151
|
Tay WT, Elfekih S, Court LN, Gordon KHJ, Delatte H, De Barro PJ. The Trouble with MEAM2: Implications of Pseudogenes on Species Delimitation in the Globally Invasive Bemisia tabaci (Hemiptera: Aleyrodidae) Cryptic Species Complex. Genome Biol Evol 2018; 9:2732-2738. [PMID: 28985301 PMCID: PMC5647793 DOI: 10.1093/gbe/evx173] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/29/2017] [Indexed: 11/23/2022] Open
Abstract
Molecular species identification using suboptimal PCR primers can over-estimate species diversity due to coamplification of nuclear mitochondrial (NUMT) DNA/pseudogenes. For the agriculturally important whitefly Bemisia tabaci cryptic pest species complex, species identification depends primarily on characterization of the mitochondrial DNA cytochrome oxidase I (mtDNA COI) gene. The lack of robust PCR primers for the mtDNA COI gene can undermine correct species identification which in turn compromises management strategies. This problem is identified in the B. tabaci Africa/Middle East/Asia Minor clade which comprises the globally invasive Mediterranean (MED) and Middle East Asia Minor I (MEAM1) species, Middle East Asia Minor 2 (MEAM2), and the Indian Ocean (IO) species. Initially identified from the Indian Ocean island of Réunion, MEAM2 has since been reported from Japan, Peru, Turkey and Iraq. We identified MEAM2 individuals from a Peruvian population via Sanger sequencing of the mtDNA COI gene. In attempting to characterize the MEAM2 mitogenome, we instead characterized mitogenomes of MEAM1. We also report on the mitogenomes of MED, AUS, and IO thereby increasing genomic resources for members of this complex. Gene synteny (i.e., same gene composition and orientation) was observed with published B. tabaci cryptic species mitogenomes. Pseudogene fragments matching MEAM2 partial mtDNA COI gene exhibited low frequency single nucleotide polymorphisms that matched low copy number DNA fragments (<3%) of MEAM1 genomes, whereas presence of internal stop codons, loss of expected stop codons and poor primer annealing sites, all suggested MEAM2 as a pseudogene artifact and so not a real species.
Collapse
Affiliation(s)
- Wee Tek Tay
- CSIRO, Black Mountain Science and Innovation Park, Acton, Australia
| | - Samia Elfekih
- CSIRO, Black Mountain Science and Innovation Park, Acton, Australia
| | - Leon N Court
- CSIRO, Black Mountain Science and Innovation Park, Acton, Australia
| | - Karl H J Gordon
- CSIRO, Black Mountain Science and Innovation Park, Acton, Australia
| | | | - Paul J De Barro
- CSIRO, Ecosciences Precinct, Brisbane, Queensland, Australia
| |
Collapse
|
152
|
Cuperfain AB, Zhang ZL, Kennedy JL, Gonçalves VF. The Complex Interaction of Mitochondrial Genetics and Mitochondrial Pathways in Psychiatric Disease. MOLECULAR NEUROPSYCHIATRY 2018; 4:52-69. [PMID: 29998118 DOI: 10.1159/000488031] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 02/27/2018] [Indexed: 12/18/2022]
Abstract
While accounting for only 2% of the body's weight, the brain utilizes up to 20% of the body's total energy. Not surprisingly, metabolic dysfunction and energy supply-and-demand mismatch have been implicated in a variety of neurological and psychiatric disorders. Mitochondria are responsible for providing the brain with most of its energetic demands, and the brain uses glucose as its exclusive energy source. Exploring the role of mitochondrial dysfunction in the etiology of psychiatric disease is a promising avenue to investigate further. Genetic analysis of mitochondrial activity is a cornerstone in understanding disease pathogenesis related to metabolic dysfunction. In concert with neuroimaging and pathological study, genetics provides an important bridge between biochemical findings and clinical correlates in psychiatric disease. Mitochondrial genetics has several unique aspects to its analysis, and corresponding special considerations. Here, we review the components of mitochondrial genetic analysis - nuclear DNA, mitochon-drial DNA, mitochondrial pathways, pseudogenes, nuclear-mitochondrial mismatch, and microRNAs - that could contribute to an observable clinical phenotype. Throughout, we highlight psychiatric diseases that can arise due to dysfunction in these processes, with a focus on schizophrenia and bipolar disorder.
Collapse
Affiliation(s)
- Ari B Cuperfain
- Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada.,Neuroscience Section, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Zhi Lun Zhang
- Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada.,Neuroscience Section, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - James L Kennedy
- Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada.,Neuroscience Section, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Vanessa F Gonçalves
- Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada.,Neuroscience Section, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| |
Collapse
|
153
|
Munds RA, Titus CL, Eggert LS, Blomquist GE. Using a multi-gene approach to infer the complicated phylogeny and evolutionary history of lorises (Order Primates: Family Lorisidae). Mol Phylogenet Evol 2018; 127:556-567. [PMID: 29807155 DOI: 10.1016/j.ympev.2018.05.025] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 04/19/2018] [Accepted: 05/18/2018] [Indexed: 11/25/2022]
Abstract
Extensive phylogenetic studies have found robust phylogenies are modeled by using a multi-gene approach and sampling from the majority of the taxa of interest. Yet, molecular studies focused on the lorises, a cryptic primate family, have often relied on one gene, or just mitochondrial DNA, and many were unable to include all four genera in the analyses, resulting in inconclusive phylogenies. Past phylogenetic loris studies resulted in lorises being monophyletic, paraphyletic, or an unresolvable trichotomy with the closely related galagos. The purpose of our study is to improve our understanding of loris phylogeny and evolutionary history by using a multi-gene approach. We used the mitochondrial genes cytochrome b, and cytochrome c oxidase subunit 1, along with a nuclear intron (recombination activating gene 2) and nuclear exon (the melanocortin 1 receptor). Maximum Likelihood and Bayesian phylogenetic analyses were conducted based on data from each locus, as well as on the concatenated sequences. The robust, concatenated results found lorises to be a monophyletic family (Lorisidae) (PP ≥ 0.99) with two distinct subfamilies: the African Perodictinae (PP ≥ 0.99) and the Asian Lorisinae (PP ≥ 0.99). Additionally, from these analyses all four genera were all recovered as monophyletic (PP ≥ 0.99). Some of our single-gene analyses recovered monophyly, but many had discordances, with some showing paraphyly or a deep-trichotomy. Bayesian partitioned analyses inferred the most recent common ancestors of lorises emerged ∼42 ± 6 million years ago (mya), the Asian Lorisinae separated ∼30 ± 9 mya, and Perodictinae arose ∼26 ± 10 mya. These times fit well with known historical tectonic shifts of the area, as well as with the sparse loris fossil record. Additionally, our results agree with previous multi-gene studies on Lorisidae which found lorises to be monophyletic and arising ∼40 mya (Perelman et al., 2011; Pozzi et al., 2014). By taking a multi-gene approach, we were able to recover a well-supported, monophyletic loris phylogeny and inferred the evolutionary history of this cryptic family.
Collapse
Affiliation(s)
- Rachel A Munds
- Department of Anthropology, University of Missouri, Columbia, MO 65211, United States; Nocturnal Primate Research Group, Oxford Brookes University, Oxford OX3 0BP, UK.
| | - Chelsea L Titus
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, United States
| | - Lori S Eggert
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, United States
| | - Gregory E Blomquist
- Department of Anthropology, University of Missouri, Columbia, MO 65211, United States
| |
Collapse
|
154
|
Raupach MJ, Hannig K, Moriniére J, Hendrich L. A DNA barcode library for ground beetles of Germany: the genus Amara Bonelli, 1810 (Insecta, Coleoptera, Carabidae). Zookeys 2018; 759:57-80. [PMID: 29853775 PMCID: PMC5968077 DOI: 10.3897/zookeys.759.24129] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 03/27/2018] [Indexed: 01/08/2023] Open
Abstract
The genus Amara Bonelli, 1810 is a very speciose and taxonomically difficult genus of the Carabidae. The identification of many of the species is accomplished with considerable difficulty, in particular for females and immature stages. In this study the effectiveness of DNA barcoding, the most popular method for molecular species identification, was examined to discriminate various species of this genus from Central Europe. DNA barcodes from 690 individuals and 47 species were analysed, including sequences from previous studies and more than 350 newly generated DNA barcodes. Our analysis revealed unique BINs for 38 species (81%). Interspecific K2P distances below 2.2% were found for three species pairs and one species trio, including haplotype sharing between Amara alpina/Amara torrida and Amara communis/Amara convexior/Amara makolskii. This study represents another step in generating an extensive reference library of DNA barcodes for carabids, highly valuable bioindicators for characterizing disturbances in various habitats.
Collapse
Affiliation(s)
- Michael J. Raupach
- Institute for Biology and Environmental Sciences, Carl von Ossietzky University Oldenburg, Carl von Ossietzky Straße 9-11, 26111 Oldenburg, Germany
| | | | - Jérôme Moriniére
- Taxonomic coordinator – German Barcode of Life (GBOL), Bavarian State Collection of Zoology (SNSB – ZSM), Münchhausenstraße 21, 81247 München, Germany
| | - Lars Hendrich
- Sektion Insecta varia, Bavarian State Collection of Zoology (SNSB – ZSM), Münchhausenstraße 21, 81247 München, Germany
| |
Collapse
|
155
|
QAYOOM UBAID, PAWAR RAVINDRAA, MOHITE SWAPNAJAA, SAWANT MILINDS, NIRMALE VIVEKH, PAWAR SHRIKANTP, GOSWAMI MUKUNDA, LAKRA WAZIRS. DNA barcoding of some commonly exploited fishes from the northern Western Ghats, India. THE INDIAN JOURNAL OF ANIMAL SCIENCES 2018. [DOI: 10.56093/ijans.v88i2.79354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The Western Ghats, being very rich in freshwater fish diversity, has recently been confirmed as a globallysignificant centre of diversity and endemism for freshwater species and comprise one of the 34 global biodiversityhotspots. Owing to its extreme ichthyofaunal diversity, the present study was designed to generate cytochromeoxidase I (COI) DNA barcodes for the identification of some commonly exploited fishes from the west-flowingrivers of northern Western Ghats. Twenty-three fish specimens representing 6 families and 10 species were barcodedfrom the major west-flowing rivers of the northern Western Ghats. The obtained barcodes discriminated all thespecies with sufficient barcode gap. The average Kimura two parameter (K2P) values for within species, the genusand family distances were 0.37, 17.74 and 18.51% respectively. The neighbour-joining tree revealed distinct clusterscorresponding to the taxonomic status of the species. Generated barcodes are expected to provide the much-neededbaseline reference for the ichthyofaunal biodiversity of the global biodiversity hotspot.
