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Uvizl M, Puechmaille SJ, Power S, Pippel M, Carthy S, Haerty W, Myers EW, Teeling EC, Huang Z. Comparative Genome Microsynteny Illuminates the Fast Evolution of Nuclear Mitochondrial Segments (NUMTs) in Mammals. Mol Biol Evol 2024; 41:msad278. [PMID: 38124445 PMCID: PMC10764098 DOI: 10.1093/molbev/msad278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 11/16/2023] [Accepted: 12/12/2023] [Indexed: 12/23/2023] Open
Abstract
The escape of DNA from mitochondria into the nuclear genome (nuclear mitochondrial DNA, NUMT) is an ongoing process. Although pervasively observed in eukaryotic genomes, their evolutionary trajectories in a mammal-wide context are poorly understood. The main challenge lies in the orthology assignment of NUMTs across species due to their fast evolution and chromosomal rearrangements over the past 200 million years. To address this issue, we systematically investigated the characteristics of NUMT insertions in 45 mammalian genomes and established a novel, synteny-based method to accurately predict orthologous NUMTs and ascertain their evolution across mammals. With a series of comparative analyses across taxa, we revealed that NUMTs may originate from nonrandom regions in mtDNA, are likely found in transposon-rich and intergenic regions, and unlikely code for functional proteins. Using our synteny-based approach, we leveraged 630 pairwise comparisons of genome-wide microsynteny and predicted the NUMT orthology relationships across 36 mammals. With the phylogenetic patterns of NUMT presence-and-absence across taxa, we constructed the ancestral state of NUMTs given the mammal tree using a coalescent method. We found support on the ancestral node of Fereuungulata within Laurasiatheria, whose subordinal relationships are still controversial. This study broadens our knowledge on NUMT insertion and evolution in mammalian genomes and highlights the merit of NUMTs as alternative genetic markers in phylogenetic inference.
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Affiliation(s)
- Marek Uvizl
- Department of Zoology, National Museum, 19300 Prague, Czech Republic
- Department of Zoology, Faculty of Science, Charles University, 12844 Prague, Czech Republic
| | - Sebastien J Puechmaille
- Institut des Sciences de l’Evolution de Montpellier (ISEM), University of Montpellier, 34095 Montpellier, France
- Institut Universitaire de France, Paris, France
| | - Sarahjane Power
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Martin Pippel
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
- National Bioinformatics Infrastructure Sweden, Uppsala, Sweden
| | - Samuel Carthy
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Wilfried Haerty
- Earlham Institute, Norwich Research Park, Colney Ln, NR4 7UZ Norwich, UK
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Eugene W Myers
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Emma C Teeling
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Zixia Huang
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
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2
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Protachevicz AP, Paulitsch F, Klepa MS, Hainosz J, Olchanheski LR, Hungria M, Stefania da Silva Batista J. Pioneering Desmodium spp. are nodulated by natural populations of stress-tolerant alpha- and beta-rhizobia. Braz J Microbiol 2023; 54:3127-3135. [PMID: 37673840 PMCID: PMC10689651 DOI: 10.1007/s42770-023-01113-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 08/23/2023] [Indexed: 09/08/2023] Open
Abstract
The rhizobia-Desmodium (Leguminosae, Papilionoideae) symbiosis is generally described by its specificity with alpha-rhizobia, especially with Bradyrhizobium. Our study aimed to isolate rhizobia from root nodules of native D. barbatum, D. incanum, and D. discolor, collected in remnants of the biomes of Atlantic Forest and Cerrado in protected areas of the Paraná State, southern Brazil. Based on the 16S rRNA phylogeny, 18 out of 29 isolates were classified as Alphaproteobacteria (Bradyrhizobium and Allorhizobium/Rhizobium) and 11 as Betaproteobacteria (Paraburkholderia). Phylogeny of the recA gene of the alpha-rhizobia resulted in ten main clades, of which two did not group with any described rhizobial species. In the 16S rRNA phylogeny of the beta-rhizobia, Paraburkholderia strains from the same host and conservation unity occupied the same clade. Phenotypic characterization of representative strains revealed the ability of Desmodium rhizobia to grow under stressful conditions such as high temperature, salinity, low pH conditions, and tolerance of heavy metals and xenobiotic compounds. Contrasting with previous reports, our results revealed that Brazilian native Desmodium can exploit symbiotic interactions with stress-tolerant strains of alpha- and beta-rhizobia. Stress tolerance can highly contribute to the ecological success of Desmodium in this phytogeographic region, possibly relating to its pioneering ability in Brazil. We propose Desmodium as a promising model for studies of plant-rhizobia interactions.
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Affiliation(s)
- Ana Paolla Protachevicz
- Departamento de Biologia Estrutural, Molecular E Genética, Universidade Estadual de Ponta Grossa, C.P. 6001, Ponta Grossa, PR, 84030-900, Brazil
| | - Fabiane Paulitsch
- Departamento de Biologia Estrutural, Molecular E Genética, Universidade Estadual de Ponta Grossa, C.P. 6001, Ponta Grossa, PR, 84030-900, Brazil
| | | | - Jessica Hainosz
- Departamento de Biologia Estrutural, Molecular E Genética, Universidade Estadual de Ponta Grossa, C.P. 6001, Ponta Grossa, PR, 84030-900, Brazil
| | - Luiz Ricardo Olchanheski
- Departamento de Biologia Estrutural, Molecular E Genética, Universidade Estadual de Ponta Grossa, C.P. 6001, Ponta Grossa, PR, 84030-900, Brazil
| | | | - Jesiane Stefania da Silva Batista
- Departamento de Biologia Estrutural, Molecular E Genética, Universidade Estadual de Ponta Grossa, C.P. 6001, Ponta Grossa, PR, 84030-900, Brazil.
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3
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Tao Y, He C, Lin D, Gu Z, Pu W. Comprehensive Identification of Mitochondrial Pseudogenes (NUMTs) in the Human Telomere-to-Telomere Reference Genome. Genes (Basel) 2023; 14:2092. [PMID: 38003036 PMCID: PMC10671835 DOI: 10.3390/genes14112092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 11/09/2023] [Accepted: 11/12/2023] [Indexed: 11/26/2023] Open
Abstract
Practices related to mitochondrial research have long been hindered by the presence of mitochondrial pseudogenes within the nuclear genome (NUMTs). Even though partially assembled human reference genomes like hg38 have included NUMTs compilation, the exhaustive NUMTs within the only complete reference genome (T2T-CHR13) remain unknown. Here, we comprehensively identified the fixed NUMTs within the reference genome using human pan-mitogenome (HPMT) from GeneBank. The inclusion of HPMT serves the purpose of establishing an authentic mitochondrial DNA (mtDNA) mutational spectrum for the identification of NUMTs, distinguishing it from the polymorphic variations found in NUMTs. Using HPMT, we identified approximately 10% of additional NUMTs in three human reference genomes under stricter thresholds. And we also observed an approximate 6% increase in NUMTs in T2T-CHR13 compared to hg38, including NUMTs on the short arms of chromosomes 13, 14, and 15 that were not assembled previously. Furthermore, alignments based on 20-mer from mtDNA suggested the presence of more mtDNA-like short segments within the nuclear genome, which should be avoided for short amplicon or cell free mtDNA detection. Finally, through the assay of transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) on cell lines before and after mtDNA elimination, we concluded that NUMTs have a minimal impact on bulk ATAC-seq, even though 16% of sequencing data originated from mtDNA.
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Affiliation(s)
- Yichen Tao
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200438, China; (Y.T.); (D.L.)
| | - Chengpeng He
- Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, Nansha District, Guangzhou 511458, China;
| | - Deng Lin
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200438, China; (Y.T.); (D.L.)
| | - Zhenglong Gu
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200438, China; (Y.T.); (D.L.)
- Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, Nansha District, Guangzhou 511458, China;
| | - Weilin Pu
- Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, Nansha District, Guangzhou 511458, China;
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Frolova AA, Merkel AY, Kevbrin VV, Kopitsyn DS, Slobodkin AI. Sulfurospirillum tamanensis sp. nov., a Facultatively Anaerobic Alkaliphilic Bacterium from a Terrestrial Mud Volcano. Microbiology (Reading) 2023. [DOI: 10.1134/s0026261722602226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023] Open
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Lucas T, Vincent B, Eric P. Translocation of mitochondrial DNA into the nuclear genome blurs phylogeographic and conservation genetic studies in seabirds. ROYAL SOCIETY OPEN SCIENCE 2022; 9:211888. [PMID: 35719890 PMCID: PMC9198517 DOI: 10.1098/rsos.211888] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 04/19/2022] [Indexed: 05/03/2023]
Abstract
Mitochondrial DNA (mtDNA) translocated into the nuclear genome (numt), when co-analysed with genuine mtDNA, could plague phylogeographic studies. To evaluate numt-related biases in population genetics parameters in birds, which are prone to accumulating numts, we targeted the mitochondrial mt-cytb gene. We looked at 13 populations of Audubon's shearwater (Puffinus lherminieri), including five mitochondrial lineages. mt-cytb homologue and paralogue (numt) sequences were determined by Sanger sequencing with and without prior exonuclease digestion of nuclear DNA. Numts formed monophyletic clades corresponding to three of the five mitochondrial lineages tested (the remaining two forming a paraphyletic group). Nineteen percent of numt alleles fell outside of their expected mitochondrial clade, a pattern consistent with multiple translocation events, incomplete lineage sorting (ILS), and/or introgression. When co-analysing mt-cytb paralogues and homologues, excluding individuals with ambiguities underestimates genetic diversity (4%) and differentiation (11%) among least-sampled populations. Removing ambiguous sites drops the proportion of inter-lineage genetic variance by 63%. While co-analysing numts with mitochondrial sequences can lead to severe bias and information loss in bird phylogeographic studies, the separate analysis of genuine mitochondrial loci and their nuclear paralogues can shed light on numt molecular evolution, as well as evolutionary processes such as ILS and introgression.
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Affiliation(s)
- Torres Lucas
- Centre d'Etudes Biologiques de Chizé, UMR 7372, CNRS - La Rochelle Universite, Villiers en Bois, France
- Littoral, Environnement et Sociétés, UMR 7266 CNRS - La Rochelle Université, La Rochelle, France
| | - Bretagnolle Vincent
- Centre d'Etudes Biologiques de Chizé, UMR 7372, CNRS - La Rochelle Universite, Villiers en Bois, France
| | - Pante Eric
- Littoral, Environnement et Sociétés, UMR 7266 CNRS - La Rochelle Université, La Rochelle, France
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6
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Hazkani-Covo E. A Burst of Numt Insertion in the Dasyuridae Family During Marsupial Evolution. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.844443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Nuclear pseudogenes of mitochondrial origin (numts) are common in all eukaryotes. Our previous scan of numts in sequenced nuclear genomes suggested that the highest numt content currently known in animals is that in the gray short-tailed opossum. The present work sought to determine numt content in marsupials and to compare it to those in placental and monothematic mammals as well as in non-mammalian vertebrates. To achieve this, 70 vertebrate species with available nuclear and mitochondrial genomes were scanned for numt content. An extreme numt content was found in the Dasyuridae, with 3,450 in Sarcophilus harrisii (1,955 kb) and 2,813 in Antechinus flavipes (847 kb). The evolutionarily closest species analyzed, the extinct Thylacinus cynocephalus belonging to the Thylacindae family, had only 435 numts (238 kb). These two Dasyuridae genomes featured the highest numt content identified in animals to date. A phylogenetic analysis of numts longer than 300 bp, using a Diprotodonita mitochondrial tree, indicated a burst of numt insertion that began before the divergence of the Dasyurini and Phascogalini, reaching a peak in the early evolution of the two tribes. No comparable increase was found in the early divergent species T. cynocephalus. Divergence of the Dasyuridae tribes has been previously dated to shortly after the Miocene climate transition, characterized by a rapid temperature decline. Interestingly, deviation from optimal growth temperature is one of the environmental factors reported to increase numt insertions in a laboratory setting.
