplicon sequence variants (ASVs) retrieved from such studies do not get a taxonomic assignment with a reference sequence. To assess and investigate such sequences, we have developed the Dark mAtteR iNvestigator (DARN) software tool. For this purpose, a reference COI-oriented phylogenetic tree was built from 1,593 consensus sequences covering all the three domains of life. With respect to eukaryotes, consensus sequences at the family level were constructed from 183,330 sequences retrieved from the Midori reference 2 database, which represented 70% of the initial number of reference sequences. Similarly, sequences from 431 bacterial and 15 archaeal taxa at the family level (29% and 1% of the initial number of reference sequences respectively) were retrieved from the BOLD and the PFam databases. DARN makes use of this phylogenetic tree to investigate COI pre-processed sequences of amplicon samples to provide both a tabular and a graphical overview of their phylogenetic assignments. To evaluate DARN, both environmental and bulk metabarcoding samples from different aquatic environments using various primer sets were analysed. We demonstrate that a large proportion of non-target prokaryotic organisms, such as bacteria and archaea, are also amplified in eDNA samples and we suggest prokaryotic COI sequences to be included in the reference databases used for the taxonomy assignment to allow for further analyses of dark matter. DARN source code is available on GitHub at https://github.com/hariszaf/darn and as a Docker image at https://hub.docker.com/r/hariszaf/darn.
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Ghosh A, Jangra S, Dietzgen RG, Yeh WB. Frontiers Approaches to the Diagnosis of Thrips (Thysanoptera): How Effective Are the Molecular and Electronic Detection Platforms? INSECTS 2021; 12:insects12100920. [PMID: 34680689 PMCID: PMC8540714 DOI: 10.3390/insects12100920] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 10/01/2021] [Accepted: 10/04/2021] [Indexed: 11/23/2022]
Abstract
Simple Summary Thrips are important agricultural and forest pests. They cause damage by sucking plant sap and transmitting several plant viruses. Correct identification is the key for epidemiological studies and formulating appropriate management strategies. The application of molecular and electronic detection platforms has improved the morphological character-based diagnosis of thrips species. This article reviews research on molecular and automated identification of thrips species and discusses future research strategies for rapid and high throughput thrips diagnosis. Abstract Thrips are insect pests of economically important agricultural, horticultural, and forest crops. They cause damage by sucking plant sap and by transmitting several tospoviruses, ilarviruses, carmoviruses, sobemoviruses, and machlomoviruses. Accurate and timely identification is the key to successful management of thrips species. However, their small size, cryptic nature, presence of color and reproductive morphs, and intraspecies genetic variability make the identification of thrips species challenging. The use of molecular and electronic detection platforms has made thrips identification rapid, precise, sensitive, high throughput, and independent of developmental stages. Multi-locus phylogeny based on mitochondrial, nuclear, and other markers has resolved ambiguities in morphologically indistinguishable thrips species. Microsatellite, RFLP, RAPD, AFLP, and CAPS markers have helped to explain population structure, gene flow, and intraspecies heterogeneity. Recent techniques such as LAMP and RPA have been employed for sensitive and on-site identification of thrips. Artificial neural networks and high throughput diagnostics facilitate automated identification. This review also discusses the potential of pyrosequencing, microarrays, high throughput sequencing, and electronic sensors in delimiting thrips species.
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Affiliation(s)
- Amalendu Ghosh
- Insect Vector Laboratory, Advanced Centre for Plant Virology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India; (A.G.); (S.J.)
| | - Sumit Jangra
- Insect Vector Laboratory, Advanced Centre for Plant Virology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India; (A.G.); (S.J.)