Collapse
|
156
|
Marlétaz F, Le Parco Y, Liu S, Peijnenburg KTCA. Extreme Mitogenomic Variation in Natural Populations of Chaetognaths. Genome Biol Evol 2018; 9:1374-1384. [PMID: 28854623 PMCID: PMC5470650 DOI: 10.1093/gbe/evx090] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/09/2017] [Indexed: 12/15/2022] Open
Abstract
The extent of within-species genetic variation across the diversity of animal life is an underexplored problem in ecology and evolution. Although neutral genetic variation should scale positively with population size, mitochondrial diversity levels are believed to show little variation across animal species. Here, we report an unprecedented case of extreme mitochondrial diversity within natural populations of two morphospecies of chaetognaths (arrow worms). We determine that this diversity is composed of deep sympatric mitochondrial lineages, which are in some cases as divergent as human and platypus. Additionally, based on 54 complete mitogenomes, we observed mitochondrial gene order differences between several of these lineages. We examined nuclear divergence patterns (18S, 28S, and an intron) to determine the possible origin of these lineages, but did not find congruent patterns between mitochondrial and nuclear markers. We also show that extreme mitochondrial divergence in chaetognaths is not driven by positive selection. Hence, we propose that the extreme levels of mitochondrial variation could be the result of either a complex scenario of reproductive isolation, or a combination of large population size and accelerated mitochondrial mutation rate. These findings emphasize the importance of characterizing genome-wide levels of nuclear variation in these species and promote chaetognaths as a remarkable model to study mitochondrial evolution.
Collapse
Affiliation(s)
- Ferdinand Marlétaz
- Department of Zoology, University of Oxford, United Kingdom.,Molecular Genetics Unit, Okinawa Institute of Science and Technology, Onna, Japan
| | - Yannick Le Parco
- Institut Méditerranéen d'Océanologie (CNRS UMR 7294), Aix-Marseille Université, Campus de Luminy, Marseille, France
| | - Shenglin Liu
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, The Netherlands
| | - Katja T C A Peijnenburg
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, The Netherlands.,Naturalis Biodiversity Center, Marine Biodiversity, Leiden, The Netherlands
| |
Collapse
|
157
|
Detwiler KM. Mitochondrial DNA Analyses of Cercopithecus Monkeys Reveal a Localized Hybrid Origin for C. mitis doggetti in Gombe National Park, Tanzania. INT J PRIMATOL 2018. [DOI: 10.1007/s10764-018-0029-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
|
158
|
Bista I, Carvalho GR, Tang M, Walsh K, Zhou X, Hajibabaei M, Shokralla S, Seymour M, Bradley D, Liu S, Christmas M, Creer S. Performance of amplicon and shotgun sequencing for accurate biomass estimation in invertebrate community samples. Mol Ecol Resour 2018; 18:1020-1034. [PMID: 29667329 DOI: 10.1111/1755-0998.12888] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Revised: 03/11/2018] [Accepted: 03/29/2018] [Indexed: 01/10/2023]
Abstract
New applications of DNA and RNA sequencing are expanding the field of biodiversity discovery and ecological monitoring, yet questions remain regarding precision and efficiency. Due to primer bias, the ability of metabarcoding to accurately depict biomass of different taxa from bulk communities remains unclear, while PCR-free whole mitochondrial genome (mitogenome) sequencing may provide a more reliable alternative. Here, we used a set of documented mock communities comprising 13 species of freshwater macroinvertebrates of estimated individual biomass, to compare the detection efficiency of COI metabarcoding (three different amplicons) and shotgun mitogenome sequencing. Additionally, we used individual COI barcoding and de novo mitochondrial genome sequencing, to provide reference sequences for OTU assignment and metagenome mapping (mitogenome skimming), respectively. We found that, even though both methods occasionally failed to recover very low abundance species, metabarcoding was less consistent, by failing to recover some species with higher abundances, probably due to primer bias. Shotgun sequencing results provided highly significant correlations between read number and biomass in all but one species. Conversely, the read-biomass relationships obtained from metabarcoding varied across amplicons. Specifically, we found significant relationships for eight of 13 (amplicons B1FR-450 bp, FF130R-130 bp) or four of 13 (amplicon FFFR, 658 bp) species. Combining the results of all three COI amplicons (multiamplicon approach) improved the read-biomass correlations for some of the species. Overall, mitogenomic sequencing yielded more informative predictions of biomass content from bulk macroinvertebrate communities than metabarcoding. However, for large-scale ecological studies, metabarcoding currently remains the most commonly used approach for diversity assessment.
Collapse
Affiliation(s)
- Iliana Bista
- School of Biological Sciences, Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, UK
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Gary R Carvalho
- School of Biological Sciences, Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, UK
| | - Min Tang
- Department of Entomology, China Agricultural University, Beijing, China
| | - Kerry Walsh
- Environment Agency, Horizon House, Bristol, UK
| | - Xin Zhou
- Department of Entomology, China Agricultural University, Beijing, China
| | - Mehrdad Hajibabaei
- Department of Integrative Biology & Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Shadi Shokralla
- Department of Integrative Biology & Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Mathew Seymour
- School of Biological Sciences, Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, UK
| | | | - Shanlin Liu
- Natural History Museum of Denmark, Copenhagen, Denmark
- BGI-Shenzhen, Shenzhen, China
| | | | - Simon Creer
- School of Biological Sciences, Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, UK
| |
Collapse
|
159
|
Mansonella ozzardi mitogenome and pseudogene characterisation provides new perspectives on filarial parasite systematics and CO-1 barcoding. Sci Rep 2018; 8:6158. [PMID: 29670192 PMCID: PMC5906601 DOI: 10.1038/s41598-018-24382-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 03/15/2018] [Indexed: 11/26/2022] Open
Abstract
Despite the broad distribution of M. ozzardi in Latin America and the Caribbean, there is still very little DNA sequence data available to study this neglected parasite’s epidemiology. Mitochondrial DNA (mtDNA) sequences, especially the cytochrome oxidase (CO1) gene’s barcoding region, have been targeted successfully for filarial diagnostics and for epidemiological, ecological and evolutionary studies. MtDNA-based studies can, however, be compromised by unrecognised mitochondrial pseudogenes, such as Numts. Here, we have used shot-gun Illumina-HiSeq sequencing to recover the first complete Mansonella genus mitogenome and to identify several mitochondrial-origin pseudogenes. Mitogenome phylogenetic analysis placed M. ozzardi in the Onchocercidae “ONC5” clade and suggested that Mansonella parasites are more closely related to Wuchereria and Brugia genera parasites than they are to Loa genus parasites. DNA sequence alignments, BLAST searches and conceptual translations have been used to compliment phylogenetic analysis showing that M. ozzardi from the Amazon and Caribbean regions are near-identical and that previously reported Peruvian M. ozzardi CO1 reference sequences are probably of pseudogene origin. In addition to adding a much-needed resource to the Mansonella genus’s molecular tool-kit and providing evidence that some M. ozzardi CO1 sequence deposits are pseudogenes, our results suggest that all Neotropical M. ozzardi parasites are closely related.
Collapse
|
160
|
Elbrecht V, Vamos EE, Steinke D, Leese F. Estimating intraspecific genetic diversity from community DNA metabarcoding data. PeerJ 2018; 6:e4644. [PMID: 29666773 PMCID: PMC5896493 DOI: 10.7717/peerj.4644] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Accepted: 03/28/2018] [Indexed: 12/18/2022] Open
Abstract
Background DNA metabarcoding is used to generate species composition data for entire communities. However, sequencing errors in high-throughput sequencing instruments are fairly common, usually requiring reads to be clustered into operational taxonomic units (OTUs), losing information on intraspecific diversity in the process. While Cytochrome c oxidase subunit I (COI) haplotype information is limited in resolving intraspecific diversity it is nevertheless often useful e.g. in a phylogeographic context, helping to formulate hypotheses on taxon distribution and dispersal. Methods This study combines sequence denoising strategies, normally applied in microbial research, with additional abundance-based filtering to extract haplotype information from freshwater macroinvertebrate metabarcoding datasets. This novel approach was added to the R package "JAMP" and can be applied to COI amplicon datasets. We tested our haplotyping method by sequencing (i) a single-species mock community composed of 31 individuals with 15 different haplotypes spanning three orders of magnitude in biomass and (ii) 18 monitoring samples each amplified with four different primer sets and two PCR replicates. Results We detected all 15 haplotypes of the single specimens in the mock community with relaxed filtering and denoising settings. However, up to 480 additional unexpected haplotypes remained in both replicates. Rigorous filtering removes most unexpected haplotypes, but also can discard expected haplotypes mainly from the small specimens. In the monitoring samples, the different primer sets detected 177-200 OTUs, each containing an average of 2.40-3.30 haplotypes per OTU. The derived intraspecific diversity data showed population structures that were consistent between replicates and similar between primer pairs but resolution depended on the primer length. A closer look at abundant taxa in the dataset revealed various population genetic patterns, e.g. the stonefly Taeniopteryx nebulosa and the caddisfly Hydropsyche pellucidula showed a distinct north-south cline with respect to haplotype distribution, while the beetle Oulimnius tuberculatus and the isopod Asellus aquaticus displayed no clear population pattern but differed in genetic diversity. Discussion We developed a strategy to infer intraspecific genetic diversity from bulk invertebrate metabarcoding data. It needs to be stressed that at this point this metabarcoding-informed haplotyping is not capable of capturing the full diversity present in such samples, due to variation in specimen size, primer bias and loss of sequence variants with low abundance. Nevertheless, for a high number of species intraspecific diversity was recovered, identifying potentially isolated populations and taxa for further more detailed phylogeographic investigation. While we are currently lacking large-scale metabarcoding datasets to fully take advantage of our new approach, metabarcoding-informed haplotyping holds great promise for biomonitoring efforts that not only seek information about species diversity but also underlying genetic diversity.
Collapse
Affiliation(s)
- Vasco Elbrecht
- Aquatic Ecosystem Research, University of Duisburg-Essen, Essen, North Rhine-Westphalia, Germany.,Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Ecaterina Edith Vamos
- Aquatic Ecosystem Research, University of Duisburg-Essen, Essen, North Rhine-Westphalia, Germany
| | - Dirk Steinke
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Florian Leese
- Aquatic Ecosystem Research, University of Duisburg-Essen, Essen, North Rhine-Westphalia, Germany.,Centre for Water and Environmental Research (ZWU) Essen, University of Duisburg-Essen, Essen, North Rhine-Westphalia, Germany
| |
Collapse
|
161
|
Loewen CA, Ganetzky B. Mito-Nuclear Interactions Affecting Lifespan and Neurodegeneration in a Drosophila Model of Leigh Syndrome. Genetics 2018; 208:1535-1552. [PMID: 29496745 PMCID: PMC5887147 DOI: 10.1534/genetics.118.300818] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 02/19/2018] [Indexed: 12/18/2022] Open
Abstract
Proper mitochondrial activity depends upon proteins encoded by genes in the nuclear and mitochondrial genomes that must interact functionally and physically in a precisely coordinated manner. Consequently, mito-nuclear allelic interactions are thought to be of crucial importance on an evolutionary scale, as well as for manifestation of essential biological phenotypes, including those directly relevant to human disease. Nonetheless, detailed molecular understanding of mito-nuclear interactions is still lacking, and definitive examples of such interactions in vivo are sparse. Here we describe the characterization of a mutation in Drosophila ND23, a nuclear gene encoding a highly conserved subunit of mitochondrial complex 1. This characterization led to the discovery of a mito-nuclear interaction that affects the ND23 mutant phenotype. ND23 mutants exhibit reduced lifespan, neurodegeneration, abnormal mitochondrial morphology, and decreased ATP levels. These phenotypes are similar to those observed in patients with Leigh syndrome, which is caused by mutations in a number of nuclear genes that encode mitochondrial proteins, including the human ortholog of ND23 A key feature of Leigh syndrome, and other mitochondrial disorders, is unexpected and unexplained phenotypic variability. We discovered that the phenotypic severity of ND23 mutations varies depending on the maternally inherited mitochondrial background. Sequence analysis of the relevant mitochondrial genomes identified several variants that are likely candidates for the phenotypic interaction with mutant ND23, including a variant affecting a mitochondrially encoded component of complex I. Thus, our work provides an in vivo demonstration of the phenotypic importance of mito-nuclear interactions in the context of mitochondrial disease.