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Han Y, Hou Z, He Q, Zhang X, Yan K, Han R, Liang Z. Genome-Wide Characterization and Expression Analysis of bZIP Gene Family Under Abiotic Stress in Glycyrrhiza uralensis. Front Genet 2021; 12:754237. [PMID: 34675967 PMCID: PMC8525656 DOI: 10.3389/fgene.2021.754237] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 09/13/2021] [Indexed: 11/24/2022] Open
Abstract
bZIP gene family is one of the largest transcription factor families. It plays an important role in plant growth, metabolic, and environmental response. However, complete genome-wide investigation of bZIP gene family in Glycyrrhiza uralensis remains unexplained. In this study, 66 putative bZIP genes in the genome of G. uralensis were identified. And their evolutionary classification, physicochemical properties, conserved domain, functional differentiation, and the expression level under different stress conditions were further analyzed. All the members were clustered into 13 subfamilies (A–K, M, and S). A total of 10 conserved motifs were found in GubZIP proteins. Members from the same subfamily shared highly similar gene structures and conserved domains. Tandem duplication events acted as a major driving force for the evolution of bZIP gene family in G. uralensis. Cis-acting elements and protein–protein interaction networks showed that GubZIPs in one subfamily are involved in multiple functions, while some GubZIPs from different subfamilies may share the same functional category. The miRNA network targeting GubZIPs showed that the regulation at the transcriptional level may affect protein–protein interaction networks. We suspected that domain-mediated interactions may categorize a protein family into subfamilies in G. uralensis. Furthermore, the tissue-specific gene expression patterns of GubZIPs were analyzed using the public RNA-seq data. Moreover, gene expression level of 66 bZIP family members under abiotic stress treatments was quantified by using qRT-PCR. The results of this study may serve as potential candidates for functional characterization in the future.
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Affiliation(s)
- Yuxuan Han
- The Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Zhuoni Hou
- The Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Qiuling He
- The Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Xuemin Zhang
- Tasly R&D Institute, Tasly Holding Group Co., Ltd., Tianjin, China
| | - Kaijing Yan
- Tasly R&D Institute, Tasly Holding Group Co., Ltd., Tianjin, China
| | - Ruilian Han
- Institute of Landscape and Plant Ecology, The School of Engineering and Architecture, Zhejiang Sci-tech University, Hangzhou, China
| | - Zongsuo Liang
- The Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
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8
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Zhang G, Geng D, Guo Q, Liu W, Li S, Gao W, Wang Y, Zhang M, Wang Y, Bu Y, Niu H. Genomic landscape of mitochondrial DNA insertions in 23 bat genomes: characteristics, loci, phylogeny, and polymorphism. Integr Zool 2021; 17:890-903. [PMID: 34496458 DOI: 10.1111/1749-4877.12582] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The transfer of mitochondrial DNA to the nuclear genome gives rise to the nuclear DNA sequences of mitochondrial origin (NUMTs), considered as a driving force in genome evolution. In this study, NUMTs in 23 bat genomes were investigated and compared systematically. The results showed that NUMTs existed in 22 genomes except for Noctilio leporinus, suggesting that mitochondrial fragment insertion in the nuclear genome was a common event in bat genomes. However, remarkable variations in NUMTs number, cumulative length, and proportion in the nuclear genome were discovered across bat species. Further orthologous NUMT loci analysis of the Phyllostomidae family indicated that the NUMTs insertion events in bat genomes were homoplasy-free. The NUMTs were mainly inserted into the intergenic regions, particularly, co-localized with repetitive sequences (especially transposable elements). However, several NUMTs were inserted into genes, some of which were in the exon region of functional genes. One NUMT in the genome of Pteropus alecto surprisingly matched with cDNA of ATP8B3 that provided evidence of NUMTs with coding function. Phylogenic analysis on NUMTs originating from COXI and COXII loci highlighted 2 clusters of Yinpterochiroptera and Yangochiroptera for Chiroptera. Seven NUMTs from Rhinolophus ferrumequinum were amplified, and the sequencing results confirmed the reliability of the NUMT analysis. One of them was polymorphic for the presence or absence of the NUMT insertion, and each genotype of NUMT loci showed a distinct regional distribution pattern. The information obtained in this study provides novel insights into the NUMT organization and features in bat genomes and establishes a basis for further studying of the evolution of bat species.
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Affiliation(s)
- Guojun Zhang
- College of Life Sciences, Henan Normal University, Xinxiang, China.,School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, China
| | - Deqi Geng
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Qiulin Guo
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Wei Liu
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Shufen Li
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Wujun Gao
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Yongfei Wang
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Min Zhang
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Yilin Wang
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Yanzhen Bu
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Hongxing Niu
- College of Life Sciences, Henan Normal University, Xinxiang, China
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Pseudodesulfovibrio alkaliphilus, sp. nov., an alkaliphilic sulfate-reducing bacterium isolated from a terrestrial mud volcano. Antonie van Leeuwenhoek 2021; 114:1387-1397. [PMID: 34212258 DOI: 10.1007/s10482-021-01608-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 06/23/2021] [Indexed: 10/21/2022]
Abstract
The diversity of anaerobic microorganisms in terrestrial mud volcanoes is largely unexplored. Here we report the isolation of a novel sulfate-reducing alkaliphilic bacterium (strain F-1T) from a terrestrial mud volcano located at the Taman peninsula, Russia. Cells of strain F-1T were Gram-negative motile vibrios with a single polar flagellum; 2.0-4.0 µm in length and 0.5 µm in diameter. The temperature range for growth was 6-37 °C, with an optimum at 24 °C. The pH range for growth was 7.0-10.5, with an optimum at pH 9.5. Strain F-1T utilized lactate, pyruvate, and molecular hydrogen as electron donors and sulfate, sulfite, thiosulfate, elemental sulfur, fumarate or arsenate as electron acceptors. In the presence of sulfate, the end products of lactate oxidation were acetate, H2S and CO2. Lactate and pyruvate could also be fermented. The major product of lactate fermentation was acetate. The main cellular fatty acids were anteiso-C15:0, C16:0, C18:0, and iso-C17:1ω8. Phylogenetic analysis revealed that strain F-1T was most closely related to Pseudodesulfovibrio aespoeensis (98.05% similarity). The total size of the genome of the novel isolate was 3.23 Mb and the genomic DNA G + C content was 61.93 mol%. The genome contained all genes essential for dissimilatory sulfate reduction. We propose to assign strain F-1T to the genus Pseudodesulfovibrio, as a new species, Pseudodesulfovibrio alkaliphilus sp. nov. The type strain is F-1T (= KCTC 15918T = VKM B-3405T).
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Smart U, Cihlar JC, Budowle B. International Wildlife Trafficking: A perspective on the challenges and potential forensic genetics solutions. Forensic Sci Int Genet 2021; 54:102551. [PMID: 34134047 DOI: 10.1016/j.fsigen.2021.102551] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 06/03/2021] [Accepted: 06/04/2021] [Indexed: 12/29/2022]
Abstract
International wildlife trafficking (IWT) is a thriving and pervasive illegal enterprise that adversely affects modern societies. Yet, despite being globally recognized as a threat to biodiversity, national security, economy, and biosecurity, IWT remains largely unabated and is proliferating at an alarming rate. The increase in IWT is generally attributed to a lack of prioritization to curb wildlife crime through legal and scientific infrastructure. This review: (1) lays out the damaging scope and influence of IWT; (2) discusses the potential of DNA marker systems, barcodes, and emerging molecular technologies, such as long-read portable sequencing, to facilitate rapid, in situ identification of species and individuals; and (3) encourages initiatives that promote quality and innovation. Interdisciplinary collaboration promises to be one of the most effective ways forward to surmounting the complex scientific and legal challenges posed by IWT.
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Affiliation(s)
- Utpal Smart
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp, Bowie Blvd., Fort Worth, TX 76107, USA.
| | - Jennifer Churchill Cihlar
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp, Bowie Blvd., Fort Worth, TX 76107, USA; Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA
| | - Bruce Budowle
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp, Bowie Blvd., Fort Worth, TX 76107, USA; Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA
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Anaerotalea alkaliphila gen. nov., sp. nov., an alkaliphilic, anaerobic, fermentative bacterium isolated from a terrestrial mud volcano. Extremophiles 2021; 25:301-309. [PMID: 33891175 DOI: 10.1007/s00792-021-01229-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 04/12/2021] [Indexed: 02/03/2023]
Abstract
Diversity of extremophilic microorganisms in mud volcanoes is largely unexplored. Here, we report the isolation of a novel alkaliphilic, mesophilic, fermentative bacterium (strain F-3apT) from a terrestrial mud volcano located at the Taman peninsula, Russia. Cells of strain F-3apT are Gram-stain-positive non-motile rods. The formation of endospores is not observed. The temperature range for growth is 14-42 °C, with an optimum at 37 °C. The pH range for growth is 7.5-11.0, with an optimum at pH 9.0. The isolate utilizes various organic polymeric substances, organic acids, carbohydrates, and proteinaceous compounds. The end products of glucose fermentation are ethanol, CO2, and H2. The major cellular fatty acids of strain F-3apT are C16:0, C16:1, and C14:0. Phylogenetic analysis reveals that strain F-3apT belongs to the order Clostridiales, with less than 91% of 16S rRNA gene sequence similarity to any species with a validly published name. The total size of the genome of strain F-3apT is 2.98 Mb, and a genomic DNA G + C content is 56.78 mol%. The whole-genome phylogenetic analysis confirms that strain F-3apT forms a distinct lineage within Clostridia. We propose to assign strain F-3apT to a new species of a novel genus Anaerotalea alkaliphila gen. nov., sp. nov. The type strain is F-3apT (= KCTC 15917 T = VKM B-3406 T).
