1
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Macdonald E, Whibley A, Waters PD, Patel H, Edwards RJ, Ganley ARD. Origin and maintenance of large ribosomal RNA gene repeat size in mammals. Genetics 2024; 228:iyae121. [PMID: 39044674 PMCID: PMC11373518 DOI: 10.1093/genetics/iyae121] [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: 06/14/2024] [Revised: 07/15/2024] [Accepted: 07/16/2024] [Indexed: 07/25/2024] Open
Abstract
The genes encoding ribosomal RNA are highly conserved across life and in almost all eukaryotes are present in large tandem repeat arrays called the rDNA. rDNA repeat unit size is conserved across most eukaryotes but has expanded dramatically in mammals, principally through the expansion of the intergenic spacer region that separates adjacent rRNA coding regions. Here, we used long-read sequence data from representatives of the major amniote lineages to determine where in amniote evolution rDNA unit size increased. We find that amniote rDNA unit sizes fall into two narrow size classes: "normal" (∼11-20 kb) in all amniotes except monotreme, marsupial, and eutherian mammals, which have "large" (∼35-45 kb) sizes. We confirm that increases in intergenic spacer length explain much of this mammalian size increase. However, in stark contrast to the uniformity of mammalian rDNA unit size, mammalian intergenic spacers differ greatly in sequence. These results suggest a large increase in intergenic spacer size occurred in a mammalian ancestor and has been maintained despite substantial sequence changes over the course of mammalian evolution. This points to a previously unrecognized constraint on the length of the intergenic spacer, a region that was thought to be largely neutral. We finish by speculating on possible causes of this constraint.
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Affiliation(s)
- Emma Macdonald
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Annabel Whibley
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
- Grapevine Improvement, Bragato Research Institute, RFH Building, Engineering Drive, Lincoln University, Lincoln 7647, New Zealand
| | - Paul D Waters
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Chancellery Walk, Kensington, NSW 2033, Australia
| | - Hardip Patel
- John Curtin School of Medical Research, Australian National University, 131 Garran Rd, Acton, ACT 2601, Australia
| | - Richard J Edwards
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Chancellery Walk, Kensington, NSW 2033, Australia
- Minderoo OceanOmics Centre at UWA, UWA Oceans Institute, University of Western Australia, Crawley WA 6009, Australia
| | - Austen R D Ganley
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
- Digital Life Institute, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
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2
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Elguweidi A, Crease T. Copy number and sequence variation in rDNA of Daphnia pulex from natural populations: insights from whole-genome sequencing. G3 (BETHESDA, MD.) 2024; 14:jkae105. [PMID: 38771699 PMCID: PMC11228840 DOI: 10.1093/g3journal/jkae105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Revised: 02/17/2024] [Accepted: 05/10/2024] [Indexed: 05/23/2024]
Abstract
Ribosomal DNA (rDNA) has a vital role in ribosome biogenesis as it contains the genes that encode ribosomal RNA (rRNA) separated by intergenic spacers (IGSs). The rRNA genes occur in hundreds to tens of thousands of copies per haploid genome in eukaryotes and are generally highly conserved with low variation within species. Due to the repetitive nature and large size of rDNA arrays, detecting intraindividual variation can be difficult. In this study, we use whole-genome sequences of 169 Daphnia pulex individuals from 10 natural populations to measure the copy number and sequence variation in rDNA. This revealed that variation in rDNA copy number between individuals spans an order of magnitude. We further observed a substantial level of sequence variation within individual genomes. As expected, single-nucleotide polymorphisms occurred in regions of lower functional constraint such as the IGS and expansion segments of the rRNA genes. The presence of strong linkage disequilibrium among variants facilitated identification of haplotypes within each population. Although there was evidence of recombination among haplotypes from different populations, it is insufficient to eliminate linkage disequilibrium within populations. Estimating copy number and haplotype diversity within individuals revealed that the level of intraindividual sequence variation is not strongly correlated with copy number. The observed patterns of variation highlight a complex evolutionary history of rDNA in D. pulex. Future research should explore the functional implications of rDNA copy number and sequence variation on organismal phenotypes.