Collapse
Affiliation(s)
- Carin A Loewen
- Laboratory of Genetics, University of Wisconsin-Madison, Wisconsin 53706-1580
| | - Barry Ganetzky
- Laboratory of Genetics, University of Wisconsin-Madison, Wisconsin 53706-1580
| |
Collapse
|
162
|
Strange RM, Delaney KJ. First Report of a Mitochondrial Pseudogene in Agnathan Vertebrates (Cyclostomata: Petromyzontidae). J Mol Evol 2018; 86:187-189. [PMID: 29564489 DOI: 10.1007/s00239-018-9835-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 03/15/2018] [Indexed: 11/28/2022]
Abstract
We report herein the characterization of a nuclear paralog of a fragment of the mitochondrial genome (a numt) in two closely related species of lampreys (Ichthyomyzon spp.). Although numts have been characterized in several vertebrate taxa, numts have yet to be reported for fishes in general. Given the phylogenetic position of lampreys relative to other vertebrates, the presence of numts within the lamprey genome is either evidence of an ancestral trait lost in other fishes but uniquely retained in agnathans and amniotes, or (more intriguingly) a product of the genome rearrangements these animals undergo during development.
Collapse
Affiliation(s)
- Rex Meade Strange
- Department of Biology, University of Southern Indiana, 8600 University Blvd., Evansville, IN, 47712, USA.
| | - Kimberly J Delaney
- Department of Biology, University of Southern Indiana, 8600 University Blvd., Evansville, IN, 47712, USA
| |
Collapse
|
163
|
Schiavo G, Strillacci MG, Ribani A, Bovo S, Roman-Ponce SI, Cerolini S, Bertolini F, Bagnato A, Fontanesi L. Few mitochondrial DNA sequences are inserted into the turkey (Meleagris gallopavo) nuclear genome: evolutionary analyses and informativity in the domestic lineage. Anim Genet 2018. [PMID: 29521475 DOI: 10.1111/age.12648] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mitochondrial DNA (mtDNA) insertions have been detected in the nuclear genome of many eukaryotes. These sequences are pseudogenes originated by horizontal transfer of mtDNA fragments into the nuclear genome, producing nuclear DNA sequences of mitochondrial origin (numt). In this study we determined the frequency and distribution of mtDNA-originated pseudogenes in the turkey (Meleagris gallopavo) nuclear genome. The turkey reference genome (Turkey_2.01) was aligned with the reference linearized mtDNA sequence using last. A total of 32 numt sequences (corresponding to 18 numt regions derived by unique insertional events) were identified in the turkey nuclear genome (size ranging from 66 to 1415 bp; identity against the modern turkey mtDNA corresponding region ranging from 62% to 100%). Numts were distributed in nine chromosomes and in one scaffold. They derived from parts of 10 mtDNA protein-coding genes, ribosomal genes, the control region and 10 tRNA genes. Seven numt regions reported in the turkey genome were identified in orthologues positions in the Gallus gallus genome and therefore were present in the ancestral genome that in the Cretaceous originated the lineages of the modern crown Galliformes. Five recently integrated turkey numts were validated by PCR in 168 turkeys of six different domestic populations. None of the analysed numts were polymorphic (i.e. absence of the inserted sequence, as reported in numts of recent integration in other species), suggesting that the reticulate speciation model is not useful for explaining the origin of the domesticated turkey lineage.
Collapse
Affiliation(s)
- G Schiavo
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale G. Fanin 46, 40127, Bologna, Italy
| | - M G Strillacci
- Department of Veterinary Medicine, University of Milan, Via Celoria 10, 20133, Milano, Italy
| | - A Ribani
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale G. Fanin 46, 40127, Bologna, Italy
| | - S Bovo
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale G. Fanin 46, 40127, Bologna, Italy.,Biocomputing Group, Department of Biological, Geological, and Environmental Sciences, University of Bologna, Via San Giacomo 9/2, 40126, Bologna, Italy
| | - S I Roman-Ponce
- Centro Nacional de Investigación en Fisiología y Mejoramiento Animal, Instituto Nacional de Investigaciones Forestales, Agricola y Pecuarias (INIFAP), Km.1 Carretera a Colón, Auchitlán, 76280, Querétaro, Mexico
| | - S Cerolini
- Department of Veterinary Medicine, University of Milan, Via Celoria 10, 20133, Milano, Italy
| | - F Bertolini
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale G. Fanin 46, 40127, Bologna, Italy.,Department of Animal Science, Iowa State University, 2255 Kildee Hall, 50011, Ames, IA, USA
| | - A Bagnato
- Department of Veterinary Medicine, University of Milan, Via Celoria 10, 20133, Milano, Italy
| | - L Fontanesi
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale G. Fanin 46, 40127, Bologna, Italy
| |
Collapse
|
164
|
Kumlert R, Chaisiri K, Anantatat T, Stekolnikov AA, Morand S, Prasartvit A, Makepeace BL, Sungvornyothin S, Paris DH. Autofluorescence microscopy for paired-matched morphological and molecular identification of individual chigger mites (Acari: Trombiculidae), the vectors of scrub typhus. PLoS One 2018; 13:e0193163. [PMID: 29494599 PMCID: PMC5832206 DOI: 10.1371/journal.pone.0193163] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 02/06/2018] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Conventional gold standard characterization of chigger mites involves chemical preparation procedures (i.e. specimen clearing) for visualization of morphological features, which however contributes to destruction of the arthropod host DNA and any endosymbiont or pathogen DNA harbored within the specimen. METHODOLOGY/PRINCIPAL FINDINGS In this study, a novel work flow based on autofluorescence microscopy was developed to enable identification of trombiculid mites to the species level on the basis of morphological traits without any special preparation, while preserving the mite DNA for subsequent genotyping. A panel of 16 specifically selected fluorescence microscopy images of mite features from available identification keys served for complete chigger morphological identification to the species level, and was paired with corresponding genotype data. We evaluated and validated this method for paired chigger morphological and genotypic ID using the mitochondrial cytochrome c oxidase subunit I gene (coi) in 113 chigger specimens representing 12 species and 7 genera (Leptotrombidium, Ascoschoengastia, Gahrliepia, Walchia, Blankaartia, Schoengastia and Schoutedenichia) from the Lao People's Democratic Republic (Lao PDR) to the species level (complete characterization), and 153 chiggers from 5 genera (Leptotrombidium, Ascoschoengastia, Helenicula, Schoengastiella and Walchia) from Thailand, Cambodia and Lao PDR to the genus level. A phylogenetic tree constructed from 77 coi gene sequences (approximately 640 bp length, n = 52 new coi sequences and n = 25 downloaded from GenBank), demonstrated clear grouping of assigned morphotypes at the genus levels, although evidence of both genetic polymorphism and morphological plasticity was found. CONCLUSIONS/SIGNIFICANCE With this new methodology, we provided the largest collection of characterized coi gene sequences for trombiculid mites to date, and almost doubled the number of available characterized coi gene sequences with a single study. The ability to provide paired phenotypic-genotypic data is of central importance for future characterization of mites and dissecting the molecular epidemiology of mites transmitting diseases like scrub typhus.
Collapse
Affiliation(s)
- Rawadee Kumlert
- Faculty of Tropical Medicine, Mahidol University, Ratchathewi, Bangkok, Thailand
- Department of Disease Control, Ministry of Public Health, Nonthaburi, Bangkok, Thailand
| | - Kittipong Chaisiri
- Faculty of Tropical Medicine, Mahidol University, Ratchathewi, Bangkok, Thailand
- Department of Infection Biology, Institute of Infection & Global Health, University of Liverpool, Liverpool Science Park IC2, Liverpool, United Kingdom
| | - Tippawan Anantatat
- Mahidol Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Alexandr A. Stekolnikov
- Zoological Institute of the Russian Academy of Sciences, Universitetskaya Embankment 1, Saint Petersburg, Russia
| | - Serge Morand
- CNRS ISEM—CIRAD ASTRE, Faculty of Veterinary Technology, Kasetsart University, Bangkok, Thailand
| | - Anchana Prasartvit
- Department of Disease Control, Ministry of Public Health, Nonthaburi, Bangkok, Thailand
| | - Benjamin L. Makepeace
- Department of Infection Biology, Institute of Infection & Global Health, University of Liverpool, Liverpool Science Park IC2, Liverpool, United Kingdom
| | | | - Daniel H. Paris
- Mahidol Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
- Nuffield Department of Medicine, Oxford University, Oxford, United Kingdom
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- Faculty of Medicine, University Basel, Basel, Switzerland
| |
Collapse
|
165
|
Bennett KL, Kaddumukasa M, Shija F, Djouaka R, Misinzo G, Lutwama J, Linton YM, Walton C. Comparative phylogeography of Aedes mosquitoes and the role of past climatic change for evolution within Africa. Ecol Evol 2018; 8:3019-3036. [PMID: 29531714 PMCID: PMC5838080 DOI: 10.1002/ece3.3668] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 10/26/2017] [Accepted: 10/27/2017] [Indexed: 01/01/2023] Open
Abstract
The study of demographic processes involved in species diversification and evolution ultimately provides explanations for the complex distribution of biodiversity on earth, indicates regions important for the maintenance and generation of biodiversity, and identifies biological units important for conservation or medical consequence. African and forest biota have both received relatively little attention with regard to understanding their diversification, although one possible mechanism is that this has been driven by historical climate change. To investigate this, we implemented a standard population genetics approach along with Approximate Bayesian Computation, using sequence data from two exon-primed intron-crossing (EPIC) nuclear loci and mitochondrial cytochrome oxidase subunit I, to investigate the evolutionary history of five medically important and inherently forest dependent mosquito species of the genus Aedes. By testing different demographic hypotheses, we show that Aedes bromeliae and Aedes lilii fit the same model of lineage diversification, admixture, expansion, and recent population structure previously inferred for Aedes aegypti. In addition, analyses of population structure show that Aedes africanus has undergone lineage diversification and expansion while Aedes hansfordi has been impacted by population expansion within Uganda. This congruence in evolutionary history is likely to relate to historical climate-driven habitat change within Africa during the late Pleistocene and Holocene epoch. We find differences in the population structure of mosquitoes from Tanzania and Uganda compared to Benin and Uganda which could relate to differences in the historical connectivity of forests across the continent. Our findings emphasize the importance of recent climate change in the evolution of African forest biota.