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Osman MM, Hassan HY, Elnour MA, Makkan H, Gebremeskel EI, Gais T, Koko ME, Soodyall H, Ibrahim ME. Mitochondrial HVRI and whole mitogenome sequence variations portray similar scenarios on the genetic structure and ancestry of northeast Africans. Meta Gene 2021. [DOI: 10.1016/j.mgene.2020.100837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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13
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Pereira RJ, Ruiz‐Ruano FJ, Thomas CJ, Pérez‐Ruiz M, Jiménez‐Bartolomé M, Liu S, Torre J, Bella JL. Mind the
numt
: Finding informative mitochondrial markers in a giant grasshopper genome. J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12446] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Ricardo J. Pereira
- Division of Evolutionary Biology Faculty of Biology II Ludwig‐ Maximilians‐Universität München Planegg‐Martinsried Germany
| | - Francisco J. Ruiz‐Ruano
- Department of Genetics University of Granada Granada Spain
- Department of Ecology and Genetics – Evolutionary Biology Evolutionary Biology Centre (EBC) Uppsala University Uppsala Sweden
- Department of Organismal Biology – Systematic Biology Evolutionary Biology Centre (EBC) Uppsala University Uppsala Sweden
| | - Callum J.E. Thomas
- Division of Evolutionary Biology Faculty of Biology II Ludwig‐ Maximilians‐Universität München Planegg‐Martinsried Germany
| | - Mar Pérez‐Ruiz
- Departamento de Biología (Genética) Facultad de Ciencias Universidad Autónoma de Madrid Madrid Spain
| | - Miguel Jiménez‐Bartolomé
- Departamento de Biología (Genética) Facultad de Ciencias Universidad Autónoma de Madrid Madrid Spain
| | - Shanlin Liu
- Department of Entomology College of Plant Protection China Agricultural University Beijing China
| | - Joaquina Torre
- Departamento de Biología (Genética) Facultad de Ciencias Universidad Autónoma de Madrid Madrid Spain
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC‐UAM) Universidad Autónoma de Madrid Madrid Spain
| | - José L. Bella
- Departamento de Biología (Genética) Facultad de Ciencias Universidad Autónoma de Madrid Madrid Spain
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC‐UAM) Universidad Autónoma de Madrid Madrid Spain
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Hoser SM, Hoffmann A, Meindl A, Gamper M, Fallmann J, Bernhart SH, Müller L, Ploner M, Misslinger M, Kremser L, Lindner H, Geley S, Schaal H, Stadler PF, Huettenhofer A. Intronic tRNAs of mitochondrial origin regulate constitutive and alternative splicing. Genome Biol 2020; 21:299. [PMID: 33292386 PMCID: PMC7722341 DOI: 10.1186/s13059-020-02199-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 11/09/2020] [Indexed: 02/19/2023] Open
Abstract
BACKGROUND The presence of nuclear mitochondrial DNA (numtDNA) has been reported within several nuclear genomes. Next to mitochondrial protein-coding genes, numtDNA sequences also encode for mitochondrial tRNA genes. However, the biological roles of numtDNA remain elusive. RESULTS Employing in silico analysis, we identify 281 mitochondrial tRNA homologs in the human genome, which we term nimtRNAs (nuclear intronic mitochondrial-derived tRNAs), being contained within introns of 76 nuclear host genes. Despite base changes in nimtRNAs when compared to their mtRNA homologs, a canonical tRNA cloverleaf structure is maintained. To address potential functions of intronic nimtRNAs, we insert them into introns of constitutive and alternative splicing reporters and demonstrate that nimtRNAs promote pre-mRNA splicing, dependent on the number and positioning of nimtRNA genes and splice site recognition efficiency. A mutational analysis reveals that the nimtRNA cloverleaf structure is required for the observed splicing increase. Utilizing a CRISPR/Cas9 approach, we show that a partial deletion of a single endogenous nimtRNALys within intron 28 of the PPFIBP1 gene decreases inclusion of the downstream-located exon 29 of the PPFIBP1 mRNA. By employing a pull-down approach followed by mass spectrometry, a 3'-splice site-associated protein network is identified, including KHDRBS1, which we show directly interacts with nimtRNATyr by an electrophoretic mobility shift assay. CONCLUSIONS We propose that nimtRNAs, along with associated protein factors, can act as a novel class of intronic splicing regulatory elements in the human genome by participating in the regulation of splicing.
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Affiliation(s)
- Simon M Hoser
- Division of Genomics and RNomics, Biocenter, Medical University of Innsbruck, 6020, Innsbruck, Austria.
| | - Anne Hoffmann
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München at the University of Leipzig and University Hospital Leipzig, Philipp-Rosenthal-Str. 27, 04103, Leipzig, Germany
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, 04107, Leipzig, Germany
| | - Andreas Meindl
- Division of Genomics and RNomics, Biocenter, Medical University of Innsbruck, 6020, Innsbruck, Austria
| | - Maximilian Gamper
- Division of Genomics and RNomics, Biocenter, Medical University of Innsbruck, 6020, Innsbruck, Austria
| | - Jörg Fallmann
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, 04107, Leipzig, Germany
| | - Stephan H Bernhart
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, 04107, Leipzig, Germany
| | - Lisa Müller
- Institute for Virology, Medical Faculty Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
| | - Melanie Ploner
- Division of Genomics and RNomics, Biocenter, Medical University of Innsbruck, 6020, Innsbruck, Austria
| | - Matthias Misslinger
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Leopold Kremser
- Division of Clinical Biochemistry, Protein Micro-Analysis Facility, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Herbert Lindner
- Division of Clinical Biochemistry, Protein Micro-Analysis Facility, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Stephan Geley
- Institute of Pathophysiology, Biocenter, Medical University of Innsbruck, 6020, Innsbruck, Austria
| | - Heiner Schaal
- Institute for Virology, Medical Faculty Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, 04107, Leipzig, Germany
- Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, 04103, Leipzig, Germany
| | - Alexander Huettenhofer
- Division of Genomics and RNomics, Biocenter, Medical University of Innsbruck, 6020, Innsbruck, Austria.
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Munlela B, João ED, Donato CM, Strydom A, Boene SS, Chissaque A, Bauhofer AFL, Langa J, Cassocera M, Cossa-Moiane I, Chilaúle JJ, O’Neill HG, de Deus N. Whole Genome Characterization and Evolutionary Analysis of G1P[8] Rotavirus A Strains during the Pre- and Post-Vaccine Periods in Mozambique (2012-2017). Pathogens 2020; 9:pathogens9121026. [PMID: 33291333 PMCID: PMC7762294 DOI: 10.3390/pathogens9121026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 12/03/2020] [Accepted: 12/03/2020] [Indexed: 11/22/2022] Open
Abstract
Mozambique introduced the Rotarix® vaccine (GSK Biologicals, Rixensart, Belgium) into the National Immunization Program in September 2015. Although G1P[8] was one of the most prevalent genotypes between 2012 and 2017 in Mozambique, no complete genomes had been sequenced to date. Here we report whole genome sequence analysis for 36 G1P[8] strains using an Illumina MiSeq platform. All strains exhibited a Wa-like genetic backbone (G1-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1). Phylogenetic analysis showed that most of the Mozambican strains clustered closely together in a conserved clade for the entire genome. No distinct clustering for pre- and post-vaccine strains were observed. These findings may suggest no selective pressure by the introduction of the Rotarix® vaccine in 2015. Two strains (HJM1646 and HGM0544) showed varied clustering for the entire genome, suggesting reassortment, whereas a further strain obtained from a rural area (MAN0033) clustered separately for all gene segments. Bayesian analysis for the VP7 and VP4 encoding gene segments supported the phylogenetic analysis and indicated a possible introduction from India around 2011.7 and 2013.0 for the main Mozambican clade. Continued monitoring of rotavirus strains in the post-vaccine period is required to fully understand the impact of vaccine introduction on the diversity and evolution of rotavirus strains.
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Affiliation(s)
- Benilde Munlela
- Instituto Nacional de Saúde (INS), Distrito de Marracuene, Maputo 3943, Mozambique; (S.S.B.); (A.C.); (A.F.L.B.); (J.L.); (M.C.); (I.C.-M.); (J.J.C.); (N.d.D.)
- Centro de Biotecnologia, Universidade Eduardo Mondlane, Maputo 3453, Mozambique
- Correspondence: or (B.M.); (E.D.J.); Tel.: +258-848814087 (B.M.); +258-827479229 (E.D.J.)
| | - Eva D. João
- Instituto Nacional de Saúde (INS), Distrito de Marracuene, Maputo 3943, Mozambique; (S.S.B.); (A.C.); (A.F.L.B.); (J.L.); (M.C.); (I.C.-M.); (J.J.C.); (N.d.D.)
- Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa, UNL, Rua da Junqueira 100, 1349-008 Lisbon, Portugal
- Correspondence: or (B.M.); (E.D.J.); Tel.: +258-848814087 (B.M.); +258-827479229 (E.D.J.)
| | - Celeste M. Donato
- Enteric Diseases Group, Murdoch Children’s Research Institute, 50 Flemington Road, Parkville, Melbourne 3052, Australia;
- Department of Paediatrics, the University of Melbourne, Parkville 3010, Australia
- Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton 3800, Australia
| | - Amy Strydom
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, 205 Nelson Mandela Avenue, Bloemfontein 9301, South Africa; (A.S.); (H.G.O.)
| | - Simone S. Boene
- Instituto Nacional de Saúde (INS), Distrito de Marracuene, Maputo 3943, Mozambique; (S.S.B.); (A.C.); (A.F.L.B.); (J.L.); (M.C.); (I.C.-M.); (J.J.C.); (N.d.D.)
- Centro de Biotecnologia, Universidade Eduardo Mondlane, Maputo 3453, Mozambique
| | - Assucênio Chissaque
- Instituto Nacional de Saúde (INS), Distrito de Marracuene, Maputo 3943, Mozambique; (S.S.B.); (A.C.); (A.F.L.B.); (J.L.); (M.C.); (I.C.-M.); (J.J.C.); (N.d.D.)
- Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa, UNL, Rua da Junqueira 100, 1349-008 Lisbon, Portugal
| | - Adilson F. L. Bauhofer
- Instituto Nacional de Saúde (INS), Distrito de Marracuene, Maputo 3943, Mozambique; (S.S.B.); (A.C.); (A.F.L.B.); (J.L.); (M.C.); (I.C.-M.); (J.J.C.); (N.d.D.)
- Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa, UNL, Rua da Junqueira 100, 1349-008 Lisbon, Portugal
| | - Jerónimo Langa
- Instituto Nacional de Saúde (INS), Distrito de Marracuene, Maputo 3943, Mozambique; (S.S.B.); (A.C.); (A.F.L.B.); (J.L.); (M.C.); (I.C.-M.); (J.J.C.); (N.d.D.)
| | - Marta Cassocera
- Instituto Nacional de Saúde (INS), Distrito de Marracuene, Maputo 3943, Mozambique; (S.S.B.); (A.C.); (A.F.L.B.); (J.L.); (M.C.); (I.C.-M.); (J.J.C.); (N.d.D.)
- Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa, UNL, Rua da Junqueira 100, 1349-008 Lisbon, Portugal
| | - Idalécia Cossa-Moiane
- Instituto Nacional de Saúde (INS), Distrito de Marracuene, Maputo 3943, Mozambique; (S.S.B.); (A.C.); (A.F.L.B.); (J.L.); (M.C.); (I.C.-M.); (J.J.C.); (N.d.D.)