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Affiliation(s)
- Abir Elguweidi
- Department of Integrative Biology, University of Guelph, Guelph, ON, N1G2W1, Canada
| | - Teresa Crease
- Department of Integrative Biology, University of Guelph, Guelph, ON, N1G2W1, Canada
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3
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Mazurkiewicz M, Pawłowska J, Barrenechea Angeles I, Grzelak K, Deja K, Zaborska A, Pawłowski J, Włodarska-Kowalczuk M. Sediment DNA metabarcoding and morphology provide complementary insight into macrofauna and meiobenthos response to environmental gradients in an Arctic glacial fjord. MARINE ENVIRONMENTAL RESEARCH 2024; 198:106552. [PMID: 38788477 DOI: 10.1016/j.marenvres.2024.106552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 05/09/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024]
Abstract
Arctic fjords ecosystems are highly dynamic, with organisms exposed to various natural stressors along with productivity clines driven by advection of water masses from shelves. The benthic response to these environmental clines has been extensively studied using traditional, morphology-based approaches mostly focusing on macroinvertebrates. In this study we analyse the effects of glacially mediated disturbance on the biodiversity of benthic macrofauna and meiobenthos (meiofauna and Foraminifera) in a Svalbard fjord by comparing morphology and eDNA metabarcoding. Three genetic markers targeting metazoans (COI), meiofauna (18S V1V2) and Foraminifera (18S 37f) were analyzed. Univariate measures of alpha diversity and multivariate compositional dissimilarities were calculated and tested for similarities in response to environmental gradients using correlation analysis. Our study showed different taxonomic composition of morphological and molecular datasets for both macrofauna and meiobenthos. Some taxonomic groups while abundant in metabarcoding data were almost absent in morphology-based inventory and vice versa. In general, species richness and diversity measures in macrofauna morphological data were higher than in metabarcoding, and similar for the meiofauna. Both methodological approaches showed different patterns of response to the glacially mediated disturbance for the macrofauna and the meiobenthos. Macrofauna showed an evident distinction in taxonomic composition and a dramatic cline in alpha diversity indices between the outer and inner parts of fjord, while the meiobenthos showed a gradual change and more subtle responses to environmental changes along the fjord axis. The two methods can be seen as complementing rather than replacing each other. Morphological approach provides more accurate inventory of larger size species and more reliable quantitative data, while metabarcoding allows identification of inconspicuous taxa that are overlooked in morphology-based studies. As different taxa may show different sensitivities to environmental changes, both methods shall be used to monitor marine biodiversity in Arctic ecosystems and its response to dramatically changing environmental conditions.
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Affiliation(s)
- Mikołaj Mazurkiewicz
- Institute of Oceanology Polish Academy of Sciences, Powstańców Warszawy 55, 81-712, Sopot, Poland.
| | - Joanna Pawłowska
- Institute of Oceanology Polish Academy of Sciences, Powstańców Warszawy 55, 81-712, Sopot, Poland
| | - Inés Barrenechea Angeles
- Department of Geosciences, The Arctic University of Norway, Dramsvegen 201, 9010, Tromsø, Norway
| | - Katarzyna Grzelak
- Institute of Oceanology Polish Academy of Sciences, Powstańców Warszawy 55, 81-712, Sopot, Poland
| | - Kajetan Deja
- Institute of Oceanology Polish Academy of Sciences, Powstańców Warszawy 55, 81-712, Sopot, Poland
| | - Agata Zaborska
- Institute of Oceanology Polish Academy of Sciences, Powstańców Warszawy 55, 81-712, Sopot, Poland
| | - Jan Pawłowski
- Institute of Oceanology Polish Academy of Sciences, Powstańców Warszawy 55, 81-712, Sopot, Poland; ID-Gene Ecodiagnostics, Chemin du Pont-du-Centenaire 109, 1228, Plan-les-Ouates, Switzerland
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4
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Lobanov VA, Konecsni KA, Scandrett WB, Jenkins EJ. Identification of Trichinella taxa by ITS-1 amplicon next-generation sequencing with an improved resolution for detecting underrepresented genotypes in mixed natural infections. Parasit Vectors 2023; 16:466. [PMID: 38129932 PMCID: PMC10734138 DOI: 10.1186/s13071-023-06035-1] [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: 07/06/2023] [Accepted: 10/29/2023] [Indexed: 12/23/2023] Open
Abstract
BACKGROUND Amplicon-based next-generation sequencing (NGS) has rapidly gained popularity as a powerful method for delineating taxa in complex communities, including helminths. Here, we applied this approach to identify species and genotypes of zoonotic nematodes of the Trichinella genus. A known limitation of the current multiplex PCR (mPCR) assay recommended by the International Commission on Trichinellosis is that it does not differentiate Trichinella nativa from T. chanchalensis. METHODS The new assay entails deep sequencing of an amplified variable fragment of the ribosomal cistron's (rDNA) internal transcribed spacer 1 using the Illumina platform. The assay was evaluated using first-stage larvae (L1) of select laboratory strains of various Trichinella taxa mixed in known proportions and then validated using archived L1 from 109 wildlife hosts. The species/genotypes of these L1 isolates from wildlife were previously determined using mPCR. RESULTS NGS data analysis for Trichinella laboratory strains selected as representative of North American fauna revealed a sequence representation bias. Trichinella pseudospiralis, a non-encapsulated species, was the most underrepresented when mixed with T. spiralis, T. murrelli, T. nativa and Trichinella T6 in equal quantities. However, five L1 of T. pseudospiralis were readily revealed by NGS in a mix with 2000 L1 of T. nativa (1:400 ratio). From naturally infected wildlife, all Trichinella taxa revealed by mPCR were also identified by NGS in 103 of 107 (96.3%) samples amplified on both assays. NGS identified additional taxa in 11 (10.3%) samples, whereas additional taxa were revealed by mPCR in only four (3.7%) samples. Most isolates comprised single or mixed infections of T. nativa and Trichinella T6. On NGS, T. chanchalensis (T13) was detected in combination with Trichinella T6 in a wolverine (Gulo gulo) and in combination with T. nativa and Trichinella T6 in a marten (Martes americana) from the Northwest Territories, Canada. CONCLUSIONS This new NGS assay demonstrates strong potential as a single assay for identifying all recognised Trichinella taxa as well as improved sensitivity for detecting under-represented and novel genotypes in mixed infections. In addition, we report a new host record for T. chanchalensis in American marten.