Collapse
Affiliation(s)
- Kelly Louise Bennett
- Faculty of Life SciencesComputational Evolutionary Biology GroupUniversity of ManchesterManchesterUK
| | - Martha Kaddumukasa
- Department of Arbovirology, Emerging and Re‐emerging InfectionsUganda Virus Research InstituteEntebbeUganda
- WITS Institute for Malaria ResearchSchool of Pathology Faculty of Health SciencesUniversity of WitwatersrandParktownJohannesburg
| | - Fortunate Shija
- Faculty of Life SciencesComputational Evolutionary Biology GroupUniversity of ManchesterManchesterUK
- Department of Veterinary Microbiology and ParasitologySokoine University of AgricultureMorogoroTanzania
| | - Rousseau Djouaka
- Agro‐Eco‐Health Platform for West and Central AfricaInternational Institute for Tropical AgricultureCotonouRepublic of Benin
| | - Gerald Misinzo
- Agro‐Eco‐Health Platform for West and Central AfricaInternational Institute for Tropical AgricultureCotonouRepublic of Benin
| | - Julius Lutwama
- Department of Arbovirology, Emerging and Re‐emerging InfectionsUganda Virus Research InstituteEntebbeUganda
| | - Yvonne Marie Linton
- Department of EntomologyNational Museum of Natural HistorySmithsonian InstitutionWashingtonDCUSA
- Walter Reed Biosystematics UnitSmithsonian Institution Museum Support CenterSuitlandMDUSA
- Walter Reed Army Institute of ResearchSilver SpringMDUSA
- Uniformed Services University of Health SciencesBethesdaMDUSA
| | - Catherine Walton
- Faculty of Life SciencesComputational Evolutionary Biology GroupUniversity of ManchesterManchesterUK
| |
Collapse
|
166
|
Gidlund EK, von Walden F, Venojärvi M, Risérus U, Heinonen OJ, Norrbom J, Sundberg CJ. Humanin skeletal muscle protein levels increase after resistance training in men with impaired glucose metabolism. Physiol Rep 2018; 4:4/23/e13063. [PMID: 27923980 PMCID: PMC5357820 DOI: 10.14814/phy2.13063] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 11/01/2016] [Accepted: 11/03/2016] [Indexed: 11/24/2022] Open
Abstract
Humanin (HN) is a mitochondrially encoded and secreted peptide linked to glucose metabolism and tissue protecting mechanisms. Whether skeletal muscle HN gene or protein expression is influenced by exercise remains unknown. In this intervention study we show, for the first time, that HN protein levels increase in human skeletal muscle following 12 weeks of resistance training in persons with prediabetes. Male subjects (n = 55) with impaired glucose regulation (IGR) were recruited and randomly assigned to resistance training, Nordic walking or a control group. The exercise interventions were performed three times per week for 12 weeks with progressively increased intensity during the intervention period. Biopsies from the vastus lateralis muscle and venous blood samples were taken before and after the intervention. Skeletal muscle and serum protein levels of HN were analyzed as well as skeletal muscle gene expression of the mitochondrially encoded gene MT‐RNR2, containing the open reading frame for HN. To elucidate mitochondrial training adaptation, mtDNA, and nuclear DNA as well as Citrate synthase were measured. Skeletal muscle HN protein levels increased by 35% after 12 weeks of resistance training. No change in humanin protein levels was seen in serum in any of the intervention groups. There was a significant correlation between humanin levels in serum and the improvements in the 2 h glucose loading test in the resistance training group. The increase in HN protein levels in skeletal muscle after regular resistance training in prediabetic males may suggest a role for HN in the regulation of glucose metabolism. Given the preventative effect of exercise on diabetes type 2, the role of HN as a mitochondrially derived peptide and an exercise‐responsive mitokine warrants further investigation.
Collapse
Affiliation(s)
- Eva-Karin Gidlund
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Ferdinand von Walden
- Neuropediatrics Unit, Department of Women's and Children's Health, Karolinska Institutet and Astrid Lindgren's Pediatric Hospital, Stockholm, Sweden
| | - Mika Venojärvi
- Institute of Biomedicine, Sports and exercise medicine, University of Eastern Finland, Kuopio, Finland
| | - Ulf Risérus
- Clinical Nutrition and Metabolism, Department of Public Health and Caring Sciences, Uppsala University, Uppsala, Sweden
| | - Olli J Heinonen
- Paavo Nurmi Centre and Departmen of Health & Physical Activity, University of Turku, Turku, Finland
| | - Jessica Norrbom
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Carl Johan Sundberg
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| |
Collapse
|
167
|
Mustafa SI, Schwarzacher T, Heslop-Harrison JS. Complete mitogenomes from Kurdistani sheep: abundant centromeric nuclear copies representing diverse ancestors. Mitochondrial DNA A DNA Mapp Seq Anal 2018; 29:1180-1193. [DOI: 10.1080/24701394.2018.1431226] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Sarbast Ihsan Mustafa
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
- Department of Animal Production, University of Duhok, Duhok, Iraq
| | - Trude Schwarzacher
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | | |
Collapse
|
168
|
Krehenwinkel H, Fong M, Kennedy S, Huang EG, Noriyuki S, Cayetano L, Gillespie R. The effect of DNA degradation bias in passive sampling devices on metabarcoding studies of arthropod communities and their associated microbiota. PLoS One 2018; 13:e0189188. [PMID: 29304124 PMCID: PMC5755739 DOI: 10.1371/journal.pone.0189188] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2017] [Accepted: 11/21/2017] [Indexed: 11/18/2022] Open
Abstract
PCR amplification bias is a well-known problem in metagenomic analysis of arthropod communities. In contrast, variation of DNA degradation rates is a largely neglected source of bias. Differential degradation of DNA molecules could cause underrepresentation of taxa in a community sequencing sample. Arthropods are often collected by passive sampling devices, like malaise traps. Specimens in such a trap are exposed to varying periods of suboptimal storage and possibly different rates of DNA degradation. Degradation bias could thus be a significant issue, skewing diversity estimates. Here, we estimate the effect of differential DNA degradation on the recovery of community diversity of Hawaiian arthropods and their associated microbiota. We use a simple DNA size selection protocol to test for degradation bias in mock communities, as well as passively collected samples from actual Malaise traps. We compare the effect of DNA degradation to that of varying PCR conditions, including primer choice, annealing temperature and cycle number. Our results show that DNA degradation does indeed bias community analyses. However, the effect of this bias is of minor importance compared to that induced by changes in PCR conditions. Analyses of the macro and microbiome from passively collected arthropod samples are thus well worth pursuing.
Collapse
Affiliation(s)
- Henrik Krehenwinkel
- Department of Environmental Sciences, Policy and Management, University of California, Mulford Hall, Berkeley, California, United States of America
- Center for Comparative Genomics, California Academy of Sciences, San Francisco, California, United States of America
| | - Marisa Fong
- Department of Environmental Sciences, Policy and Management, University of California, Mulford Hall, Berkeley, California, United States of America
| | - Susan Kennedy
- Department of Environmental Sciences, Policy and Management, University of California, Mulford Hall, Berkeley, California, United States of America
| | - Edward Greg Huang
- Department of Environmental Sciences, Policy and Management, University of California, Mulford Hall, Berkeley, California, United States of America
| | - Suzuki Noriyuki
- Department of Environmental Sciences, Policy and Management, University of California, Mulford Hall, Berkeley, California, United States of America
- Center for Geo-Environmental Science, Rissho University, Saitama, Japan
| | - Luis Cayetano
- Department of Environmental Sciences, Policy and Management, University of California, Mulford Hall, Berkeley, California, United States of America
| | - Rosemary Gillespie
- Department of Environmental Sciences, Policy and Management, University of California, Mulford Hall, Berkeley, California, United States of America
| |
Collapse
|
169
|
Krehenwinkel H, Wolf M, Lim JY, Rominger AJ, Simison WB, Gillespie RG. Estimating and mitigating amplification bias in qualitative and quantitative arthropod metabarcoding. Sci Rep 2017; 7:17668. [PMID: 29247210 PMCID: PMC5732254 DOI: 10.1038/s41598-017-17333-x] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 11/16/2017] [Indexed: 11/09/2022] Open
Abstract
Amplicon based metabarcoding promises rapid and cost-efficient analyses of species composition. However, it is disputed whether abundance estimates can be derived from metabarcoding due to taxon specific PCR amplification biases. PCR-free approaches have been suggested to mitigate this problem, but come with considerable increases in workload and cost. Here, we analyze multilocus datasets of diverse arthropod communities, to evaluate whether amplification bias can be countered by (1) targeting loci with highly degenerate primers or conserved priming sites, (2) increasing PCR template concentration, (3) reducing PCR cycle number or (4) avoiding locus specific amplification by directly sequencing genomic DNA. Amplification bias is reduced considerably by degenerate primers or targeting amplicons with conserved priming sites. Surprisingly, a reduction of PCR cycles did not have a strong effect on amplification bias. The association of taxon abundance and read count was actually less predictable with fewer cycles. Even a complete exclusion of locus specific amplification did not exclude bias. Copy number variation of the target loci may be another explanation for read abundance differences between taxa, which would affect amplicon based and PCR free methods alike. As read abundance biases are taxon specific and predictable, the application of correction factors allows abundance estimates.
Collapse
Affiliation(s)
- Henrik Krehenwinkel
- Department of Environmental Sciences, Policy and Management University of California Berkeley Mulford Hall, Berkeley, California, USA.
- Center for Comparative Genomics California Academy of Sciences Music Concourse Drive, San Francisco, California, USA.
| | - Madeline Wolf
- Department of Environmental Sciences, Policy and Management University of California Berkeley Mulford Hall, Berkeley, California, USA
| | - Jun Ying Lim
- Department of Environmental Sciences, Policy and Management University of California Berkeley Mulford Hall, Berkeley, California, USA
| | - Andrew J Rominger
- Department of Environmental Sciences, Policy and Management University of California Berkeley Mulford Hall, Berkeley, California, USA
| | - Warren B Simison
- Center for Comparative Genomics California Academy of Sciences Music Concourse Drive, San Francisco, California, USA
| | - Rosemary G Gillespie
- Department of Environmental Sciences, Policy and Management University of California Berkeley Mulford Hall, Berkeley, California, USA
| |
Collapse
|
170
|
Schiavo G, Hoffmann OI, Ribani A, Utzeri VJ, Ghionda MC, Bertolini F, Geraci C, Bovo S, Fontanesi L. A genomic landscape of mitochondrial DNA insertions in the pig nuclear genome provides evolutionary signatures of interspecies admixture. DNA Res 2017; 24:487-498. [PMID: 28460080 PMCID: PMC5737481 DOI: 10.1093/dnares/dsx019] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 04/02/2017] [Indexed: 12/26/2022] Open
Abstract
Nuclear DNA sequences of mitochondrial origin (numts) are derived by insertion of mitochondrial DNA (mtDNA), into the nuclear genome. In this study, we provide, for the first time, a genome picture of numts inserted in the pig nuclear genome. The Sus scrofa reference nuclear genome (Sscrofa10.2) was aligned with circularized and consensus mtDNA sequences using LAST software. A total of 430 numt sequences that may represent 246 different numt integration events (57 numt regions determined by at least two numt sequences and 189 singletons) were identified, covering about 0.0078% of the nuclear genome. Numt integration events were correlated (0.99) to the chromosome length. The longest numt sequence (about 11 kbp) was located on SSC2. Six numts were sequenced and PCR amplified in pigs of European commercial and local pig breeds, of the Chinese Meishan breed and in European wild boars. Three of them were polymorphic for the presence or absence of the insertion. Surprisingly, the estimated age of insertion of two of the three polymorphic numts was more ancient than that of the speciation time of the Sus scrofa, supporting that these polymorphic sites were originated from interspecies admixture that contributed to shape the pig genome.