- Institute of Tropical Medicine (ITM), Kronenburgstraat 43, 2000 Antwerp, Belgium
| | - Jorfélia J. Chilaúle
- Instituto Nacional de Saúde (INS), Distrito de Marracuene, Maputo 3943, Mozambique; (S.S.B.); (A.C.); (A.F.L.B.); (J.L.); (M.C.); (I.C.-M.); (J.J.C.); (N.d.D.)
| | - Hester G. O’Neill
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, 205 Nelson Mandela Avenue, Bloemfontein 9301, South Africa; (A.S.); (H.G.O.)
| | - Nilsa de Deus
- Instituto Nacional de Saúde (INS), Distrito de Marracuene, Maputo 3943, Mozambique; (S.S.B.); (A.C.); (A.F.L.B.); (J.L.); (M.C.); (I.C.-M.); (J.J.C.); (N.d.D.)
- Departamento de Ciências Biológicas, Universidade Eduardo Mondlane, Maputo 3453, Mozambique
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16
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Dayama G, Zhou W, Prado-Martinez J, Marques-Bonet T, Mills RE. Characterization of nuclear mitochondrial insertions in the whole genomes of primates. NAR Genom Bioinform 2020; 2:lqaa089. [PMID: 33575633 PMCID: PMC7671390 DOI: 10.1093/nargab/lqaa089] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 05/04/2020] [Accepted: 10/15/2020] [Indexed: 12/30/2022] Open
Abstract
The transfer and integration of whole and partial mitochondrial genomes into the nuclear genomes of eukaryotes is an ongoing process that has facilitated the transfer of genes and contributed to the evolution of various cellular pathways. Many previous studies have explored the impact of these insertions, referred to as NumtS, but have focused primarily on older events that have become fixed and are therefore present in all individual genomes for a given species. We previously developed an approach to identify novel Numt polymorphisms from next-generation sequence data and applied it to thousands of human genomes. Here, we extend this analysis to 79 individuals of other great ape species including chimpanzee, bonobo, gorilla, orang-utan and also an old world monkey, macaque. We show that recent Numt insertions are prevalent in each species though at different apparent rates, with chimpanzees exhibiting a significant increase in both polymorphic and fixed Numt sequences as compared to other great apes. We further assessed positional effects in each species in terms of evolutionary time and rate of insertion and identified putative hotspots on chromosome 5 for Numt integration, providing insight into both recent polymorphic and older fixed reference NumtS in great apes in comparison to human events.
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Affiliation(s)
- Gargi Dayama
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Weichen Zhou
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | | | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, 08010, Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, 08193 Cerdanyola del Vallès, Barcelona, Spain
| | - Ryan E Mills
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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17
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de Melo KP, Camargo M. Mechanisms for sperm mitochondrial removal in embryos. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1868:118916. [PMID: 33276010 DOI: 10.1016/j.bbamcr.2020.118916] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 11/23/2020] [Accepted: 11/25/2020] [Indexed: 12/24/2022]
Abstract
BACKGROUND Different animal species have different characteristics regarding the transmission of mitochondrial DNA. While some species have biparental mitochondrial inheritance, others have developed pathways to remove paternal mtDNA. These pathways guarantee the uniparental mitochondrial inheritance, so far well known in mammals, avoiding heteroplasmy, which may have the potential to cause certain mitochondrial diseases in the offspring. SCOPE OF REVIEW This review aims to address the main mechanisms that involve mitochondrial degradation in different animal species, as well as to describe what is present in the literature on the mechanisms involved in mitochondrial inheritance. MAJOR CONCLUSIONS Two theories are proposed to explain the uniparental inheritance of mtDNA: (i) active degradation, where mechanisms for paternal mitochondrial DNA elimination involve mitochondrial degradation pathway by autophagy and, in some species, may also involve the endocytic degradation pathway; and (ii) passive dilution, where the paternal mitochondria are diluted in the cells of the embryo according to cell division, until becoming undetectable. GENERAL SIGNIFICANCE This work brings a wide review of the already published evidence on mitochondrial inheritance in the animal kingdom and the possible mechanisms to mtDNA transmission already described in literature.
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Affiliation(s)
- Karla Pacheco de Melo
- Department of Surgery, Division of Urology, Human Reproduction Section, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Mariana Camargo
- Department of Surgery, Division of Urology, Human Reproduction Section, Universidade Federal de São Paulo, São Paulo, Brazil.
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18
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Kowal K, Tkaczyk A, Pierzchała M, Bownik A, Ślaska B. Identification of Mitochondrial DNA (NUMTs) in the Nuclear Genome of Daphnia magna. Int J Mol Sci 2020; 21:E8725. [PMID: 33218217 PMCID: PMC7699184 DOI: 10.3390/ijms21228725] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 11/06/2020] [Accepted: 11/16/2020] [Indexed: 01/30/2023] Open
Abstract
This is the first study in which the Daphnia magna (D. magna) nuclear genome (nDNA) obtained from the GenBank database was analyzed for pseudogene sequences of mitochondrial origin. To date, there is no information about pseudogenes localized in D. magna genome. This study aimed to identify NUMTs, their length, homology, and location for potential use in evolutionary studies and to check whether their occurrence causes co-amplification during mitochondrial genome (mtDNA) analyses. Bioinformatic analysis showed 1909 fragments of the mtDNA of D. magna, of which 1630 were located in ten linkage groups (LG) of the nDNA. The best-matched NUMTs covering >90% of the gene sequence have been identified for two mt-tRNA genes, and they may be functional nuclear RNA molecules. Isolating the total DNA in mtDNA studies, co-amplification of nDNA fragments is unlikely in the case of amplification of the whole tRNA genes as well as fragments of other genes. It was observed that TRNA-MET fragments had the highest level of sequence homology, thus they could be evolutionarily the youngest. The lowest homology was found in the D-loop-derived pseudogene. It may probably be the oldest NUMT incorporated into the nDNA; however, further analysis is necessary.
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Affiliation(s)
- Krzysztof Kowal
- Faculty of Animal Sciences and Bioeconomy, Institute of Biological Bases of Animal Production, University of Life Sciences in Lublin, Akademicka 13 Str., 20-950 Lublin, Poland; (K.K.); (A.T.)
| | - Angelika Tkaczyk
- Faculty of Animal Sciences and Bioeconomy, Institute of Biological Bases of Animal Production, University of Life Sciences in Lublin, Akademicka 13 Str., 20-950 Lublin, Poland; (K.K.); (A.T.)
| | - Mariusz Pierzchała
- Department of Genomics and Biodiversity, Institute of Genetics and Animal Biotechnology of the Polish Academy of Sciences, Postępu 36a Str., 05-552 Jastrzębiec, Poland;
| | - Adam Bownik
- Faculty of Environmental Biology, Department of Hydrobiology and Protection of Ecosystems, University of Life Sciences in Lublin, Dobrzańskiego 37 Str., 20-262 Lublin, Poland;
| | - Brygida Ślaska
- Faculty of Animal Sciences and Bioeconomy, Institute of Biological Bases of Animal Production, University of Life Sciences in Lublin, Akademicka 13 Str., 20-950 Lublin, Poland; (K.K.); (A.T.)
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19
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Dhruw C, Husain K, Kumar V, Sonawane VC. Novel xylanase producing Bacillus strain X2: molecular phylogenetic analysis and its application for production of xylooligosaccharides. 3 Biotech 2020; 10:328. [PMID: 32656061 PMCID: PMC7334322 DOI: 10.1007/s13205-020-02322-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 06/24/2020] [Indexed: 11/24/2022] Open
Abstract
A Bacillus strain X2 that produced extracellular endo-xylanase (GH 11) (EC: 3.2.1.8) was isolated from the soil of the Northeast India region. This aerobic culture was Gram positive and endospore forming. Chemotaxonomic characterization showed variance with the fatty acid profile of related species in the Bacillus subtilis group. In Bacillus strain X2, distinct occurrence of iso-C14:0 lipids is absent in other related species. The 16S rRNA gene sequence homology showed 99% similarity with Bacillus subtilis subsp. inaquosorum. The phylogenetic analysis by the multilocus sequence analysis (MLSA) of the nucleotide sequence of six concatenated genes (16S rRNA, groEL, gyrA, polC, purH and rpoB) resolved the taxonomic position of the Bacillus strain X2 in the Bacillus subtilis subsp. group. The MLSA showed that it is a member of a clade that includes Bacillus subtilis subsp. stercoris. In in silico DNA-DNA hybridization (DDH), the highest matching score was obtained with Bacillus subtilis subsp. stercoris (87%). The in silico DDH of the genome (G + C 43.7 mol %) shared 48.5%, with Bacillus subtilis subsp. inaquosorum. The MLSA phylogenetic tree and the highest degree of DNA hybridization, indicating that it belongs to the Bacillus subtilis subspecies stercoris.
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Affiliation(s)
- Chandrabhan Dhruw
- BERPDC, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, 160036 India
| | - Khadim Husain
- BERPDC, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, 160036 India
| | - Vyas Kumar
- BERPDC, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, 160036 India
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20
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Genotyping-by-sequencing reveals the effects of riverscape, climate and interspecific introgression on the genetic diversity and local adaptation of the endangered Mexican golden trout (Oncorhynchus chrysogaster). CONSERV GENET 2020. [DOI: 10.1007/s10592-020-01297-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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21
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Wang D, Xiang H, Ning C, Liu H, Liu JF, Zhao X. Mitochondrial DNA enrichment reduced NUMT contamination in porcine NGS analyses. Brief Bioinform 2020; 21:1368-1377. [PMID: 31204429 DOI: 10.1093/bib/bbz060] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 04/19/2019] [Indexed: 12/24/2022] Open
Abstract
Genetic associations between mitochondrial DNA (mtDNA) and economic traits have been widely reported for pigs, which indicate the importance of mtDNA. However, studies on mtDNA heteroplasmy in pigs are rare. Next generation sequencing (NGS) methodologies have emerged as a promising genomic approach for detection of mitochondrial heteroplasmy. Due to the short reads, flexible bioinformatic analyses and the contamination of nuclear mitochondrial sequences (NUMTs), NGS was expected to increase false-positive detection of heteroplasmy. In this study, Sanger sequencing was performed as a gold standard to detect heteroplasmy with a detection sensitivity of 5% in pigs and then one whole-genome sequencing method (WGS) and two mtDNA enrichment sequencing methods (Capture and LongPCR) were carried out. The aim of this study was to determine whether mitochondrial heteroplasmy identification from NGS data was affected by NUMTs. We find that WGS generated more false intra-individual polymorphisms and less mapping specificity than the two enrichment sequencing methods, suggesting NUMTs indeed led to false-positive mitochondrial heteroplasmies from NGS data. In addition, to accurately detect mitochondrial diversity, three commonly used tools-SAMtools, VarScan and GATK-with different parameter values were compared. VarScan achieved the best specificity and sensitivity when considering the base alignment quality re-computation and the minimum variant frequency of 0.25. It also suggested bioinformatic workflow interfere in the identification of mtDNA SNPs. In conclusion, intra-individual polymorphism in pig mitochondria from NGS data was confused with NUMTs, and mtDNA-specific enrichment is essential before high-throughput sequencing in the detection of mitochondrial genome sequences.