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Affiliation(s)
- Vladislav A Lobanov
- Center for Food-borne and Animal Parasitology, Canadian Food Inspection Agency, Saskatoon, SK, Canada.
| | - Kelly A Konecsni
- Center for Food-borne and Animal Parasitology, Canadian Food Inspection Agency, Saskatoon, SK, Canada
| | - W Brad Scandrett
- Center for Food-borne and Animal Parasitology, Canadian Food Inspection Agency, Saskatoon, SK, Canada
| | - Emily J Jenkins
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
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5
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Macheriotou L, Derycke S, Vanreusel A. Environmental filtering along a bathymetric gradient: A metabarcoding meta-analysis of free-living nematodes. Mol Ecol 2023; 32:6177-6189. [PMID: 37971160 DOI: 10.1111/mec.17201] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 10/20/2023] [Accepted: 10/26/2023] [Indexed: 11/19/2023]
Abstract
Identifying and understanding patterns of biological diversity is crucial at a time when even the most remote and pristine marine ecosystems are threatened by resource exploitation such as deep-seabed mining. Metabarcoding provides the means through which one can perform comprehensive investigations of diversity by examining entire assemblages simultaneously. Nematodes commonly represent the most abundant infaunal metazoan group in marine soft sediments. In this meta-analysis, we compiled all publicly available metabarcoding datasets targeting the 18S rRNA v1-v2 region from sediment samples to conduct a global-scale examination of nematode amplicon sequence variant (ASV) alpha diversity patterns and phylogenetic community structure at different depths and habitats. We found that nematode ASV richness followed a parabolic trend, increasing from the intertidal to the shelf, reaching a maximum in the bathyal and decreasing in the abyssal zone. No depth- or habitat-specific assemblages were identified as a large fraction of genera were shared. Contrastingly, the vast majority of ASVs were unique to each habitat and/or depth zone; genetic diversity was thus highly localized. Overwhelmingly, nematode ASVs in all habitats exhibited phylogenetic clustering, pointing to environmental filtering as the primary force defining community assembly rather than competitive interactions. This finding stresses the importance of habitat preservation for the maintenance of marine nematode diversity.
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Affiliation(s)
- Lara Macheriotou
- Marine Biology Research Group, Department of Biology, Ghent University, Ghent, Belgium
| | - Sofie Derycke
- Marine Biology Research Group, Department of Biology, Ghent University, Ghent, Belgium
- Aquatic Environment and Quality, Institute for Agricultural and Fisheries Research (ILVO), Oostende, Belgium
| | - Ann Vanreusel
- Marine Biology Research Group, Department of Biology, Ghent University, Ghent, Belgium
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6
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Bukin YS, Mikhailov IS, Petrova DP, Galachyants YP, Zakharova YR, Likhoshway YV. The effect of metabarcoding 18S rRNA region choice on diversity of microeukaryotes including phytoplankton. World J Microbiol Biotechnol 2023; 39:229. [PMID: 37341802 DOI: 10.1007/s11274-023-03678-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 06/13/2023] [Indexed: 06/22/2023]
Abstract
Metabarcoding using high throughput sequencing of amplicons of the 18S rRNA gene is one of the widely used methods for assessing the diversity of microeukaryotes in various ecosystems. We investigated the effectiveness of the V4 and V8-V9 regions of the 18S rRNA gene by comparing the results of metabarcoding microeukaryotic communities using the DADA2 (ASV), USEARCH-UNOISE3 (ZOTU), and USEARCH-UPARSE (OTU with 97% similarity) algorithms. Both regions showed similar levels of genetic variability and taxa identification accuracy. Richness for DADA2 datasets of both regions was lower than for UNOISE3 and UPARSE datasets, which is due to more accurate error correction in amplicons. Microeukaryotic communities (autotrophs and heterotrophs) structure identified using both regions showed a significant relationship with phytoplankton (autotrophs) communities structure based on microscopy in a seasonal freshwater sample series. The strongest relationship was found between the phytoplankton species and V8-V9 ASVs produced by DADA2.