Collapse
Affiliation(s)
- Giuseppina Schiavo
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, 40127 Bologna, Italy
| | - Orsolya Ivett Hoffmann
- Ruminant Genome Biology Group, NARIC, Agricultural Biotechnology Center, H-2100?Gödöllo, Hungary
| | - Anisa Ribani
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, 40127 Bologna, Italy
| | - Valerio Joe Utzeri
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, 40127 Bologna, Italy
| | - Marco Ciro Ghionda
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, 40127 Bologna, Italy
| | - Francesca Bertolini
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, 40127 Bologna, Italy
| | - Claudia Geraci
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, 40127 Bologna, Italy
| | - Samuele Bovo
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, 40127 Bologna, Italy
| | - Luca Fontanesi
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, 40127 Bologna, Italy
| |
Collapse
|
171
|
Hazkani-Covo E, Martin WF. Quantifying the Number of Independent Organelle DNA Insertions in Genome Evolution and Human Health. Genome Biol Evol 2017; 9:1190-1203. [PMID: 28444372 PMCID: PMC5570036 DOI: 10.1093/gbe/evx078] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/20/2017] [Indexed: 12/28/2022] Open
Abstract
Fragments of organelle genomes are often found as insertions in nuclear DNA. These fragments of mitochondrial DNA (numts) and plastid DNA (nupts) are ubiquitous components of eukaryotic genomes. They are, however, often edited out during the genome assembly process, leading to systematic underestimation of their frequency. Numts and nupts, once inserted, can become further fragmented through subsequent insertion of mobile elements or other recombinational events that disrupt the continuity of the inserted sequence relative to the genuine organelle DNA copy. Because numts and nupts are typically identified through sequence comparison tools such as BLAST, disruption of insertions into smaller fragments can lead to systematic overestimation of numt and nupt frequencies. Accurate identification of numts and nupts is important, however, both for better understanding of their role during evolution, and for monitoring their increasingly evident role in human disease. Human populations are polymorphic for 141 numt loci, five numts are causal to genetic disease, and cancer genomic studies are revealing an abundance of numts associated with tumor progression. Here, we report investigation of salient parameters involved in obtaining accurate estimates of numt and nupt numbers in genome sequence data. Numts and nupts from 44 sequenced eukaryotic genomes reveal lineage-specific differences in the number, relative age and frequency of insertional events as well as lineage-specific dynamics of their postinsertional fragmentation. Our findings outline the main technical parameters influencing accurate identification and frequency estimation of numts in genomic studies pertinent to both evolution and human health.
Collapse
Affiliation(s)
- Einat Hazkani-Covo
- Department of Natural and Life Sciences, The Open University of Israel, Ra'anana, Israel
| | - William F Martin
- Institute of Molecular Evolution, Heinrich-Heine University, Düsseldorf, Germany
| |
Collapse
|
172
|
Kumar V, Dickey AM, Seal DR, Shatters RG, Osborne LS, McKenzie CL. Unexpected High Intragenomic Variation in Two of Three Major Pest Thrips Species Does Not Affect Ribosomal Internal Transcribed Spacer 2 (ITS2) Utility for Thrips Identification. Int J Mol Sci 2017; 18:ijms18102100. [PMID: 28984819 PMCID: PMC5666782 DOI: 10.3390/ijms18102100] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 09/28/2017] [Accepted: 09/30/2017] [Indexed: 11/16/2022] Open
Abstract
The mitochondrial cytochrome oxidase I gene (mtCO1) and the ribosomal internal transcribed spacer 2 region (ITS2) are among the most widely used molecular markers for insect taxonomic characterization. Three economically important species of thrips, Scirtothripsdorsalis, Thripspalmi, and Frankliniellaoccidentalis were selected to examine the extent of intragenomic variation within these two marker regions in the family Thripidae, and determine if this variation would affect the utility of markers in thrips molecular diagnostics. For each species, intragenomic (within individual) variation and intergenomic (among individuals) variation was assessed by cloning and sequencing PCR-amplified copies. Intergenomic variation was generally higher than intragenomic variation except in cases where intergenomic variation was very low, as in mtCO1 from S.dorsalis and F.occidentalis. Intragenomic variation was detected in both markers in all three of the thrips species, however, 2-3 times more intragenomic variation was observed for ITS2 than mtCO1 in both S.dorsalis and T.palmi. Furthermore, levels of intragenomic variation were low for both of the genes in F.occidentalis. In all of the three thrips species, no sex-based clustering of haplotypes was observed in either marker. Unexpected high intragenomic variation in ITS2 for two of three thrips species did not interfere with thrips diagnostics. However, caution should be taken in applying ITS2 to certain studies of S.dorsalis and T.palmi when high levels of intragenomic variation could be problematic or confounding. In such studies, mtCO1 may be a preferable marker. Possible reasons for discrepancies in intragenomic variation among genomic regions are discussed.
Collapse
Affiliation(s)
- Vivek Kumar
- Department of Entomology and Nematology, Mid-Florida Research and Education Center, University of Florida, Apopka, FL 32703, USA; (A.M.D.); (L.S.O.)
- U.S. Horticultural Research Laboratory, USDA-ARS, Fort Pierce, FL 34945, USA; (R.G.S.); (C.L.M.)
- Department of Entomology and Nematology, Tropical Research and Education Center, University of Florida, Homestead, FL 33031, USA;
- Correspondence: ; Tel.: +1-772-462-5978
| | - Aaron M. Dickey
- Department of Entomology and Nematology, Mid-Florida Research and Education Center, University of Florida, Apopka, FL 32703, USA; (A.M.D.); (L.S.O.)
- U.S. Horticultural Research Laboratory, USDA-ARS, Fort Pierce, FL 34945, USA; (R.G.S.); (C.L.M.)
- Present Address: U.S. Meat Animal Research Center, USDA-ARS, Clay Center, NE 68933, USA
| | - Dakshina R. Seal
- Department of Entomology and Nematology, Tropical Research and Education Center, University of Florida, Homestead, FL 33031, USA;
| | - Robert G. Shatters
- U.S. Horticultural Research Laboratory, USDA-ARS, Fort Pierce, FL 34945, USA; (R.G.S.); (C.L.M.)
| | - Lance S. Osborne
- Department of Entomology and Nematology, Mid-Florida Research and Education Center, University of Florida, Apopka, FL 32703, USA; (A.M.D.); (L.S.O.)
| | - Cindy L. McKenzie
- U.S. Horticultural Research Laboratory, USDA-ARS, Fort Pierce, FL 34945, USA; (R.G.S.); (C.L.M.)
| |
Collapse
|
173
|
Szafranski P. Intercompartmental Piecewise Gene Transfer. Genes (Basel) 2017; 8:genes8100260. [PMID: 28984842 PMCID: PMC5664110 DOI: 10.3390/genes8100260] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 09/25/2017] [Accepted: 09/28/2017] [Indexed: 11/16/2022] Open
Abstract
Gene relocation from the residual genomes of organelles to the nuclear genome still continues, although as a scaled down evolutionary phenomenon, limited in occurrence mostly to protists (sensu lato) and land plants. During this process, the structural integrity of transferred genes is usually preserved. However, the relocation of mitochondrial genes that code for respiratory chain and ribosomal proteins is sometimes associated with their fragmentation into two complementary genes. Herein, this review compiles cases of piecewise gene transfer from the mitochondria to the nucleus, and discusses hypothesized mechanistic links between the fission and relocation of those genes.
Collapse
Affiliation(s)
- Przemyslaw Szafranski
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.
| |
Collapse
|
174
|
Vamos E, Elbrecht V, Leese F. Short COI markers for freshwater macroinvertebrate metabarcoding. METABARCODING AND METAGENOMICS 2017. [DOI: 10.3897/mbmg.1.14625] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
|
175
|
Ancient mitochondrial pseudogenes reveal hybridization between distant lineages in the evolution of the Rupicapra genus. Gene 2017; 628:63-71. [DOI: 10.1016/j.gene.2017.07.035] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 07/07/2017] [Accepted: 07/11/2017] [Indexed: 11/23/2022]
|
176
|
Melvin RG, Ballard JWO. Cellular and population level processes influence the rate, accumulation and observed frequency of inherited and somatic mtDNA mutations. Mutagenesis 2017; 32:323-334. [PMID: 28521046 DOI: 10.1093/mutage/gex004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Mitochondria are found in all animals and have the unique feature of containing multiple copies of their own small, circular DNA genome (mtDNA). The rate and pattern of mutation accumulation in the mtDNA are influenced by molecular, cellular and population level processes. We distinguish between inherited and somatic mtDNA mutations and review evidence for the often-made assumption that mutations accumulate at a higher rate in mtDNA than in nuclear DNA (nDNA). We conclude that the whole genome mutation accumulation rate is higher for mtDNA than for nDNA but include the caveat that rates overlap considerably between the individual mtDNA- and nDNA-encoded genes. Next, we discuss the postulated causal mechanisms for the high rate of mtDNA mutation accumulation in both inheritance and in somatic cells. Perhaps unexpectedly, mtDNA is resilient to many mutagens of nDNA but is prone to errors of replication. We then consider the influence of maternal inheritance, recombination and selection on the observed accumulation pattern of inherited mtDNA mutations. Finally, we discuss environmental influences of temperature and diet on the observed frequency of inherited and somatic mtDNA mutations. We conclude that it is necessary to understand the cellular processes to fully interpret the pattern of mutations and how they influence our interpretations of evolution and disease.
Collapse
Affiliation(s)
- Richard G Melvin
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - John William O Ballard
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
| |
Collapse
|
177
|
Pozzi A, Plazzi F, Milani L, Ghiselli F, Passamonti M. SmithRNAs: Could Mitochondria "Bend" Nuclear Regulation? Mol Biol Evol 2017; 34:1960-1973. [PMID: 28444389 PMCID: PMC5850712 DOI: 10.1093/molbev/msx140] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Typically, animal mitochondria have very compact genomes, with few short intergenic regions, and no introns. Hence, it may seem that there is little space for unknown functions in mitochondrial DNA (mtDNA). However, mtDNA can also operate through RNA interference, as small non coding RNAs (sncRNAs) produced by mtDNA have already been proposed for humans. We sequenced sncRNA libraries from isolated mitochondria of Ruditapes philippinarum (Mollusca Bivalvia) gonads, a species with doubly uniparental inheritance of mitochondria, and identified several putative sncRNAs of mitochondrial origin. Some sncRNAs are transcribed by intergenic regions that form stable stem-hairpin structures, which makes them good miRNA-like candidates. We decided to name them small mitochondrial highly-transcribed RNAs (smithRNAs). Many concurrent data support that we have recovered sncRNAs of mitochondrial origin that might be involved in gonad formation and able to affect nuclear gene expression. This possibility has been never suggested before. If mtDNA can affect nuclear gene expression through RNA interference, this opens a plethora of new possibilities for it to interact with the nucleus, and makes metazoan mtDNA a much more complex genome than previously thought.