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Affiliation(s)
- Dan Wang
- National Engineering Laboratory for Animal Breeding; Ministry of Agricultural Key Laboratory of Animal Genetics, Breeding and Reproduction; College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Hai Xiang
- College of Life Science and Engineering, Foshan University, Foshan, Guangdong 528231, China
| | - Chao Ning
- National Engineering Laboratory for Animal Breeding; Ministry of Agricultural Key Laboratory of Animal Genetics, Breeding and Reproduction; College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Hao Liu
- National Engineering Laboratory for Animal Breeding; Ministry of Agricultural Key Laboratory of Animal Genetics, Breeding and Reproduction; College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jian-Feng Liu
- National Engineering Laboratory for Animal Breeding; Ministry of Agricultural Key Laboratory of Animal Genetics, Breeding and Reproduction; College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xingbo Zhao
- National Engineering Laboratory for Animal Breeding; Ministry of Agricultural Key Laboratory of Animal Genetics, Breeding and Reproduction; College of Animal Science and Technology, China Agricultural University, Beijing, China
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22
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Abstract
Khadi is a popular traditional alcoholic beverage in rural households in Botswana. The product is produced by fermentation of ripened sun-dried Grewia flava (Malvaceae) fruits supplemented with brown table sugar. Despite its popularity, its growing consumer acceptance, its potential nutritional value, and its contribution to the socio-economic lifestyle of Botswana, the production process remains non-standardized. Non-standardized production processes lead to discrepancies in product quality and safety as well as varying shelf life. Identification of unknown fermentative microorganisms of khadi is an important step towards standardization of its brewing process for entrance into commercial markets. The aim of this study was to isolate and identify bacteria and yeasts responsible for fermentation of khadi. Yeasts and bacteria harbored in 18 khadi samples from 18 brewers in central and northern Botswana were investigated using classic culture-dependent techniques and DNA sequencing methods. Additionally, we used the same techniques to investigate the presence of bacteria and yeasts on six batches of ripened-dried G. flava fruits used for production of the sampled brews. Our results revealed that Saccharomyces cerevisiae closely related to a commercial baker’s yeast strain sold locally was the most predominant yeast species in khadi suggesting a possible non-spontaneous brewing process. However, we also detected diverse non-Saccharomyces yeasts, which are not available commercially in retail shops in Botswana. This suggests that spontaneous fermentation is partially responsible for fermentation of khadi. This study, presenting the first microbiological characterization of a prominent traditional alcoholic beverage in Botswana, is vital for development of starter cultures for the production of a consistent product towards the commercialization of khadi.
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Paraburkholderia atlantica sp. nov. and Paraburkholderia franconis sp. nov., two new nitrogen-fixing nodulating species isolated from Atlantic forest soils in Brazil. Arch Microbiol 2020; 202:1369-1380. [PMID: 32166359 DOI: 10.1007/s00203-020-01843-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 02/18/2020] [Accepted: 02/21/2020] [Indexed: 12/26/2022]
Abstract
A polyphasic study was conducted with 11 strains trapped by Mimosa pudica and Phaseolus vulgaris grown in soils of the Brazilian Atlantic Forest. In the phylogenetic analysis of the 16S rRNA gene, one clade of strains (Psp1) showed higher similarity with Paraburkholderia piptadeniae STM7183T (99.6%), whereas the second (Psp6) was closely related to Paraburkholderia tuberum STM678T (99%). An MLSA (multilocus sequence analysis) with four (recA, gyrB, trpB and gltB) housekeeping genes placed both Psp1 and Psp6 strains in new clades, and BOX-PCR profiles indicated high intraspecific genetic diversity within each clade. Values of digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) of the whole genome sequences were of 56.9 and 94.4% between the Psp1 strain CNPSo 3157T and P. piptadeniae; and of 49.7% and 92.7% between the Psp6 strain CNPSo 3155T and P. tuberum, below the threshold for species delimitation. In the nodC analysis, Psp1 strains clustered together with P. piptadeniae, while Psp6 did not group with any symbiotic Paraburkholderia. Other phenotypic, genotypic and symbiotic properties were evaluated. The polyphasic analysis supports that the strains represent two novel species, for which the names Paraburkholderia franconis sp. nov. with type strain CNPSo 3157T (= ABIP 241, = LMG 31644) and Paraburkholderia atlantica sp. nov. with type strain CNPSo 3155T (= ABIP 236, = LMG 31643) are proposed.
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Zhang GJ, Dong R, Lan LN, Li SF, Gao WJ, Niu HX. Nuclear Integrants of Organellar DNA Contribute to Genome Structure and Evolution in Plants. Int J Mol Sci 2020; 21:ijms21030707. [PMID: 31973163 PMCID: PMC7037861 DOI: 10.3390/ijms21030707] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 01/16/2020] [Accepted: 01/18/2020] [Indexed: 11/16/2022] Open
Abstract
The transfer of genetic material from the mitochondria and plastid to the nucleus gives rise to nuclear integrants of mitochondrial DNA (NUMTs) and nuclear integrants of plastid DNA (NUPTs). This frequently occurring DNA transfer is ongoing and has important evolutionary implications. In this review, based on previous studies and the analysis of NUMT/NUPT insertions of more than 200 sequenced plant genomes, we analyzed and summarized the general features of NUMTs/NUPTs and highlighted the genetic consequence of organellar DNA insertions. The statistics of organellar DNA integrants among various plant genomes revealed that organellar DNA-derived sequence content is positively correlated with the nuclear genome size. After integration, the nuclear organellar DNA could undergo different fates, including elimination, mutation, rearrangement, fragmentation, and proliferation. The integrated organellar DNAs play important roles in increasing genetic diversity, promoting gene and genome evolution, and are involved in sex chromosome evolution in dioecious plants. The integrating mechanisms, involving non-homologous end joining at double-strand breaks were also discussed.
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Affiliation(s)
- Guo-Jun Zhang
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; (G.-J.Z.); (R.D.); (L.-N.L.); (S.-F.L.)
- School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang 453003, China
| | - Ran Dong
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; (G.-J.Z.); (R.D.); (L.-N.L.); (S.-F.L.)
| | - Li-Na Lan
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; (G.-J.Z.); (R.D.); (L.-N.L.); (S.-F.L.)
| | - Shu-Fen Li
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; (G.-J.Z.); (R.D.); (L.-N.L.); (S.-F.L.)
| | - Wu-Jun Gao
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; (G.-J.Z.); (R.D.); (L.-N.L.); (S.-F.L.)
- Correspondence: (W.-J.G.); (H.-X.N.)
| | - Hong-Xing Niu
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; (G.-J.Z.); (R.D.); (L.-N.L.); (S.-F.L.)
- Correspondence: (W.-J.G.); (H.-X.N.)
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Smart U, Budowle B, Ambers A, Soares Moura-Neto R, Silva R, Woerner AE. A novel phylogenetic approach for de novo discovery of putative nuclear mitochondrial (pNumt) haplotypes. Forensic Sci Int Genet 2019; 43:102146. [DOI: 10.1016/j.fsigen.2019.102146] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 08/09/2019] [Accepted: 08/13/2019] [Indexed: 10/26/2022]
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Paraburkholderia guartelaensis sp. nov., a nitrogen-fixing species isolated from nodules of Mimosa gymnas in an ecotone considered as a hotspot of biodiversity in Brazil. Arch Microbiol 2019; 201:1435-1446. [PMID: 31428824 DOI: 10.1007/s00203-019-01714-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 07/14/2019] [Accepted: 08/10/2019] [Indexed: 10/26/2022]
Abstract
A polyphasic approach was used to infer the phylogenetic position of six nitrogen-fixing symbiotic bacteria isolated from Mimosa gymnas nodules grown in an ecotone between the Brazilian biomes of Atlantic Forest and Cerrado, considered as a hotspot of biodiversity. The 16S rRNA gene phylogeny indicated the highest similarity with Paraburkholderia oxyphila (98.7-98.9%), but similar values were found with other Paraburkholderia species. The multilocus sequence analysis (MLSA) of five (recA, gyrB, trpB, gltB, and atpD) housekeeping genes indicated that the CNPSo strains represent a novel lineage, sharing less than 95.7% of nucleotide identity (NI) with other Paraburkholderia species, being more closely related to P. nodosa. Genome parameters were analyzed for strain CNPSo 3008T, and DNA-DNA hybridization revealed a maximum of 55.9% of DNA-DNA relatedness with P. nodosa, while average nucleotide identity with the two closest species was of 93.84% with P. nodosa and of 87.93% with P. mimosarum, both parameters confirming that the strain represents a new species. In the analysis of the nodulation nodC gene, all CNPSo strains showed the highest similarity with P. nodosa, and nodulation tests indicated host specificity with Mimosa. Other phylogenetic, physiological, and chemotaxonomic properties were evaluated. All data obtained support the description of the novel species Paraburkholderia guartelaensis sp. nov., with CNPSo 3008T (= U13000T = G29.01T) indicated as the type strain.
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Li SF, Li JR, Wang J, Dong R, Jia KL, Zhu HW, Li N, Yuan JH, Deng CL, Gao WJ. Cytogenetic and genomic organization analyses of chloroplast DNA invasions in the nuclear genome of Asparagus officinalis L. provides signatures of evolutionary complexity and informativity in sex chromosome evolution. BMC PLANT BIOLOGY 2019; 19:361. [PMID: 31419941 PMCID: PMC6698032 DOI: 10.1186/s12870-019-1975-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 08/13/2019] [Indexed: 05/03/2023]
Abstract
BACKGROUND The transfer of chloroplast DNA into nuclear genome is a common process in plants. These transfers form nuclear integrants of plastid DNAs (NUPTs), which are thought to be driving forces in genome evolution, including sex chromosome evolution. In this study, NUPTs in the genome of a dioecious plant Asparagus officinalis L. were systematically analyzed, in order to investigate the characteristics of NUPTs in the nuclear genome and the relationship between NUPTs and sex chromosome evolution in this species. RESULTS A total of 3155 NUPT insertions were detected, and they represented approximated 0.06% of the nuclear genome. About 45% of the NUPTs were organized in clusters. These clusters were derived from various evolutionary events. The Y chromosome contained the highest number and largest proportion of NUPTs, suggesting more accumulation of NUPTs on sex chromosomes. NUPTs were distributed widely in all of the chromosomes, and some regions preferred these insertions. The highest density of NUPTs was found in a 47 kb region in the Y chromosome; more than 75% of this region was occupied by NUPTs. Further cytogenetic and sequence alignment analysis revealed that this region was likely the centromeric region of the sex chromosomes. On the other hand, the male-specific region of the Y chromosome (MSY) and the adjacent regions did not have NUPT insertions. CONCLUSIONS These results indicated that NUPTs were involved in shaping the genome of A. officinalis through complicated process. NUPTs may play important roles in the centromere shaping of the sex chromosomes of A. officinalis, but were not implicated in MSY formation.