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Affiliation(s)
- Yuri S Bukin
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Ivan S Mikhailov
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia.
| | - Darya P Petrova
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Yuri P Galachyants
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Yulia R Zakharova
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Yelena V Likhoshway
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
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7
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Rinaldi L, Krücken J, Martinez-Valladares M, Pepe P, Maurelli MP, de Queiroz C, Castilla Gómez de Agüero V, Wang T, Cringoli G, Charlier J, Gilleard JS, von Samson-Himmelstjerna G. Advances in diagnosis of gastrointestinal nematodes in livestock and companion animals. ADVANCES IN PARASITOLOGY 2022; 118:85-176. [PMID: 36088084 DOI: 10.1016/bs.apar.2022.07.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Diagnosis of gastrointestinal nematodes in livestock and companion animals has been neglected for years and there has been an historical underinvestment in the development and improvement of diagnostic tools, undermining the undoubted utility of surveillance and control programmes. However, a new impetus by the scientific community and the quickening pace of technological innovations, are promoting a renaissance of interest in developing diagnostic capacity for nematode infections in veterinary parasitology. A cross-cutting priority for diagnostic tools is the development of pen-side tests and associated decision support tools that rapidly inform on the levels of infection and morbidity. This includes development of scalable, parasite detection using artificial intelligence for automated counting of parasitic elements and research towards establishing biomarkers using innovative molecular and proteomic methods. The aim of this review is to assess the state-of-the-art in the diagnosis of helminth infections in livestock and companion animals and presents the current advances of diagnostic methods for intestinal parasites harnessing (i) automated methods for copromicroscopy based on artificial intelligence, (ii) immunodiagnosis, and (iii) molecular- and proteome-based approaches. Regardless of the method used, multiple factors need to be considered before diagnostics test results can be interpreted in terms of control decisions. Guidelines on how to apply diagnostics and how to interpret test results in different animal species are increasingly requested and some were recently made available in veterinary parasitology for the different domestic species.
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Affiliation(s)
- Laura Rinaldi
- Department of Veterinary Medicine and Animal Production, University of Naples "Federico II", Naples, Italy.
| | - J Krücken
- Institute for Parasitology and Tropical Veterinary Medicine, Veterinary Centre for Resistance Research, Freie Universität Berlin, Berlin, Germany
| | - M Martinez-Valladares
- Instituto de Ganadería de Montaña (CSIC-Universidad de León), Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad de León, León, Spain
| | - P Pepe
- Department of Veterinary Medicine and Animal Production, University of Naples "Federico II", Naples, Italy
| | - M P Maurelli
- Department of Veterinary Medicine and Animal Production, University of Naples "Federico II", Naples, Italy
| | - C de Queiroz
- Faculty of Veterinary Medicine, 3331 Hospital Drive, Host-Parasite Interactions (HPI) Program University of Calgary, Calgary, Alberta, Canada; Faculty of Veterinary Medicine, St Georges University, Grenada
| | - V Castilla Gómez de Agüero
- Instituto de Ganadería de Montaña (CSIC-Universidad de León), Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad de León, León, Spain
| | - T Wang
- Kreavet, Kruibeke, Belgium
| | - Giuseppe Cringoli
- Department of Veterinary Medicine and Animal Production, University of Naples "Federico II", Naples, Italy
| | | | - J S Gilleard
- Faculty of Veterinary Medicine, 3331 Hospital Drive, Host-Parasite Interactions (HPI) Program University of Calgary, Calgary, Alberta, Canada
| | - G von Samson-Himmelstjerna
- Institute for Parasitology and Tropical Veterinary Medicine, Veterinary Centre for Resistance Research, Freie Universität Berlin, Berlin, Germany
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Yu F, Luo W, Xie W, Li Y, Meng S, Kan J, Ye X, Peng T, Wang H, Huang T, Hu Z. Community reassemblies of eukaryotes, prokaryotes, and viruses in the hexabromocyclododecanes-contaminated microcosms. JOURNAL OF HAZARDOUS MATERIALS 2022; 436:129159. [PMID: 35643009 DOI: 10.1016/j.jhazmat.2022.129159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 04/28/2022] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
The microbial community in seriously contaminated environment were not well known. This research investigated the community reassemblies in microcosms made of two distinct mangrove sediments amended with high levels of hexabromocyclododecanes (HBCDs). After eight months of contamination, the transformation of HBCDs yielded various lower brominated products and resulted in acidification (pH ~2). Therefore, the degraders and dehalogenase homologous genes involved in transformation of HBCDs only presented in low abundance to avoid further deterioration of the habitats. Moreover, in these deteriorated habitats, 1344 bacterial, 969 archaeal, 599 eukaryotic (excluded fungi), 187 fungal OTUs, and 10 viral genera, were reduced compared with controls. Specifically, in two groups of microcosms, Zetaproteobacteria, Deinococcus-Thermus, Spirochaetes, Bacteroidetes, Euryarchaeota, and Ascomycota, were positively responding taxa to HBCDs. Caloneis (Bacillariophyta) and Ascomycota turned to the dominant eukaryotic and fungal taxa. Most of predominant taxa were related to the contamination of brominated flame retardants (BFRs). Microbial communities were reassembled in divergent and sediment-dependent manner. The long-term contamination of HBCDs leaded to the change of relations between many taxa, included some of the environmental viruses and their known hosts. This research highlight the importance of monitoring the ecological effects around plants producing or processing halogenated compounds.