Collapse
Affiliation(s)
- Andrea Pozzi
- Department of Biological Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Federico Plazzi
- Department of Biological Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Liliana Milani
- Department of Biological Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Fabrizio Ghiselli
- Department of Biological Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Marco Passamonti
- Department of Biological Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| |
Collapse
|
178
|
Cryptic genetic diversity of Neverita didyma in the coast of China revealed by phylogeographic analysis: implications for management and conservation. CONSERV GENET 2017. [DOI: 10.1007/s10592-017-0998-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
179
|
Striking pseudogenization in avian phylogenetics: Numts are large and common in falcons. Mol Phylogenet Evol 2017; 115:1-6. [PMID: 28690127 DOI: 10.1016/j.ympev.2017.07.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 06/23/2017] [Accepted: 07/05/2017] [Indexed: 11/21/2022]
Abstract
Nuclear copies of mitochondrial genes (numts) are a well-known feature of eukaryotic genomes and a concern in systematics, as they can mislead phylogenetic inferences when inadvertently used. Studies on avian numts initially based on the chicken genome suggest that numts may be uncommon and relatively short among birds. Here we ask how common numts are in falcons, based on recently sequenced genomes of the Saker falcon (Falco cherrug) and Peregrine falcon (F. peregrinus). We identified numts by BLASTN searches and then extracted CYTB, ND2 and COI sequences from them, which were then used for phylogeny inference along with several sequences from other species in Falconiformes. Our results indicate that avian numts may be much more frequent and longer than previously thought. Phylogenetic inferences revealed multiple independent nuclear insertions throughout the history of the Falconiformes, including cases of sequences available in public databases and wrongly identified as authentic mtDNA. New sequencing technologies and ongoing efforts for whole genome sequencing will provide exciting opportunities for avian numt research in the near future.
Collapse
|
180
|
Singh KK, Choudhury AR, Tiwari HK. Numtogenesis as a mechanism for development of cancer. Semin Cancer Biol 2017; 47:101-109. [PMID: 28511886 DOI: 10.1016/j.semcancer.2017.05.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 04/20/2017] [Accepted: 10/14/2016] [Indexed: 01/10/2023]
Abstract
Transfer of genetic material from cytoplasmic organelles to the nucleus, an ongoing process, has implications in evolution, aging, and human pathologies such as cancer. The transferred mitochondrial DNA (mtDNA) fragments in the nuclear genome are called nuclear mtDNA or NUMTs. We have named the process numtogenesis, defining the term as the transfer of mtDNA into the nuclear genome, or, less specifically, the transfer of mitochondria or mitochondrial components into the nucleus. There is increasing evidence of the involvement of NUMTs in human biology and pathology. Although information pertaining to NUMTs and numtogenesis is sparse, the role of this aspect of mitochondrial biology to human cancers is apparent. In this review, we present available knowledge about the origin and mechanisms of numtogenesis, with special emphasis on the role of NUMTs in human malignancies. We describe studies undertaken in our laboratory and in others and discuss the influence of NUMTs in tumor initiation and progression and in survival of cancer patients. We describe suppressors of numtogenesis and evolutionary conserved mechanisms underlying numtogenesis in cancer. An understanding the emerging field of numtogenesis should allow comprehension of this process in various malignancies and other diseases and, more generally, in human health.
Collapse
Affiliation(s)
- Keshav K Singh
- Departments of Genetics, Birmingham, AL, 35294, USA; Departments of Pathology, Birmingham, AL, 35294, USA; Departments of Environmental Health, Center for Free Radical Biology, Birmingham, AL, 35294, USA; Center for Aging, Birmingham, AL, 35294, USA; UAB Comprehensive Cancer Center, University of Alabama at Birmingham, AL, 35294, USA; Birmingham Veterans Affairs Medical Center, AL, 35294, USA.
| | | | - Hemant K Tiwari
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| |
Collapse
|
181
|
Screening for the ancient polar bear mitochondrial genome reveals low integration of mitochondrial pseudogenes ( numts) in bears. MITOCHONDRIAL DNA PART B-RESOURCES 2017; 2:251-254. [PMID: 33644382 PMCID: PMC7894413 DOI: 10.1080/23802359.2017.1318673] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Phylogenetic analyses of nuclear and mitochondrial genomes indicate that polar bears captured the brown bear mitochondrial genome 160,000 years ago, leading to an extinction of the original polar bear mitochondrial genome. However, mitochondrial DNA occasionally integrates into the nuclear genome, forming pseudogenes called numts (nuclear mitochondrial integrations). Screening the polar bear genome identified only 13 numts. Genomic analyses of two additional ursine bears and giant panda indicate that all except one of the discovered numts entered the bear lineage at least 14 million years ago. However, short read genome assemblies might lead to an under-representation of numts or other repetitive sequences. Our findings suggest low integration rates of numts in bears and a loss of the original polar bear mitochondrial genome.
Collapse
|
182
|
Wallis GP, Cameron-Christie SR, Kennedy HL, Palmer G, Sanders TR, Winter DJ. Interspecific hybridization causes long-term phylogenetic discordance between nuclear and mitochondrial genomes in freshwater fishes. Mol Ecol 2017; 26:3116-3127. [DOI: 10.1111/mec.14096] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 02/22/2017] [Accepted: 03/01/2017] [Indexed: 12/22/2022]
Affiliation(s)
- Graham P. Wallis
- Department of Zoology; University of Otago; PO Box 56 Dunedin 9054 New Zealand
| | - Sophia R. Cameron-Christie
- Women's and Children's Health; Paediatrics & Child Health; Dunedin School of Medicine; University of Otago; PO Box 56 Dunedin 9054 New Zealand
| | - Hannah L. Kennedy
- Molecular Pathology Laboratory; Canterbury Health Laboratories; PO Box 151 Christchurch 8140 New Zealand
- Department of Pathology; University of Otago; Riccarton Avenue PO Box 4345 Christchurch 8140 New Zealand
| | - Gemma Palmer
- Melbourne IVF; Suite 10 320 Victoria Parade East Melbourne Vic. 3002 Australia
| | - Tessa R. Sanders
- National Institutes of Health; 9000 Rockville Pike Bethesda MD 20892 USA
| | - David J. Winter
- Institute of Fundamental Sciences; Massey University; Private Bag 11 222 Palmerston North 4442 New Zealand
| |
Collapse
|
183
|
Soltani GG, Bénon D, Alvarez N, Praz CJ. When different contact zones tell different stories: putative ring species in the Megachile concinna species complex (Hymenoptera: Megachilidae). Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blx023] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
|
184
|
Liu X, Kang L, Xu M, Wu C, Jiang L. Phylogenetic estimation of Mytilidae in the East China Sea inferred from mitochondrial genes and nuclear DNA sequence variation. BIOCHEM SYST ECOL 2017. [DOI: 10.1016/j.bse.2017.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
185
|
Srinivasainagendra V, Sandel MW, Singh B, Sundaresan A, Mooga VP, Bajpai P, Tiwari HK, Singh KK. Migration of mitochondrial DNA in the nuclear genome of colorectal adenocarcinoma. Genome Med 2017; 9:31. [PMID: 28356157 PMCID: PMC5370490 DOI: 10.1186/s13073-017-0420-6] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 03/09/2017] [Indexed: 12/31/2022] Open
Abstract
Background Colorectal adenocarcinomas are characterized by abnormal mitochondrial DNA (mtDNA) copy number and genomic instability, but a molecular interaction between mitochondrial and nuclear genome remains unknown. Here we report the discovery of increased copies of nuclear mtDNA (NUMT) in colorectal adenocarcinomas, which supports link between mtDNA and genomic instability in the nucleus. We name this phenomenon of nuclear occurrence of mitochondrial component as numtogenesis. We provide a description of NUMT abundance and distribution in tumor versus matched blood-derived normal genomes. Methods Whole-genome sequence data were obtained for colon adenocarcinoma and rectum adenocarcinoma patients participating in The Cancer Genome Atlas, via the Cancer Genomics Hub, using the GeneTorrent file acquisition tool. Data were analyzed to determine NUMT proportion and distribution on a genome-wide scale. A NUMT suppressor gene was identified by comparing numtogenesis in other organisms. Results Our study reveals that colorectal adenocarcinoma genomes, on average, contains up to 4.2-fold more somatic NUMTs than matched normal genomes. Women colorectal tumors contained more NUMT than men. NUMT abundance in tumor predicted parallel abundance in blood. NUMT abundance positively correlated with GC content and gene density. Increased numtogenesis was observed with higher mortality. We identified YME1L1, a human homolog of yeast YME1 (yeast mitochondrial DNA escape 1) to be frequently mutated in colorectal tumors. YME1L1 was also mutated in tumors derived from other tissues. We show that inactivation of YME1L1 results in increased transfer of mtDNA in the nuclear genome. Conclusions Our study demonstrates increased somatic transfer of mtDNA in colorectal tumors. Our study also reveals sex-based differences in frequency of NUMT occurrence and that NUMT in blood reflects NUMT in tumors, suggesting NUMT may be used as a biomarker for tumorigenesis. We identify YME1L1 as the first NUMT suppressor gene in human and demonstrate that inactivation of YME1L1 induces migration of mtDNA to the nuclear genome. Our study reveals that numtogenesis plays an important role in the development of cancer. Electronic supplementary material The online version of this article (doi:10.1186/s13073-017-0420-6) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Vinodh Srinivasainagendra
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, Alabama, 35294, USA
| | - Michael W Sandel
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, Alabama, 35294, USA.,Present address: Department of Biological and Environmental Sciences, School of Natural Sciences and Mathematics, University of West Alabama, Livingston, Alabama, USA
| | - Bhupendra Singh
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, 35294, USA
| | - Aishwarya Sundaresan
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, Alabama, 35294, USA
| | - Ved P Mooga
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, 35294, USA
| | - Prachi Bajpai
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, 35294, USA
| | - Hemant K Tiwari
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, Alabama, 35294, USA.
| | - Keshav K Singh
- Departments of Genetics, Environmental Health, Center for Free Radical Biology, Center for Aging and UAB Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama, 35294, USA. .,Departments of Pathology, Environmental Health, Center for Free Radical Biology, Center for Aging and UAB Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama, 35294, USA. .,Birmingham Veterans Affairs Medical Center, Birmingham, Alabama, 35294, USA. .,Department of Genetics, School of Medicine, University of Alabama at Birmingham, Kaul Genetics Building, Suite 620, 720 20th St. South, Birmingham, AL, 35294, USA.
| |
Collapse
|
186
|
Machida RJ, Lin YY. Occurrence of mitochondrial CO1 pseudogenes in Neocalanus plumchrus (Crustacea: Copepoda): Hybridization indicated by recombined nuclear mitochondrial pseudogenes. PLoS One 2017; 12:e0172710. [PMID: 28231343 PMCID: PMC5322918 DOI: 10.1371/journal.pone.0172710] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 02/08/2017] [Indexed: 11/18/2022] Open
Abstract
A portion of the mitochondrial cytochrome c oxidase I gene was sequenced using both genomic DNA and complement DNA from three planktonic copepod Neocalanus species (N. cristatus, N. plumchrus, and N. flemingeri). Small but critical sequence differences in CO1 were observed between gDNA and cDNA from N. plumchrus. Furthermore, careful observation revealed the presence of recombination between sequences in gDNA from N. plumchrus. Moreover, a chimera of the N. cristatus and N. plumchrus sequences was obtained from N. plumchrus gDNA. The observed phenomena can be best explained by the preferential amplification of the nuclear mitochondrial pseudogenes from gDNA of N. plumchrus. Two conclusions can be drawn from the observations. First, nuclear mitochondrial pseudogenes are pervasive in N. plumchrus. Second, a mating between a female N. cristatus and a male N. plumchrus produced viable offspring, which further backcrossed to a N. plumchrus individual. These observations not only demonstrate intriguing mating behavior in these species, but also emphasize the importance of careful interpretation of species marker sequences amplified from gDNA.