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Affiliation(s)
- Shu-Fen Li
- College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
| | - Jia-Rong Li
- College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
| | - Jin Wang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
| | - Ran Dong
- College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
| | - Ke-Li Jia
- College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
- SanQuan Medical College, Xinxiang Medical University, Xinxiang, 453003 China
| | - Hong-Wei Zhu
- College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
| | - Ning Li
- College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
| | - Jin-Hong Yuan
- College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
| | - Chuan-Liang Deng
- College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
| | - Wu-Jun Gao
- College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
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Gabriela Arango B, T Pinheiro H, Rocha C, D Greene B, L Pyle R, M Copus J, Shepherd B, A Rocha L. Three new species of Chromis (Teleostei, Pomacentridae) from mesophotic coral ecosystems of the Philippines. Zookeys 2019; 835:1-15. [PMID: 31043847 PMCID: PMC6477865 DOI: 10.3897/zookeys.835.27528] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 02/24/2019] [Indexed: 11/12/2022] Open
Abstract
Three new species of Chromis (Perciformes, Pomacentridae) from the Philippines, collected between 75–150 m depth, are described by a combination of morphological features and their coloration. Chromisguntingsp. n. was found in Batangas and Oriental Mindoro, and differs from its congeners in body depth (2.1–2.2 in SL), and color of adults, light brown, with a silver area on the anterior end and a bilateral black margin along the exterior side of the tail. It is most similar to C.scotochiloptera, with a 5.3% genetic divergence in COI. Chromishangganansp. n. was found around Lubang Island. Body depth (1.9–2.0 in SL) and adult coloration (yellowish with dark black outer margins on dorsal and anal fins) also separate this species from its congeners. It is most similar to C.pembae, with a 2.5% genetic divergence. Chromisbowesisp. n. was found in Batangas, and also differs from its congeners by the combination of body depth (1.5–1.6 in SL), and color of adults (brownish grey in the dorsal side to whitish on the ventral side, with alternating dark and light stripes in the sides of body). It is most similar to C.earina, with a 3.6% genetic divergence in COI.
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Affiliation(s)
- B Gabriela Arango
- Department of Ichthyology, California Academy of Sciences, 55 Music Concourse Dr., San Francisco, CA 94118, USA Department of Ichthyology, California Academy of Sciences San Francisco United States of America
| | - Hudson T Pinheiro
- Department of Ichthyology, California Academy of Sciences, 55 Music Concourse Dr., San Francisco, CA 94118, USA Department of Ichthyology, California Academy of Sciences San Francisco United States of America
| | - Claudia Rocha
- Department of Ichthyology, California Academy of Sciences, 55 Music Concourse Dr., San Francisco, CA 94118, USA Department of Ichthyology, California Academy of Sciences San Francisco United States of America
| | - Brian D Greene
- Bernice P. Bishop Museum, Honolulu, HI 96817, USA Bernice P. Bishop Museum Honolulu United States of America
| | - Richard L Pyle
- Bernice P. Bishop Museum, Honolulu, HI 96817, USA Bernice P. Bishop Museum Honolulu United States of America
| | - Joshua M Copus
- Department of Biology, University of Hawai'i at Mānoa, Hawai'i Institute of Marine Biology, Kãne'ohe, HI 96744, USA University of Hawai'i at Mānoa Kãne'ohe United States of America
| | - Bart Shepherd
- Steinhart Aquarium, California Academy of Sciences, 55 Music Concourse Dr., San Francisco, CA 94118, USA Steinhart Aquarium, California Academy of Sciences San Francisco United States of America
| | - Luiz A Rocha
- Department of Ichthyology, California Academy of Sciences, 55 Music Concourse Dr., San Francisco, CA 94118, USA Department of Ichthyology, California Academy of Sciences San Francisco United States of America
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Loeza-Quintana T, Carr CM, Khan T, Bhatt YA, Lyon SP, Hebert PD, Adamowicz SJ. Recalibrating the molecular clock for Arctic marine invertebrates based on DNA barcodes. Genome 2019; 62:200-216. [DOI: 10.1139/gen-2018-0107] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Divergence times for species assemblages of Arctic marine invertebrates have often been estimated using a standard rate (1.4%/MY) of molecular evolution calibrated using a single sister pair of tropical crustaceans. Because rates of molecular evolution vary among taxa and environments, it is essential to obtain clock calibrations from northern lineages. The recurrent opening and closure of the Bering Strait provide an exceptional opportunity for clock calibration. Here, we apply the iterative calibration approach to investigate patterns of molecular divergence among lineages of northern marine molluscs and arthropods using publicly available sequences of the cytochrome c oxidase subunit I (COI) gene and compare these results with previous estimates of trans-Bering divergences for echinoderms and polychaetes. The wide range of Kimura two-parameter (K2P) divergences among 73 trans-Bering sister pairs (0.12%–16.89%) supports multiple pulses of migration through the Strait. Overall, the results indicate a rate of K2P divergence of 3.2%/MY in molluscs, 5%–5.2%/MY in arthropods, and 3.5%–4.7%/MY in polychaetes. While these rates are considerably higher than the often-adopted 1.4%/MY rate, they are similar to calibrations (3%–5%/MY) in several other studies of marine invertebrates. This upward revision in rates means there is a need both to reevaluate the evolutionary history of marine lineages and to reexamine the impact of prior climatic changes upon the diversification of marine life.
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Affiliation(s)
- Tzitziki Loeza-Quintana
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
- Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
| | - Christina M. Carr
- Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
- University of Northern Iowa, 187 McCollum Science Hall, Cedar Falls, IA 50614, USA
| | - Tooba Khan
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
- Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
| | - Yash A. Bhatt
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
- Faculty of Science, University of Western Ontario, 1151 Richmond St, London, ON N6A 3K7, Canada
| | - Samantha P. Lyon
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
- Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
| | - Paul D.N. Hebert
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
- Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
| | - Sarah J. Adamowicz
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
- Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
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Paulitsch F, Klepa MS, da Silva AR, do Carmo MRB, Dall’Agnol RF, Delamuta JRM, Hungria M, da Silva Batista JS. Phylogenetic diversity of rhizobia nodulating native Mimosa gymnas grown in a South Brazilian ecotone. Mol Biol Rep 2018; 46:529-540. [DOI: 10.1007/s11033-018-4506-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 11/15/2018] [Indexed: 11/29/2022]
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Methanotrophic contribution to biodegradation of phenoxy acids in cultures enriched from a groundwater-fed rapid sand filter. Appl Microbiol Biotechnol 2018; 103:1007-1019. [PMID: 30474728 DOI: 10.1007/s00253-018-9501-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 10/16/2018] [Accepted: 11/05/2018] [Indexed: 10/27/2022]
Abstract
Drinking water supply is in many parts of the world based on groundwater. Groundwater often contains methane, which can be oxidized by methanotrophs upon aeration. Sand from rapid sand filters fed with methane-rich groundwater can remove some pesticides (Hedegaard and Albrechtsen in Water Res 48:71-81, 2014). We enriched methanotrophs from filter sand and investigated whether they could drive the degradation of various pesticides. To enrich for methanotrophs, we designed and operated four laboratory-scale, continuously methane-fed column reactors, inoculated with filter sand and one control column fed with tap water. When enrichments were obtained, methane was continuously supplied to three reactors, while the fourth was starved for methane for 1 week, and the reactors were spiked with ten pesticides at groundwater-relevant concentrations (2.1-6.6 μg/L). Removal for most pesticides was not detected at the investigated contact time (1.37 min). However, the degradation of phenoxy acids was observed in the methanotrophic column reactor starved for methane, while it was not detected in the control column indicating the importance of methanotrophs. Phenoxy acid removal, using dichlorprop as a model compound, was further investigated in batch experiments with methanotrophic biomass collected from the enrichment reactors. Phenoxy acid removal (expressed per gram of matrix sand) was substantially improved in the methanotrophic enrichment compared to parent filter sand. The presence of methane did not clearly impact dichlorprop removal but did impact mineralization. We suggest that other heterotrophs are responsible for the first step in dichlorprop degradation, while the subsequent steps including ring-hydroxylation are driven by methanotrophs.
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Llamas-Arriba MG, Pérez-Ramos A, Puertas AI, López P, Dueñas MT, Prieto A. Characterization of Pediococcus ethanolidurans CUPV141: A β-D-glucan- and Heteropolysaccharide-Producing Bacterium. Front Microbiol 2018; 9:2041. [PMID: 30233527 PMCID: PMC6131198 DOI: 10.3389/fmicb.2018.02041] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Accepted: 08/13/2018] [Indexed: 12/22/2022] Open
Abstract
Pediococcus ethanolidurans CUPV141 is an exopolysaccharide (EPS)-producing lactic acid bacterium, first isolated from Basque Country cider (Spain). Physicochemical analysis of the EPS synthesized by the bacterium revealed that CUPV141 produces mostly a homopolysaccharide (HoPS), characterized as a 2-substituted (1,3)-β-D-glucan, together with a small quantity of a heteropolysaccharide (HePS) composed of glucose, galactose, glucosamine, and glycerol-3-phosphate, this being the first Pediococcus strain described to produce this kind of polymer. On the contrary, an isogenic strain CUPV141NR, generated by chemical mutagenesis of CUPV141, produced the HePS as the main extracellular polysaccharide and a barely detectable amount of 2-substituted (1,3)-β-D-glucan. This HoPS is synthesized by the transmembrane GTF glycosyltransferase (GTF), encoded by the gtf gene, which has been previously reported to be located in the pPP2 plasmid of the Pediococcus parvulus 2.6 strain. Southern blot hybridization revealed that in CUPV141 the gtf gene is located in a plasmid designated as pPE3, whose molecular mass (34.4 kbp) is different from that of pPP2 (24.5 kbp). Analysis of the influence of the EPS on the ability of the producing bacteria to adhere to the eukaryotic Caco-2 cells revealed higher affinity for the human enterocytes of CUPV141NR compared to that of CUPV141. This result indicates that, in contrast to the 2.6 strain, the presence of the HoPS does not potentiate the binding ability of P. ethanolidurans. Moreover, it supports that the phosphate-containing bacterial HePS improved the interaction between P. ethanolidurans and the eukaryotic cells.