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Affiliation(s)
- Fei Yu
- Department of Biology, College of Science, Shantou University, Guangdong Province, PR China
| | - Wenqi Luo
- Department of Biology, College of Science, Shantou University, Guangdong Province, PR China
| | - Wei Xie
- Department of Biology, College of Science, Shantou University, Guangdong Province, PR China
| | - Yuyang Li
- Department of Biology, College of Science, Shantou University, Guangdong Province, PR China
| | - Shanshan Meng
- Department of Biology, College of Science, Shantou University, Guangdong Province, PR China
| | - Jie Kan
- Department of Biology, College of Science, Shantou University, Guangdong Province, PR China
| | - Xueying Ye
- Department of Biology, College of Science, Shantou University, Guangdong Province, PR China
| | - Tao Peng
- Department of Biology, College of Science, Shantou University, Guangdong Province, PR China
| | - Hui Wang
- Department of Biology, College of Science, Shantou University, Guangdong Province, PR China
| | - Tongwang Huang
- Department of Biology, College of Science, Shantou University, Guangdong Province, PR China
| | - Zhong Hu
- Department of Biology, College of Science, Shantou University, Guangdong Province, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong, PR China.
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9
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Ding Q, Li R, Ren X, Chan LY, Ho VWS, Xie D, Ye P, Zhao Z. Genomic architecture of 5S rDNA cluster and its variations within and between species. BMC Genomics 2022; 23:238. [PMID: 35346033 PMCID: PMC8961926 DOI: 10.1186/s12864-022-08476-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 03/16/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Ribosomal DNAs (rDNAs) are arranged in purely tandem repeats, preventing them from being reliably assembled onto chromosomes during generation of genome assembly. The uncertainty of rDNA genomic structure presents a significant barrier for studying their function and evolution. RESULTS Here we generate ultra-long Oxford Nanopore Technologies (ONT) and short NGS reads to delineate the architecture and variation of the 5S rDNA cluster in the different strains of C. elegans and C. briggsae. We classify the individual rDNA's repeating units into 25 types based on the unique sequence variations in each unit of C. elegans (N2). We next perform assembly of the cluster by taking advantage of the long reads that carry these units, which led to an assembly of 5S rDNA cluster consisting of up to 167 consecutive 5S rDNA units in the N2 strain. The ordering and copy number of various rDNA units are consistent with the separation time between strains. Surprisingly, we observed a drastically reduced level of variation in the unit composition in the 5S rDNA cluster in the C. elegans CB4856 and C. briggsae AF16 strains than in the C. elegans N2 strain, suggesting that N2, a widely used reference strain, is likely to be defective in maintaining the 5S rDNA cluster stability compared with other wild isolates of C. elegans or C. briggsae. CONCLUSIONS The results demonstrate that Nanopore DNA sequencing reads are capable of generating assembly of highly repetitive sequences, and rDNA units are highly dynamic both within and between population(s) of the same species in terms of sequence and copy number. The detailed structure and variation of the 5S rDNA units within the rDNA cluster pave the way for functional and evolutionary studies.
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Affiliation(s)
- Qiutao Ding
- Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China
| | - Runsheng Li
- Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China
- Department of Infectious Diseases and Public Health, City University of Hong Kong, Hong Kong SAR, China
| | - Xiaoliang Ren
- Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China
| | - Lu-Yan Chan
- Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China
| | - Vincy W S Ho
- Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China
| | - Dongying Xie
- Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China
| | - Pohao Ye
- Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China
| | - Zhongying Zhao
- Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China.
- State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong SAR, China.
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10
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Genome Characterization and Development of Real-Time PCR Assays for Ditylenchus Dipsaci and D. Weischeri. J Nematol 2022; 54:20220058. [PMID: 36879952 PMCID: PMC9984805 DOI: 10.2478/jofnem-2022-0058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Indexed: 02/04/2023] Open
Abstract
The stem and bulb nematode Ditylenchus dipsaci is a destructive nematode pest on many crops and is internationally quarantined in many countries, whereas Ditylenchus weischeri, only known to infect a weed plant (Cirsium arvense), is an unregulated nematode species with no known economic importance. In this study, we used comparative genomics to identify multiple gene regions and developed novel real-time PCR assays for the detection of D. dipsaci and D. weischeri. We sequenced the genomes of two mixed-stage nematode populations of D. dipsaci and two mixed-stage nematode populations of D. weischeri. The assembled genomes of D. dipsaci were 228.2 Mb and 239.5 Mb, and the genomes of D. weischeri were 177.0 Mb and 196.3 Mb. Depending on the species, 21,403-27,365 gene models were predicted. Using orthologous group analysis, single-copy and species-specific genes were identified. Primers and probes were designed targeting two species-specific genes in each species. The assays detected as low as 12 pg of DNA from the target species, or as few as five nematodes, with a Cq of 31 cycles or less. Our study provides genome data for two additional D. dipsaci isolates and two D. weischeri isolates, and four new and validated molecular assays to be used for rapid detection and identification of the two species.