| | - Ralf G. Dietzgen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
- Correspondence:
| | - Wen-Bin Yeh
- Department of Entomology, National Chung Hsing University, Taichung City 402, Taiwan;
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Ruiz-García M, Jaramillo MF, López JB, Rivillas Y, Bello A, Leguizamon N, Shostell JM. Mitochondrial and karyotypic evidence reveals a lack of support for the genus Nasuella (Procyonidae, Carnivora). JOURNAL OF VERTEBRATE BIOLOGY 2021. [DOI: 10.25225/jvb.21040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Manuel Ruiz-García
- Laboratorio de Genética de Poblaciones Molecular-Biología Evolutiva, Departamento de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá DC, Colombia; e-mail: ,
| | - María F. Jaramillo
- Laboratorio de Genética de Poblaciones Molecular-Biología Evolutiva, Departamento de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá DC, Colombia; e-mail: ,
| | - Juan B. López
- Laboratorio de Genética y Citogenética, Universidad Nacional de Colombia, Sede Medellín, Medellín, Colombia; e-mail: ,
| | - Yudrum Rivillas
- Laboratorio de Genética y Citogenética, Universidad Nacional de Colombia, Sede Medellín, Medellín, Colombia; e-mail: ,
| | - Aurita Bello
- Secretaria Distrital del Ambiente (SDA), Bogotá DC, Colombia; e-mail: ,
| | | | - Joseph M. Shostell
- Math, Science and Technology Department, University of Minnesota Crookston, Crookston, USA; e-mail:
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Complete Mitochondrial Genomes of Metcalfa pruinosa and Salurnis marginella (Hemiptera: Flatidae): Genomic Comparison and Phylogenetic Inference in Fulgoroidea. Curr Issues Mol Biol 2021; 43:1391-1418. [PMID: 34698117 PMCID: PMC8929015 DOI: 10.3390/cimb43030099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 09/25/2021] [Accepted: 09/27/2021] [Indexed: 12/30/2022] Open
Abstract
The complete mitochondrial genomes (mitogenomes) of two DNA barcode-defined haplotypes of Metcalfa pruinosa and one of Salurnis marginella (Hemiptera: Flatidae) were sequenced and compared to those of other Fulgoroidea species. Furthermore, the mitogenome sequences were used to reconstruct phylogenetic relationships among fulgoroid families. The three mitogenomes, including that of the available species of Flatidae, commonly possessed distinctive structures in the 1702-1836 bp A+T-rich region, such as two repeat regions at each end and a large centered nonrepeat region. All members of the superfamily Fulgoroidea, including the Flatidae, consistently possessed a motiflike sequence (TAGTA) at the ND1 and trnS2 junction. The phylogenetic analyses consistently recovered the familial relationships of (((((Ricaniidae + Issidae) + Flatidae) + Fulgoridae) + Achilidae) + Derbidae) in the amino acid-based analysis, with the placement of Cixiidae and Delphacidae as the earliest-derived lineages of fulgoroid families, whereas the monophyly of Delphacidae was not congruent between tree-constructing algorithms.
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Lopez MLD, Lin YY, Sato M, Hsieh CH, Shiah FK, Machida RJ. Using metatranscriptomics to estimate the diversity and composition of zooplankton communities. Mol Ecol Resour 2021; 22:638-652. [PMID: 34555254 PMCID: PMC9293175 DOI: 10.1111/1755-0998.13506] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 08/18/2021] [Accepted: 09/09/2021] [Indexed: 01/04/2023]
Abstract
DNA metabarcoding is a rapid, high‐resolution tool used for biomonitoring complex zooplankton communities. However, diversity estimates derived with this approach can be biased by the co‐detection of sequences from environmental DNA (eDNA), nuclear‐encoded mitochondrial (NUMT) pseudogene contamination, and taxon‐specific PCR primer affinity differences. To avoid these methodological uncertainties, we tested the use of metatranscriptomics as an alternative approach for characterizing zooplankton communities. Specifically, we compared metatranscriptomics with PCR‐based methods using genomic (gDNA) and complementary DNA (cDNA) amplicons, and morphology‐based data for estimating species diversity and composition for both mock communities and field‐collected samples. Mock community analyses showed that the use of gDNA mitochondrial cytochrome c oxidase I (mtCO1) amplicons inflates species richness due to the co‐detection of extra‐organismal eDNA. Significantly more amplicon sequence variants, nucleotide diversity, and indels were observed with gDNA amplicons than with cDNA, indicating the presence of putative NUMT pseudogenes. Moreover, PCR‐based methods failed to detect the most abundant species in mock communities due to priming site mismatch. Overall, metatranscriptomics provided estimates of species richness and composition that closely resembled those derived from morphological data. The use of metatranscriptomics was further tested using field‐collected samples, with the results showing consistent species diversity estimates among biological and technical replicates. Additionally, temporal zooplankton species composition changes could be monitored using different mitochondrial markers. These findings demonstrate the advantages of metatranscriptomics as an effective tool for monitoring diversity in zooplankton research.
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Affiliation(s)
- Mark Louie D Lopez
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan.,Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Ya-Ying Lin
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Mitsuhide Sato
- Department of Environment and Fisheries Resources, Nagasaki University, Nagasaki, Japan
| | - Chih-Hao Hsieh
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan.,Environmental Change Research Center, Academia Sinica, Taipei, Taiwan
| | - Fuh-Kwo Shiah
- Environmental Change Research Center, Academia Sinica, Taipei, Taiwan
| | - Ryuji J Machida
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
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50
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Miller CD, Forthman M, Miller CW, Kimball RT. Extracting ‘legacy loci’ from an invertebrate sequence capture data set. ZOOL SCR 2021. [DOI: 10.1111/zsc.12513] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Caroline D. Miller
- Department of Entomology & Nematology University of Florida Gainesville FL USA
| | - Michael Forthman
- Department of Entomology & Nematology University of Florida Gainesville FL USA
- California State Collection of Arthropods Plant Pest Diagnostics Branch California Department of Food & Agriculture Sacramento CA USA
| | - Christine W. Miller
- Department of Entomology & Nematology University of Florida Gainesville FL USA
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