Collapse
Affiliation(s)
- Ryuji J. Machida
- Biodiversity Research Center, Academia Sinica, Nankang, Taipei, Taiwan
- * E-mail:
| | - Ya-Ying Lin
- Biodiversity Research Center, Academia Sinica, Nankang, Taipei, Taiwan
| |
Collapse
|
187
|
Leijs R, Batley M, Hogendoorn K. The genus Amegilla (Hymenoptera, Apidae, Anthophorini) in Australia: A revision of the subgenera Notomegilla and Zonamegilla. Zookeys 2017:79-140. [PMID: 28331394 PMCID: PMC5345376 DOI: 10.3897/zookeys.653.11177] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 01/20/2017] [Indexed: 11/12/2022] Open
Abstract
The Australian bees in the subgenera Notomegilla and Zonamegilla of the genus Amegilla are revised. Commonly in Australia the species in these subgenera are called blue-banded bees, although not all species have blue bands. A phylogeny based on mitochondrial cytochrome oxidase 1 sequence data was used to delineate the species and a set of morphological criteria was developed for species identification. Strong support was obtained for separating the Australian species into the three subgenera previously proposed on the basis of morphology. Two species, are recognised in the subgenus Notomegilla and eleven new synonymies are proposed. Twelve Australian species are recognised in the subgenus Zonamegilla including four new species: indistincta, karlba, paeninsulae and viridicingulata, and twenty new synonymies are proposed. Keys to the species of both sexes and descriptions or redescriptions of all species are provided. Distribution maps, data on flower visitation and phenology are given.
Collapse
Affiliation(s)
- Remko Leijs
- South Australian Museum, North Terrace, Adelaide, SA 5000, Australia
| | - Michael Batley
- Australian Museum, 6 College Street, Sydney NSW 2010, Australia
| | - Katja Hogendoorn
- School of Agriculture, Food and Wine, The University of Adelaide, SA 5005, Australia
| |
Collapse
|
188
|
Ruiz-García M, Chacón D, Plese T, Schuler I, Shostell JM. Mitogenomics phylogenetic relationships of the current sloth's genera and species (Bradypodidae and Megalonychidae). Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:281-299. [PMID: 28129732 DOI: 10.1080/24701394.2016.1275602] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
We sequenced the complete mitogenome of 39 sloths (19 Bradypus variegatus, 4 B. tridactylus, 1 B. pygmaeus, 1 B. torquatus, 4 Choloepus didactylus, and 10 C. hoffmanni). A Bayesian tree (BI) indicated a temporal split between Bradypus and Choloepus around 31 million years ago (MYA, Oligocene) and the other major splits within each genera during the Miocene and Pliocene. A haplotype network (MJN) estimated a lower temporal split between the sloth genera (around 23.5 MYA). Both methods detected the ancestor of B. torquatus as the first to diverge within Bradypus (21 for BI and 19 MJN), followed by that of the ancestor of B. tridactylus. The split of B. pygmaeus from the common ancestor with B. variegatus was around 12 MYA (BI) or 4.3 MYA (MJN). The splits among the previous populations of B. variegatus began around 8 MYA (BI) or 3.6 MYA (MJN). The trans-Andean population was the first to diverge from the remaining cis-Andean populations of B. variegatus. The genetic differentiation of the trans-Andean B. variegatus population relative to the cis-Andean B. variegatus is similar to that found for different species of sloths. The mitogenomic analysis resolved the differentiation of C. hoffmanni from the C. didactylus individuals of the Guiana Shield. However, one C. didactylus from the Colombian Amazon specimen was inside the C. hoffmanni clade. This could be the first example of possible natural hybridization in the Amazon of both Choloepus taxa or the existence of un-differentiable phenotypes of these two species in some Amazonian areas.
Collapse
Affiliation(s)
- Manuel Ruiz-García
- a Departamento de Biología, Facultad de Ciencias , Pontificia Universidad Javeriana , Bogotá , DC , Colombia
| | - Diego Chacón
- a Departamento de Biología, Facultad de Ciencias , Pontificia Universidad Javeriana , Bogotá , DC , Colombia
| | | | - Ingrid Schuler
- a Departamento de Biología, Facultad de Ciencias , Pontificia Universidad Javeriana , Bogotá , DC , Colombia
| | - Joseph Mark Shostell
- c Math, Science and Technology Department , University of Minnesota Crookston , Crookston , MN , USA
| |
Collapse
|
189
|
Zhang S, Wang XN, Zhang XL, Liu XZ, Zhang YJ. Complete mitochondrial genome of the endophytic fungus Pestalotiopsis fici: features and evolution. Appl Microbiol Biotechnol 2017; 101:1593-1604. [DOI: 10.1007/s00253-017-8112-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 12/11/2016] [Accepted: 12/28/2016] [Indexed: 11/25/2022]
|
190
|
Integration of mtDNA pseudogenes into the nuclear genome coincides with speciation of the human genus. A hypothesis. Mitochondrion 2016; 34:20-23. [PMID: 27979772 DOI: 10.1016/j.mito.2016.12.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 10/14/2016] [Accepted: 12/09/2016] [Indexed: 11/30/2022]
Abstract
Fragments of mitochondrial DNA are known to get inserted into nuclear DNA to form NUMTs, i.e. nuclear pseudogenes of the mtDNA. The insertion of a NUMT is a rare event. Hundreds of pseudogenes have been cataloged in the human genome. NUMTs are, in essence, a special type of mutation with their own internal timer, which is synchronized with an established molecular clock, the mtDNA. Thus insertion of NUMTs can be timed with respect to evolution milestones such as the emergence of new species. We asked whether NUMTs were inserted uniformly over time or preferentially during certain periods of evolution, as implied by the "punctuated evolution" model. To our surprise, the NUMT insertion times do appear nonrandom with at least one cluster positioned at around 2.8 million years ago (Ma). Interestingly, 2.8Ma closely corresponds to the time of emergence of the genus Homo, and to a well-documented period of major climate change ca. 2.9-2.5Ma. It is tempting to hypothesize that the insertion of NUMTs is related to the speciation process. NUMTs could be either "riders", i.e., their insertion could be facilitated by the overall higher genome rearrangement activity during speciation, or "drivers", i.e. they may more readily get fixed in the population due to positive selection associated with speciation. If correct, the hypothesis would support the idea that evolution of our genus may have happened in a rapid, punctuated manner.
Collapse
|
191
|
Quek SP, Ueda S, Gullan PJ, Kondo T, Hattori M, Itioka T, Murase K, Itino T. Nuclear DNA based species delineations ofCoccusscale insects in symbiosis with plants and ants, and the role of plant epicuticular wax in structuring associations. Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12917] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Swee-Peck Quek
- Department of Integrative Biology; University of California; Berkeley CA 94720 USA
| | - Shouhei Ueda
- Department of Biology; Faculty of Science; Shinshu University; 3-1-1 Asahi Matsumoto Nagano 390-8621 Japan
- Graduate School of Life and Environmental Science; Osaka Prefecture University; 1-1 Gakuen-cho Nakaku Sakai Osaka 599-8531 Japan
| | - Penny J. Gullan
- Division of Evolution; Ecology & Genetics; Research School of Biology; The Australian National University; Acton Canberra ACT 2601 Australia
| | - Takumasa Kondo
- Corporación Colombiana de Investigación Agropecuaria (CORPOICA); Centro de Investigación Palmira; Calle 23, Carrera 37, Continuo al Penal, Palmira Valle Colombia
| | - Mitsuru Hattori
- Department of Biology; Faculty of Science; Shinshu University; 3-1-1 Asahi Matsumoto Nagano 390-8621 Japan
- Graduate School of Fisheries and Environmental Sciences; Nagasaki University; 1-14 Bunkyo-machi Nagasaki 852-8521 Japan
| | - Takao Itioka
- Graduate School of Human and Environmental Studies; Kyoto University; Yoshida-honmachi, Sakyo- ku, Kyoto 606-8501 Japan
| | - Kaori Murase
- Graduate School of Natural Sciences, and Research Center for Biological Diversity; Nagoya City University; 1 Yamanohata, Mizuho-cho, Mizuho-ku, Nagoya Aichi 467-8501 Japan
| | - Takao Itino
- Department of Biology; Faculty of Science; Shinshu University; 3-1-1 Asahi Matsumoto Nagano 390-8621 Japan
- Institute of Mountain Science; Shinshu University; 3-1-1 Asahi, Matsumoto Nagano 390-8621 Japan
| |
Collapse
|
192
|
Layton KKS, Corstorphine EA, Hebert PDN. Exploring Canadian Echinoderm Diversity through DNA Barcodes. PLoS One 2016; 11:e0166118. [PMID: 27870868 PMCID: PMC5117606 DOI: 10.1371/journal.pone.0166118] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 10/24/2016] [Indexed: 11/19/2022] Open
Abstract
DNA barcoding has proven an effective tool for species identification in varied groups of marine invertebrates including crustaceans, molluscs, polychaetes and echinoderms. In this study, we further validate its utility by analyzing almost half of the 300 species of Echinodermata known from Canadian waters. COI sequences from 999 specimens were assigned to 145 BINs. In most cases, species discrimination was straightforward due to the large difference (25-fold) between mean intra- (0.48%) and inter- (12.0%) specific divergence. Six species were flagged for further taxonomic investigation because specimens assigned to them fell into two or three discrete sequence clusters. The potential influence of larval dispersal capacity and glacial events on patterns of genetic diversity is discussed for 19 trans-oceanic species. Although additional research is needed to clarify biogeographic patterns and resolve taxonomic questions, this study represents an important step in the assembly of a DNA barcode library for all Canadian echinoderms, a valuable resource for future biosurveillance programs.