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11
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Katju V, Konrad A, Deiss TC, Bergthorsson U. Mutation rate and spectrum in obligately outcrossing Caenorhabditis elegans mutation accumulation lines subjected to RNAi-induced knockdown of the mismatch repair gene msh-2. G3 GENES|GENOMES|GENETICS 2022; 12:6407146. [PMID: 34849777 PMCID: PMC8727991 DOI: 10.1093/g3journal/jkab364] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 10/13/2021] [Indexed: 01/09/2023]
Abstract
DNA mismatch repair (MMR), an evolutionarily conserved repair pathway shared by prokaryotic and eukaryotic species alike, influences molecular evolution by detecting and correcting mismatches, thereby protecting genetic fidelity, reducing the mutational load, and preventing lethality. Herein we conduct the first genome-wide evaluation of the alterations to the mutation rate and spectrum under impaired activity of the MutSα homolog, msh-2, in Caenorhabditis elegans male–female fog-2(lf) lines. We performed mutation accumulation (MA) under RNAi-induced knockdown of msh-2 for up to 50 generations, followed by next-generation sequencing of 19 MA lines and the ancestral control. msh-2 impairment in the male–female background substantially increased the frequency of nuclear base substitutions (∼23×) and small indels (∼328×) relative to wildtype hermaphrodites. However, we observed no increase in the mutation rates of mtDNA, and copy-number changes of single-copy genes. There was a marked increase in copy-number variation of rDNA genes under MMR impairment. In C. elegans, msh-2 repairs transitions more efficiently than transversions and increases the AT mutational bias relative to wildtype. The local sequence context, including sequence complexity, G + C-content, and flanking bases influenced the mutation rate. The X chromosome exhibited lower substitution and higher indel rates than autosomes, which can either result from sex-specific mutation rates or a nonrandom distribution of mutable sites between chromosomes. Provided the observed difference in mutational pattern is mostly due to MMR impairment, our results indicate that the specificity of MMR varies between taxa, and is more efficient in detecting and repairing small indels in eukaryotes relative to prokaryotes.
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Affiliation(s)
- Vaishali Katju
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77845, USA
| | - Anke Konrad
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77845, USA
- Faculdade de Ciência da Universidade de Lisboa (FCUL), CE3C—Centre for Ecology, Evolution and Environmental Changes, 1749-016 Lisboa, Portugal
| | - Thaddeus C Deiss
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77845, USA
| | - Ulfar Bergthorsson
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77845, USA
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12
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Amplicon-based next-generation sequencing of eukaryotic nuclear ribosomal genes (metabarcoding) for the detection of single-celled parasites in human faecal samples. Parasite Epidemiol Control 2022; 17:e00242. [PMID: 35146142 PMCID: PMC8819130 DOI: 10.1016/j.parepi.2022.e00242] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 01/26/2022] [Accepted: 01/26/2022] [Indexed: 01/12/2023] Open
Abstract
Comprehensive detection and differentiation of intestinal protists mostly rely on DNA-based methods. Here, we evaluated next-generation sequencing of eukaryotic nuclear ribosomal genes (metabarcoding) for the detection and differentiation of intestinal eukaryotic protists in the stool of healthy Tunisian individuals. Thirty-six faecal DNA samples previously evaluated by microscopy and ameboid species-specific PCRs were tested. The hypervariable regions V3-V4 and V3-V5 of the 18S rRNA gene were amplified using three universal eukaryotic primer sets and sequenced using Illumina®MiSeq sequencing. In addition, real-time PCR assays were used to detect Dientamoeba fragilis, Giardia duodenalis, and Cryptosporidium spp. The metabarcoding assay detected Blastocystis (subtypes 1, 2, and 3) and archamoebid species and subtypes (Entamoeba dispar, Entamoeba hartmanni, Entamoeba coli RL1 and RL2, Endolimax nana, Iodamoeba bütschlii RL1) in 27 (75%) and 22 (61%) of the 36 stool samples, respectively. Meanwhile, the assay had limited sensitivity for flagellates as evidenced by the fact that no Giardia-specific reads were found in any of the five Giardia-positive samples included, and Dientamoeba-specific reads were observed only in 3/13 D. fragilis-positive samples. None of the samples were positive for Cryptosporidium by any of the methods. In conclusion, a large variety of intestinal eukaryotic protists were detected and differentiated at species and subtype level; however, limited sensitivity for common flagellates was observed.