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Affiliation(s)
- María G. Llamas-Arriba
- Chemistry Faculty, Department of Applied Chemistry, University of the Basque Country (UPV/EHU), San Sebastián, Spain
- Department of Microorganisms and Plant Technology, Biological Research Center, Spanish National Research Council (CIB-CSIC), Madrid, Spain
| | - Adrián Pérez-Ramos
- Department of Microorganisms and Plant Technology, Biological Research Center, Spanish National Research Council (CIB-CSIC), Madrid, Spain
| | - Ana I. Puertas
- Chemistry Faculty, Department of Applied Chemistry, University of the Basque Country (UPV/EHU), San Sebastián, Spain
| | - Paloma López
- Department of Microorganisms and Plant Technology, Biological Research Center, Spanish National Research Council (CIB-CSIC), Madrid, Spain
| | - María T. Dueñas
- Chemistry Faculty, Department of Applied Chemistry, University of the Basque Country (UPV/EHU), San Sebastián, Spain
| | - Alicia Prieto
- Department of Microorganisms and Plant Technology, Biological Research Center, Spanish National Research Council (CIB-CSIC), Madrid, Spain
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Torre C, Donaire L, Gómez-Aix C, Juárez M, Peterschmitt M, Urbino C, Hernando Y, Agüero J, Aranda MA. Characterization of Begomoviruses Sampled during Severe Epidemics in Tomato Cultivars Carrying the Ty-1 Gene. Int J Mol Sci 2018; 19:E2614. [PMID: 30177671 PMCID: PMC6164481 DOI: 10.3390/ijms19092614] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 08/25/2018] [Accepted: 08/28/2018] [Indexed: 12/27/2022] Open
Abstract
Tomato yellow leaf curl virus (TYLCV, genus Begomovirus, family Geminiviridae) is a major species that causes a tomato disease for which resistant tomato hybrids (mainly carriers of the Ty-1/Ty-3 gene) are being used widely. We have characterized begomoviruses severely affecting resistant tomato crops in Southeast Spain. Circular DNA was prepared from samples by rolling circle amplification, and sequenced by massive sequencing (2015) or cloning and Sanger sequencing (2016). Thus, 23 complete sequences were determined, all belonging to the TYLCV Israel strain (TYLCV-IL). Massive sequencing also revealed the absence of other geminiviral and beta-satellite sequences. A phylogenetic analysis showed that the Spanish isolates belonged to two groups, one related to early TYLCV-IL isolates in the area (Group 1), and another (Group 2) closely related to El Jadida (Morocco) isolates, suggesting a recent introduction. The most parsimonious evolutionary scenario suggested that the TYLCV isolates of Group 2 are back recombinant isolates derived from TYLCV-IS76, a recombinant virus currently predominating in Moroccan epidemics. Thus, an infectious Group 2 clone (TYLCV-Mu15) was constructed and used in in planta competition assays against TYLCV-IS76. TYLCV-Mu15 predominated in single infections, whereas TYLCV-IS76 did so in mixed infections, providing credibility to a scenario of co-occurrence of both types of isolates.
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Affiliation(s)
- Covadonga Torre
- Abiopep S.L., Departamento de I + D + i, Parque Científico de Murcia, Ctra. de Madrid, Km 388, Complejo de Espinardo, Edf. R, 2°, 30100 Murcia, Spain.
| | - Livia Donaire
- Centro de Edafología y Biología Aplicada del Segura (CEBAS)-CSIC, Departamento de Biología del Estrés y Patología Vegetal, P.O. Box 164, 30100 Murcia, Spain.
| | - Cristina Gómez-Aix
- Abiopep S.L., Departamento de I + D + i, Parque Científico de Murcia, Ctra. de Madrid, Km 388, Complejo de Espinardo, Edf. R, 2°, 30100 Murcia, Spain.
| | - Miguel Juárez
- Escuela Politécnica Superior de Orihuela, Universidad Miguel Hernández de Elche, Ctra. de Beniel, Km 3.2, 03312 Alicante, Spain.
| | - Michel Peterschmitt
- Centre de Coopération Internationale en Recherche Agronomique Pour le Développement (CIRAD), UMR-BGPI, Equipe Interactions Virus-Insecte-Plante, TA A-54/K, Campus International de Baillarguet, CEDEX 5, 34398 Monptellier, France.
| | - Cica Urbino
- Centre de Coopération Internationale en Recherche Agronomique Pour le Développement (CIRAD), UMR-BGPI, Equipe Interactions Virus-Insecte-Plante, TA A-54/K, Campus International de Baillarguet, CEDEX 5, 34398 Monptellier, France.
| | - Yolanda Hernando
- Abiopep S.L., Departamento de I + D + i, Parque Científico de Murcia, Ctra. de Madrid, Km 388, Complejo de Espinardo, Edf. R, 2°, 30100 Murcia, Spain.
| | - Jesús Agüero
- Abiopep S.L., Departamento de I + D + i, Parque Científico de Murcia, Ctra. de Madrid, Km 388, Complejo de Espinardo, Edf. R, 2°, 30100 Murcia, Spain.
| | - Miguel A Aranda
- Centro de Edafología y Biología Aplicada del Segura (CEBAS)-CSIC, Departamento de Biología del Estrés y Patología Vegetal, P.O. Box 164, 30100 Murcia, Spain.
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Stewart LC, Stucker VK, Stott MB, de Ronde CEJ. Marine-influenced microbial communities inhabit terrestrial hot springs on a remote island volcano. Extremophiles 2018; 22:687-698. [PMID: 29713821 DOI: 10.1007/s00792-018-1029-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 04/19/2018] [Indexed: 11/25/2022]
Abstract
Raoul Island is a subaerial island volcano approximately 1000 km northeast of New Zealand. Its caldera contains a circumneutral closed-basin volcanic lake and several associated pools, as well as intertidal coastal hot springs, all fed by a hydrothermal system sourced from both meteoric water and seawater. Here, we report on the geochemistry, prokaryotic community diversity, and cultivatable abundance of thermophilic microorganisms of four terrestrial features and one coastal feature on Raoul. Hydrothermal fluid contributions to the volcanic lake and pools make them brackish, and consequently support unusual microbial communities dominated by Planctomycetes, Chloroflexi, Alphaproteobacteria, and Thaumarchaeota, as well as up to 3% of the rare sister phylum to Cyanobacteria, Candidatus Melainabacteria. The dominant taxa are mesophilic to moderately thermophilic, phototrophic, and heterotrophic marine groups related to marine Planctomycetaceae. The coastal hot spring/shallow hydrothermal vent community is similar to other shallow systems in the Western Pacific Ocean, potentially due to proximity and similarities of geochemistry. Although rare in community sequence data, thermophilic methanogens, sulfur-reducers, and iron-reducers are present in culture-based assays.
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Affiliation(s)
- Lucy C Stewart
- Marine Geosciences, GNS Science, PO Box 30368, Lower Hutt, 5040, New Zealand.
| | - Valerie K Stucker
- Marine Geosciences, GNS Science, PO Box 30368, Lower Hutt, 5040, New Zealand
| | - Matthew B Stott
- Marine Geosciences, GNS Science, PO Box 30368, Lower Hutt, 5040, New Zealand
- University of Canterbury, Christchurch, 8140, New Zealand
| | - Cornel E J de Ronde
- Marine Geosciences, GNS Science, PO Box 30368, Lower Hutt, 5040, New Zealand
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35
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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.
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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
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36
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Hypoxia-Inducible Factor-1α in Antarctic notothenioids contains a polyglutamine and glutamic acid insert that varies in length with phylogeny. Polar Biol 2018; 40:2537-2545. [PMID: 29430077 DOI: 10.1007/s00300-017-2164-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The long evolution of the Antarctic perciform suborder of Notothenioidei in the icy, oxygen-rich waters of the Southern Ocean may have reduced selective pressure to maintain a hypoxic response. To test this hypothesis, cDNA of the key transcriptional regulator of hypoxic genes, hypoxia-inducible factor-1α (HIF-1α), was sequenced in heart ventricles of the red-blooded notothenioid, Notothenia coriiceps, and the hemoglobinless icefish, Chaenocephalus aceratus. HIF-1α cDNA is 4500 base pairs (bp) long and encodes 755 amino acids in N. coriiceps, and in C. aceratus, HIF-1α is 3576 bp long and encodes 779 amino acids. All functional domains of HIF-1α are highly conserved compared to other teleosts, but HIF-1α contains a polyglutamine/glutamic acid (polyQ/E) insert 9 amino acids long in N. coriiceps and 34 amino acids long in C. aceratus. Sequencing of this region in four additional species, representing three families of notothenioids, revealed that the length of the polyQ/E insert varies with phylogeny. Icefishes, the crown family of notothenioids, contain the longest polyQ/E inserts, ranging between16 and 34 amino acids long, whereas the basal, cold-temperate notothenioid, Eleginops maclovinus, contains a polyQ/E insert only 4 amino acids long. PolyQ/E inserts may affect dimerization of HIF-1α and HIF-1β, HIF-1 translocation into the nucleus and/or DNA binding.
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37
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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
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38
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Calabrese FM, Balacco DL, Preste R, Diroma MA, Forino R, Ventura M, Attimonelli M. NumtS colonization in mammalian genomes. Sci Rep 2017; 7:16357. [PMID: 29180746 PMCID: PMC5703718 DOI: 10.1038/s41598-017-16750-2] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 11/14/2017] [Indexed: 12/21/2022] Open
Abstract
The colonization of the nuclear genome by mitochondrial DNA is an ongoing process in eukaryotes and plays an important role in genomic variability. Notwithstanding the DNA sequence availability of about 100 complete eukaryotic genomes, up to now NumtS distribution has been fully reported for a small number of sequenced eukaryotic species. With the aim to clarify the time and way of NumtS evolution, we explored the genomic distribution of NumtS in 23 eukaryotic species using an intra/interspecies in silico approach based on a cross-species similarity search and deeply investigate the evolution of NumtS in mammals. The intra- and interspecies analysis underlined how some mitochondrial regions that populated nuclear genomes can be considered as hotspots. Considering the large amount of NumtS we found in platypus and opossum genomes, we hypothesized the occurrence of an earlier colonization that happened prior to the Prototherian/Therian mammal divergence, approximately 160-210 million years ago. These events are still detectable due to the species-specific dynamics that have affected these genomes. Phylogenetic analyses of NumtS derived from two different mitochondrial DNA loci allowed us to recognize the unusual NumtS evolution that acted differently on primate and non-primate species' genomes.
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Affiliation(s)
- F M Calabrese
- Department of Biology, University of Bari, Bari, 70124, Italy
| | - D L Balacco
- School of Pharmacy, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - R Preste
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari, 70124, Italy
| | - M A Diroma
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari, 70124, Italy
| | - R Forino
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari, 70124, Italy
| | - M Ventura
- Department of Biology, University of Bari, Bari, 70124, Italy.
| | - M Attimonelli
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari, 70124, Italy.
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39
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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.
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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
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40
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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.
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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
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41
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Messer LF, Brown MV, Furnas MJ, Carney RL, McKinnon AD, Seymour JR. Diversity and Activity of Diazotrophs in Great Barrier Reef Surface Waters. Front Microbiol 2017. [PMID: 28638369 PMCID: PMC5461343 DOI: 10.3389/fmicb.2017.00967] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Discrepancies between bioavailable nitrogen (N) concentrations and phytoplankton growth rates in the oligotrophic waters of the Great Barrier Reef (GBR) suggest that undetermined N sources must play a significant role in supporting primary productivity. One such source could be biological dinitrogen (N2) fixation through the activity of “diazotrophic” bacterioplankton. Here, we investigated N2 fixation and diazotroph community composition over 10° S of latitude within GBR surface waters. Qualitative N2 fixation rates were found to be variable across the GBR but were relatively high in coastal, inner and outer GBR waters, reaching 68 nmol L-1 d-1. Diazotroph assemblages, identified by amplicon sequencing of the nifH gene, were dominated by the cyanobacterium Trichodesmium erythraeum, γ-proteobacteria from the Gamma A clade, and δ-proteobacterial phylotypes related to sulfate-reducing genera. However, diazotroph communities exhibited significant spatial heterogeneity, correlated with shifts in dissolved inorganic nutrient concentrations. Specifically, heterotrophic diazotrophs generally increased in relative abundance with increasing concentrations of phosphate and N, while Trichodesmium was proportionally more abundant when concentrations of these nutrients were low. This study provides the first in-depth characterization of diazotroph community composition and N2 fixation dynamics within the oligotrophic, N-limited surface waters of the GBR. Our observations highlight the need to re-evaluate N cycling dynamics within oligotrophic coral reef systems, to include diverse N2 fixing assemblages as a potentially significant source of dissolved N within the water column.