Collapse
Affiliation(s)
- Kara K. S. Layton
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, ON, N1G 2W1, Canada
- * E-mail:
| | - Erin A. Corstorphine
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Paul D. N. Hebert
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, ON, N1G 2W1, Canada
| |
Collapse
|
193
|
E GX, Zhao YJ, Huang YF. Sheep mitochondrial heteroplasmy arises from tandem motifs and unspecific PCR amplification. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 29:91-95. [PMID: 27841052 DOI: 10.1080/24701394.2016.1242582] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The mitochondrial DNA control region (D-loop) is a widely used molecular marker in evolutionary and phylogeographic research. However, the occurrence of heteroplasmy of the D-loop region within individuals has rarely been investigated. In this study, a total of 85 Chinese sheep were used to amplify a partial D-loop region, and 15 heteroplasmic animals (17.64%) were identified. A comparative analysis of the PCR amplification and cloning of the D-loop sequences from the heteroplasmic samples revealed most of the sequencing profile from the heteroplasmic regions started at the beginning of a 75-bp random repeat motif. In addition, a total of 22 nonsyngeneic sequences with a D-loop were found in 61 of the clones obtained from the 4 random heteroplasmic and 3 homozygote animals, and their genomic locations were compared for homology. In summary, the D-Loop sequencing profiles appear to be heteroplasmic and could arise from tandem repeat motifs and unspecific replication during PCR amplification; however, they are not likely due to the presence of multiple mitochondrial genomes within an individual.
Collapse
Affiliation(s)
- Guang-Xin E
- a College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Center for Herbivores Resource Protection and Utilization , Southwest University , Chongqing , China
| | - Yong-Ju Zhao
- a College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Center for Herbivores Resource Protection and Utilization , Southwest University , Chongqing , China
| | - Yong-Fu Huang
- a College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Center for Herbivores Resource Protection and Utilization , Southwest University , Chongqing , China
| |
Collapse
|
194
|
Genetic diversity and divergence in the endangered Cape Verde warbler Acrocephalus brevipennis. CONSERV GENET 2016. [DOI: 10.1007/s10592-016-0909-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
195
|
Gajić B, Stevanović J, Radulović Ž, Kulišić Z, Vejnović B, Glavinić U, Stanimirović Z. Haplotype identification and detection of mitochondrial DNA heteroplasmy in Varroa destructor mites using ARMS and PCR-RFLP methods. EXPERIMENTAL & APPLIED ACAROLOGY 2016; 70:287-297. [PMID: 27631761 DOI: 10.1007/s10493-016-0086-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 08/08/2016] [Indexed: 06/06/2023]
Abstract
In the present study, amplification refractory mutation system (ARMS) and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) methods were used for identification of recently described Serbia 1 (S1) and Peshter 1 (P1) mitochondrial haplotypes of Varroa destructor. Based on single nucleotide polymorphisms (SNPs) within cytochrome oxidase 1 (cox1) and cytochrome b (cytb) gene sequences, a total of 64 adult V. destructor females were analyzed from locations where the S1 and P1 haplotypes had been detected previously. Results of haplotype identification obtained by ARMS and PCR-RFLP methods were completely consistent with the sequencing data. Furthermore, in some analyzed samples the occurrence of site heteroplasmy at haplotype-defining sites was detected, as it was confirmed by double peaks in the sequence chromatograms. Neither mites with simultaneous nucleotide variability, nor those with combined SNP and heteroplasmy in cox1 and cytb were found. Given that this is the first occurrence of site heteroplasmy in V. destructor, the origin of this phenomenon and possible specific traits of heteroplasmic mites have yet to be determined.
Collapse
Affiliation(s)
- Bojan Gajić
- Department of Parasitology, Faculty of Veterinary Medicine, University of Belgrade, Bul. oslobodjenja 18, Belgrade, 11000, Serbia.
| | - Jevrosima Stevanović
- Department of Biology, Faculty of Veterinary Medicine, University of Belgrade, Bul. oslobodjenja 18, Belgrade, 11000, Serbia
| | - Željko Radulović
- Laboratory for Medical Entomology, Department for Parasitology, Center of Exellence for Toxoplasmosis and Medical Entomology, Institute for Medical Research, University of Belgrade, Dr. Subotića 4, POB 102, Belgrade, 11129, Serbia
| | - Zoran Kulišić
- Department of Parasitology, Faculty of Veterinary Medicine, University of Belgrade, Bul. oslobodjenja 18, Belgrade, 11000, Serbia
| | - Branislav Vejnović
- Department of Biology, Faculty of Veterinary Medicine, University of Belgrade, Bul. oslobodjenja 18, Belgrade, 11000, Serbia
| | - Uroš Glavinić
- Department of Biology, Faculty of Veterinary Medicine, University of Belgrade, Bul. oslobodjenja 18, Belgrade, 11000, Serbia
| | - Zoran Stanimirović
- Department of Biology, Faculty of Veterinary Medicine, University of Belgrade, Bul. oslobodjenja 18, Belgrade, 11000, Serbia
| |
Collapse
|
196
|
Goodall-Copestake WP. One tunic but more than one barcode: evolutionary insights from dynamic mitochondrial DNA inSalpa thompsoni(Tunicata: Salpida). Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12915] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
197
|
Ardura A, Morote E, Kochzius M, Garcia-Vazquez E. Diversity of planktonic fish larvae along a latitudinal gradient in the Eastern Atlantic Ocean estimated through DNA barcodes. PeerJ 2016; 4:e2438. [PMID: 27761307 PMCID: PMC5068340 DOI: 10.7717/peerj.2438] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 08/13/2016] [Indexed: 11/20/2022] Open
Abstract
Mid-trophic pelagic fish are essential components of marine ecosystems because they represent the link between plankton and higher predators. Moreover, they are the basis of the most important fisheries resources; for example, in African waters. In this study, we have sampled pelagic fish larvae in the Eastern Atlantic Ocean along a latitudinal gradient between 37°N and 2°S. We have employed Bongo nets for plankton sampling and sorted visually fish and fish larvae. Using the cytochrome oxidase I gene (COI) as a DNA barcode, we have identified 44 OTUs down to species level that correspond to 14 families, with Myctophidae being the most abundant. A few species were cosmopolitan and others latitude-specific, as was expected. The latitudinal pattern of diversity did not exhibit a temperate-tropical cline; instead, it was likely correlated with environmental conditions with a decline in low-oxygen zones. Importantly, gaps and inconsistencies in reference DNA databases impeded accurate identification to the species level of 49% of the individuals. Fish sampled from tropical latitudes and some orders, such as Perciformes, Myctophiformes and Stomiiformes, were largely unidentified due to incomplete references. Some larvae were identified based on morphology and COI analysis for comparing time and costs employed from each methodology. These results suggest the need of reinforcing DNA barcoding reference datasets of Atlantic bathypelagic tropical fish that, as main prey of top predators, are crucial for ecosystem-based management of fisheries resources.
Collapse
Affiliation(s)
- Alba Ardura
- USR 3278-CRIOBE-CNRS-EPHE, Laboratoire d'excellence "CORAIL", Université de Perpignan , Perpignan , France
| | - Elvira Morote
- Biologia Animal, Universidad de Almeria , Almeria , Spain
| | - Marc Kochzius
- Department of Marine Biology, Vrije Universiteit Brussel , Brussels , Belgium
| | | |
Collapse
|
198
|
Unbiased Mitoproteome Analyses Confirm Non-canonical RNA, Expanded Codon Translations. Comput Struct Biotechnol J 2016; 14:391-403. [PMID: 27830053 PMCID: PMC5094600 DOI: 10.1016/j.csbj.2016.09.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 09/28/2016] [Accepted: 09/29/2016] [Indexed: 01/14/2023] Open
Abstract
Proteomic MS/MS mass spectrometry detections are usually biased towards peptides cleaved by experimentally added digestion enzyme(s). Hence peptides resulting from spontaneous degradation and natural proteolysis usually remain undetected. Previous analyses of tryptic human proteome data (cleavage after K, R) detected non-canonical tryptic peptides translated according to tetra- and pentacodons (codons expanded by silent mono- and dinucleotides), and from transcripts systematically (a) deleting mono-, dinucleotides after trinucleotides (delRNAs), (b) exchanging nucleotides according to 23 bijective transformations. Nine symmetric and fourteen asymmetric nucleotide exchanges (X ↔ Y, e.g. A ↔ C; and X → Y → Z → X, e.g. A → C → G → A) produce swinger RNAs. Here unbiased reanalyses of these proteomic data detect preferentially non-canonical tryptic peptides despite assuming random cleavage. Unbiased analyses couldn't reconstruct experimental tryptic digestion if most detected non-canonical peptides were false positives. Detected non-tryptic non-canonical peptides map preferentially on corresponding, previously described non-canonical transcripts, as for tryptic non-canonical peptides. Hence unbiased analyses independently confirm previous trypsin-biased analyses that showed translations of del- and swinger RNA and expanded codons. Accounting for natural proteolysis completes trypsin-biased mitopeptidome analyses, independently confirms non-canonical transcriptions and translations.
Collapse
|
199
|
Malaquias MAE, Ohnheiser LT, Oskars TR, Willassen E. Diversity and systematics of philinid snails (Gastropoda: Cephalaspidea) in West Africa with remarks on the biogeography of the region. Zool J Linn Soc 2016. [DOI: 10.1111/zoj.12478] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Manuel António E. Malaquias
- Phylogenetic Systematics and Evolution Research Group; Section of Taxonomy and Evolution; Department of Natural History; University Museum of Bergen; University of Bergen; PB 7800 5020 Bergen Norway
| | - Lena T. Ohnheiser
- Phylogenetic Systematics and Evolution Research Group; Section of Taxonomy and Evolution; Department of Natural History; University Museum of Bergen; University of Bergen; PB 7800 5020 Bergen Norway
| | - Trond R. Oskars
- Phylogenetic Systematics and Evolution Research Group; Section of Taxonomy and Evolution; Department of Natural History; University Museum of Bergen; University of Bergen; PB 7800 5020 Bergen Norway
| | - Endre Willassen
- Phylogenetic Systematics and Evolution Research Group; Section of Taxonomy and Evolution; Department of Natural History; University Museum of Bergen; University of Bergen; PB 7800 5020 Bergen Norway
| |
Collapse
|
200
|
The use of DNA barcode for identifying species of Oxysarcodexia Townsend (Diptera: Sarcophagidae): A preliminary survey. Acta Trop 2016; 161:73-8. [PMID: 27260665 DOI: 10.1016/j.actatropica.2016.05.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2016] [Revised: 05/28/2016] [Accepted: 05/30/2016] [Indexed: 11/23/2022]
Abstract
Oxysarcodexia is one of the Neotropical richest genera within the Sarcophagidae family. Medical, veterinary and forensic importance of these flies are due to their association with corpses, cases of myiasis in humans and domestic animals, and being pathogen carriers. Regarding morphological identification, molecular techniques, especially the DNA-based ones, arise as useful alternatives or complementary methodologies for species identification. Thus, in this study we aimed to investigate the potential of the COI marker (barcode region) to delimit Oxysarcodexia species in comparison with the morphological identification criteria. A COI fragment was amplified and the length of the sequences after alignment were of 648bp (149 parsimoniously informative variable sites). According to the Neighbor-Joining phylogenetic tree, specimens of the same morphological species were clustered in monophyletic clades (82-100% bootstrap branch support). Species-level resolution thus achieved was successful, despite low interspecific divergence (1.8-2.3%) and since interspecific variation was higher than intraspecific divergence (0.1-1.2%). Therefore, the use of COI barcode sequences supports differentiation and identification of the Oxysarcodexia species studied.
Collapse
|