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13
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Sun X, Cheng J. Phylogenetic Signal Dissection of Heterogeneous 28S and 16S rRNA Genes in Spinicaudata (Branchiopoda, Diplostraca). Genes (Basel) 2021; 12:1705. [PMID: 34828311 PMCID: PMC8625258 DOI: 10.3390/genes12111705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 10/20/2021] [Accepted: 10/26/2021] [Indexed: 12/05/2022] Open
Abstract
It is still a challenge to reconstruct the deep phylogenetic relationships within spinicaudatans, and there are several different competing hypotheses regarding the interrelationships among Eocyzicidae, Cyzicidae s. s., Leptestheriidae, and Limnadiidae of the Suborder Spinicaudata. In order to explore the source of the inconsistencies, we focus on the sequence variation and the structure model of two rRNA genes based on extensive taxa sampling. The comparative sequence analysis revealed heterogeneity across species and the existence of conserved motifs in all spinicaudatan species. The level of intraspecific heterogeneity differed among species, which suggested that some species might have undergone a relaxed concerted evolution with respect to the 28S rRNA gene. The Bayesian analyses were performed on nuclear (28S rRNA, EF1α) and mitochondrial (16S rRNA, COI) genes. Further, we investigated compositional heterogeneity between lineages and assessed the potential for phylogenetic noise compared to signal in the combined data set. Reducing the non-phylogenetic signals and application of optimal rRNA model recovered a topology congruent with inference from the transcriptome data, whereby Limnadiidae was placed as a sister group to Leptestheriidae + Eocyzicidae with high support (topology I). Tests of alternative hypotheses provided implicit support for four competing topologies, and topology I was the best.
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Affiliation(s)
| | - Jinhui Cheng
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology and Center for Excellence in Life and Palaeoenvironment, Chinese Academy of Sciences, No. 39, Beijing Eastroad, Nanjing 210008, China;
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14
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Wahba L, Hansen L, Fire AZ. An essential role for the piRNA pathway in regulating the ribosomal RNA pool in C. elegans. Dev Cell 2021; 56:2295-2312.e6. [PMID: 34388368 PMCID: PMC8387450 DOI: 10.1016/j.devcel.2021.07.014] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 06/11/2021] [Accepted: 07/15/2021] [Indexed: 01/08/2023]
Abstract
Piwi-interacting RNAs (piRNAs) are RNA effectors with key roles in maintaining genome integrity and promoting fertility in metazoans. In Caenorhabditis elegans loss of piRNAs leads to a transgenerational sterility phenotype. The plethora of piRNAs and their ability to silence transcripts with imperfect complementarity have raised several (non-exclusive) models for the underlying drivers of sterility. Here, we report the extranuclear and transferable nature of the sterility driver, its suppression via mutations disrupting the endogenous RNAi and poly-uridylation machinery, and copy-number amplification at the ribosomal DNA locus. In piRNA-deficient animals, several small interfering RNA (siRNA) populations become increasingly overabundant in the generations preceding loss of germline function, including ribosomal siRNAs (risiRNAs). A concomitant increase in uridylated sense rRNA fragments suggests that poly-uridylation may potentiate RNAi-mediated gene silencing of rRNAs. We conclude that loss of the piRNA machinery allows for unchecked amplification of siRNA populations, originating from abundant highly structured RNAs, to deleterious levels.
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Affiliation(s)
- Lamia Wahba
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Loren Hansen
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Andrew Z Fire
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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15
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McElroy KE, Müller S, Lamatsch DK, Bankers L, Fields PD, Jalinsky JR, Sharbrough J, Boore JL, Logsdon JM, Neiman M. Asexuality Associated with Marked Genomic Expansion of Tandemly Repeated rRNA and Histone Genes. Mol Biol Evol 2021; 38:3581-3592. [PMID: 33885820 PMCID: PMC8382920 DOI: 10.1093/molbev/msab121] [Citation(s) in RCA: 4] [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] [Indexed: 12/23/2022] Open
Abstract
How does asexual reproduction influence genome evolution? Although is it clear that genomic structural variation is common and important in natural populations, we know very little about how one of the most fundamental of eukaryotic traits-mode of genomic inheritance-influences genome structure. We address this question with the New Zealand freshwater snail Potamopyrgus antipodarum, which features multiple separately derived obligately asexual lineages that coexist and compete with otherwise similar sexual lineages. We used whole-genome sequencing reads from a diverse set of sexual and asexual individuals to analyze genomic abundance of a critically important gene family, rDNA (the genes encoding rRNAs), that is notable for dynamic and variable copy number. Our genomic survey of rDNA in P. antipodarum revealed two striking results. First, the core histone and 5S rRNA genes occur between tandem copies of the 18S-5.8S-28S gene cluster, a unique architecture for these crucial gene families. Second, asexual P. antipodarum harbor dramatically more rDNA-histone copies than sexuals, which we validated through molecular and cytogenetic analysis. The repeated expansion of this genomic region in asexual P. antipodarum lineages following distinct transitions to asexuality represents a dramatic genome structural change associated with asexual reproduction-with potential functional consequences related to the loss of sexual reproduction.