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Affiliation(s)
- Lauren F Messer
- Climate Change Cluster, School of Life Sciences, University of Technology Sydney, SydneyNSW, Australia.,School of Biotechnology and Biomolecular Sciences, University of New South Wales, SydneyNSW, Australia
| | - Mark V Brown
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, SydneyNSW, Australia
| | - Miles J Furnas
- Australian Institute of Marine Science, TownsvilleQLD, Australia
| | - Richard L Carney
- Climate Change Cluster, School of Life Sciences, University of Technology Sydney, SydneyNSW, Australia
| | - A D McKinnon
- Australian Institute of Marine Science, TownsvilleQLD, Australia
| | - Justin R Seymour
- Climate Change Cluster, School of Life Sciences, University of Technology Sydney, SydneyNSW, Australia
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42
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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.
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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
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43
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Spiridonova LN, Valchuk OP, Red’kin YA, Kryukov AP. Nuclear mtDNA pseudogenes as a source of new variants of the mtDNA cytochrome b haplotypes: A case study of Siberian rubythroat Luscinia calliope (Muscicapidae, Aves). RUSS J GENET+ 2016. [DOI: 10.1134/s1022795416090131] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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44
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Chimeric mitochondrial peptides from contiguous regular and swinger RNA. Comput Struct Biotechnol J 2016; 14:283-97. [PMID: 27453772 PMCID: PMC4942731 DOI: 10.1016/j.csbj.2016.06.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 06/19/2016] [Accepted: 06/23/2016] [Indexed: 12/20/2022] Open
Abstract
Previous mass spectrometry analyses described human mitochondrial peptides entirely translated from swinger RNAs, RNAs where polymerization systematically exchanged nucleotides. Exchanges follow one among 23 bijective transformation rules, nine symmetric exchanges (X ↔ Y, e.g. A ↔ C) and fourteen asymmetric exchanges (X → Y → Z → X, e.g. A → C → G → A), multiplying by 24 DNA's protein coding potential. Abrupt switches from regular to swinger polymerization produce chimeric RNAs. Here, human mitochondrial proteomic analyses assuming abrupt switches between regular and swinger transcriptions, detect chimeric peptides, encoded by part regular, part swinger RNA. Contiguous regular- and swinger-encoded residues within single peptides are stronger evidence for translation of swinger RNA than previously detected, entirely swinger-encoded peptides: regular parts are positive controls matched with contiguous swinger parts, increasing confidence in results. Chimeric peptides are 200 × rarer than swinger peptides (3/100,000 versus 6/1000). Among 186 peptides with > 8 residues for each regular and swinger parts, regular parts of eleven chimeric peptides correspond to six among the thirteen recognized, mitochondrial protein-coding genes. Chimeric peptides matching partly regular proteins are rarer and less expressed than chimeric peptides matching non-coding sequences, suggesting targeted degradation of misfolded proteins. Present results strengthen hypotheses that the short mitogenome encodes far more proteins than hitherto assumed. Entirely swinger-encoded proteins could exist. Chimeric peptides are translated from contiguous regular and swinger RNA They are 200x rarer than mitochondrial swinger peptides Chimeric peptides integrated in regular mitochondrial proteins are downregulated Contiguous regular parts are matched positive controls for swinger parts The last point validates results beyond other statistical tests for robustness
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45
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Buddhakosai W, Klinsawat W, Smith O, Sukmak M, Kaolim N, Duangchantrasiri S, Simcharoen A, Siriaroonrat B, Wajjwalku W. Mitogenome analysis reveals a complex phylogeographic relationship within the wild tiger population of Thailand. ENDANGER SPECIES RES 2016. [DOI: 10.3354/esr00729] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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46
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Shi H, Dong J, Irwin DM, Zhang S, Mao X. Repetitive transpositions of mitochondrial DNA sequences to the nucleus during the radiation of horseshoe bats (Rhinolophus, Chiroptera). Gene 2016; 581:161-9. [DOI: 10.1016/j.gene.2016.01.035] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 01/20/2016] [Accepted: 01/21/2016] [Indexed: 10/22/2022]
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47
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Leister D. Towards understanding the evolution and functional diversification of DNA-containing plant organelles. F1000Res 2016; 5. [PMID: 26998248 PMCID: PMC4792205 DOI: 10.12688/f1000research.7915.1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/10/2016] [Indexed: 12/27/2022] Open
Abstract
Plastids and mitochondria derive from prokaryotic symbionts that lost most of their genes after the establishment of endosymbiosis. In consequence, relatively few of the thousands of different proteins in these organelles are actually encoded there. Most are now specified by nuclear genes. The most direct way to reconstruct the evolutionary history of plastids and mitochondria is to sequence and analyze their relatively small genomes. However, understanding the functional diversification of these organelles requires the identification of their complete protein repertoires – which is the ultimate goal of organellar proteomics. In the meantime, judicious combination of proteomics-based data with analyses of nuclear genes that include interspecies comparisons and/or predictions of subcellular location is the method of choice. Such genome-wide approaches can now make use of the entire sequences of plant nuclear genomes that have emerged since 2000. Here I review the results of these attempts to reconstruct the evolution and functions of plant DNA-containing organelles, focusing in particular on data from nuclear genomes. In addition, I discuss proteomic approaches to the direct identification of organellar proteins and briefly refer to ongoing research on non-coding nuclear DNAs of organellar origin (specifically, nuclear mitochondrial DNA and nuclear plastid DNA).
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Affiliation(s)
- Dario Leister
- Plant Molecular Biology, Department Biology I, Ludwig-Maximilians-Universität, Planegg-Martinsried, 82152, Germany; Copenhagen Plant Science Center (CPSC), University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
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48
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Ko YJ, Yang EC, Lee JH, Lee KW, Jeong JY, Park K, Chung O, Bhak J, Lee JH, Yim HS. Characterization of cetacean Numt and its application into cetacean phylogeny. Genes Genomics 2015. [DOI: 10.1007/s13258-015-0353-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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49
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Seligmann H. Codon expansion and systematic transcriptional deletions produce tetra-, pentacoded mitochondrial peptides. J Theor Biol 2015; 387:154-65. [PMID: 26456204 DOI: 10.1016/j.jtbi.2015.09.030] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 09/28/2015] [Accepted: 09/30/2015] [Indexed: 11/28/2022]
Abstract
Genes include occasionally isolated codons with a fourth (and fifth) silent nucleotide(s). Assuming tetracodons, translated hypothetical peptides align with regular GenBank proteins; predicted tetracodons coevolve with predicted tRNAs with expanded anticodons in each mammal, Drosophila and Lepidosauria mitogenomes, GC contents and with lepidosaurian body temperatures, suggesting that expanded codons are an adaptation of translation to high temperature. Hypothetically, continuous stretches of tetra- and pentacodons code for peptides. Both systematic nucleotide deletions during transcription, and translation by tRNAs with expanded anticodons could produce these peptides. Reanalyses of human nanoLc mass spectrometry peptidome data detect numerous tetra- and pentapeptides translated from the human mitogenome. These map preferentially on (BLAST-detected) human RNAs matching the human mitogenome, assuming systematic mono- and dinucleotide deletions after each third nucleotide (delRNAs). Translation by expanded anticodons is incompatible with silent nucleotides in the midst rather than at codon 3' extremity. More than 1/3 of detected tetra- and pentapeptides assume silent positions at codon extremity, suggesting that both mechanisms, regular translation of delRNAs and translation of regular RNAs by expanded anticodons, produce this peptide subgroup. Results show that systematically deleting polymerization occurs, and confirm serial translation of expanded codons. Non-canonical transcriptions and translations considerably expand the coding potential of DNA and RNA sequences.
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Affiliation(s)
- Hervé Seligmann
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Émergentes, Faculté de Médecine, URMITE CNRS-IRD 198 UMER 6236, Université de la Méditerranée, 13385 Marseille, France.
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50
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Ku C, Nelson-Sathi S, Roettger M, Sousa FL, Lockhart PJ, Bryant D, Hazkani-Covo E, McInerney JO, Landan G, Martin WF. Endosymbiotic origin and differential loss of eukaryotic genes. Nature 2015; 524:427-32. [PMID: 26287458 DOI: 10.1038/nature14963] [Citation(s) in RCA: 191] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 07/20/2015] [Indexed: 01/11/2023]
Abstract
Chloroplasts arose from cyanobacteria, mitochondria arose from proteobacteria. Both organelles have conserved their prokaryotic biochemistry, but their genomes are reduced, and most organelle proteins are encoded in the nucleus. Endosymbiotic theory posits that bacterial genes in eukaryotic genomes entered the eukaryotic lineage via organelle ancestors. It predicts episodic influx of prokaryotic genes into the eukaryotic lineage, with acquisition corresponding to endosymbiotic events. Eukaryotic genome sequences, however, increasingly implicate lateral gene transfer, both from prokaryotes to eukaryotes and among eukaryotes, as a source of gene content variation in eukaryotic genomes, which predicts continuous, lineage-specific acquisition of prokaryotic genes in divergent eukaryotic groups. Here we discriminate between these two alternatives by clustering and phylogenetic analysis of eukaryotic gene families having prokaryotic homologues. Our results indicate (1) that gene transfer from bacteria to eukaryotes is episodic, as revealed by gene distributions, and coincides with major evolutionary transitions at the origin of chloroplasts and mitochondria; (2) that gene inheritance in eukaryotes is vertical, as revealed by extensive topological comparison, sparse gene distributions stemming from differential loss; and (3) that continuous, lineage-specific lateral gene transfer, although it sometimes occurs, does not contribute to long-term gene content evolution in eukaryotic genomes.
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Affiliation(s)
- Chuan Ku
- Institute of Molecular Evolution, Heinrich-Heine University, 40225 Düsseldorf, Germany
| | - Shijulal Nelson-Sathi
- Institute of Molecular Evolution, Heinrich-Heine University, 40225 Düsseldorf, Germany
| | - Mayo Roettger
- Institute of Molecular Evolution, Heinrich-Heine University, 40225 Düsseldorf, Germany
| | - Filipa L Sousa
- Institute of Molecular Evolution, Heinrich-Heine University, 40225 Düsseldorf, Germany
| | - Peter J Lockhart
- Institute of Fundamental Sciences, Massey University, Palmerston North 4474, New Zealand
| | - David Bryant
- Department of Mathematics and Statistics, University of Otago, Dunedin 9054, New Zealand
| | - Einat Hazkani-Covo
- Department of Natural and Life Sciences, The Open University of Israel, Ra'anana 43107, Israel
| | - James O McInerney
- Department of Biology, National University of Ireland, Maynooth, County Kildare, Ireland.,Michael Smith Building, The University of Manchester, Oxford Rd, Manchester M13 9PL, UK
| | - Giddy Landan
- Genomic Microbiology Group, Institute of Microbiology, Christian-Albrechts-University of Kiel, 24118 Kiel, Germany
| | - William F Martin
- Institute of Molecular Evolution, Heinrich-Heine University, 40225 Düsseldorf, Germany.,Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal
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