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Affiliation(s)
- Kyle E McElroy
- Ecology, Evolutionary, and Organismal Biology, Iowa State University, Ames, IA, USA
- Department of Biology, University of Iowa, Iowa City, IA, USA
| | - Stefan Müller
- Institute of Human Genetics, Munich University Hospital, Ludwig-Maximilians University, Munich, Germany
| | - Dunja K Lamatsch
- Research Department for Limnology, University of Innsbruck, Mondsee, Mondsee, Austria
| | - Laura Bankers
- Division of Infectious Diseases, University of Colorado—Anschutz Medical Campus, Aurora, CO, USA
| | - Peter D Fields
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland
| | | | - Joel Sharbrough
- Biology Department, New Mexico Institute of Mining and Technology, Socorro, NM, USA
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Jeffrey L Boore
- Providence St. Joseph Health and Institute for Systems Biology, Seattle, WA, USA
| | - John M Logsdon
- Department of Biology, University of Iowa, Iowa City, IA, USA
| | - Maurine Neiman
- Department of Biology, University of Iowa, Iowa City, IA, USA
- Department of Gender, Women's, and Sexuality Studies, University of Iowa, Iowa City, IA, USA
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16
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Cordier T, Alonso‐Sáez L, Apothéloz‐Perret‐Gentil L, Aylagas E, Bohan DA, Bouchez A, Chariton A, Creer S, Frühe L, Keck F, Keeley N, Laroche O, Leese F, Pochon X, Stoeck T, Pawlowski J, Lanzén A. Ecosystems monitoring powered by environmental genomics: A review of current strategies with an implementation roadmap. Mol Ecol 2021; 30:2937-2958. [PMID: 32416615 PMCID: PMC8358956 DOI: 10.1111/mec.15472] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 04/25/2020] [Accepted: 05/06/2020] [Indexed: 01/02/2023]
Abstract
A decade after environmental scientists integrated high-throughput sequencing technologies in their toolbox, the genomics-based monitoring of anthropogenic impacts on the biodiversity and functioning of ecosystems is yet to be implemented by regulatory frameworks. Despite the broadly acknowledged potential of environmental genomics to this end, technical limitations and conceptual issues still stand in the way of its broad application by end-users. In addition, the multiplicity of potential implementation strategies may contribute to a perception that the routine application of this methodology is premature or "in development", hence restraining regulators from binding these tools into legal frameworks. Here, we review recent implementations of environmental genomics-based methods, applied to the biomonitoring of ecosystems. By taking a general overview, without narrowing our perspective to particular habitats or groups of organisms, this paper aims to compare, review and discuss the strengths and limitations of four general implementation strategies of environmental genomics for monitoring: (a) Taxonomy-based analyses focused on identification of known bioindicators or described taxa; (b) De novo bioindicator analyses; (c) Structural community metrics including inferred ecological networks; and (d) Functional community metrics (metagenomics or metatranscriptomics). We emphasise the utility of the three latter strategies to integrate meiofauna and microorganisms that are not traditionally utilised in biomonitoring because of difficult taxonomic identification. Finally, we propose a roadmap for the implementation of environmental genomics into routine monitoring programmes that leverage recent analytical advancements, while pointing out current limitations and future research needs.
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Affiliation(s)
- Tristan Cordier
- Department of Genetics and EvolutionScience IIIUniversity of GenevaGenevaSwitzerland
| | - Laura Alonso‐Sáez
- AZTIMarine ResearchBasque Research and Technology Alliance (BRTA)Spain
| | | | - Eva Aylagas
- Red Sea Research Center (RSRC)Biological and Environmental Sciences and Engineering (BESE)King Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
| | - David A. Bohan
- AgroécologieINRAEUniversity of BourgogneUniversity Bourgogne Franche‐ComtéDijonFrance
| | | | - Anthony Chariton
- Department of Biological SciencesMacquarie UniversitySydneyNSWAustralia
| | - Simon Creer
- School of Natural SciencesBangor UniversityGwyneddUK
| | - Larissa Frühe
- Department of EcologyTechnische Universität KaiserslauternKaiserslauternGermany
| | | | - Nigel Keeley
- Benthic Resources and Processes GroupInstitute of Marine ResearchTromsøNorway
| | - Olivier Laroche
- Benthic Resources and Processes GroupInstitute of Marine ResearchTromsøNorway
| | - Florian Leese
- Aquatic Ecosystem ResearchFaculty of BiologyUniversity of Duisburg‐EssenEssenGermany
- Centre for Water and Environmental Research (ZWU)University of Duisburg‐EssenEssenGermany
| | - Xavier Pochon
- Coastal & Freshwater GroupCawthron InstituteNelsonNew Zealand
- Institute of Marine ScienceUniversity of AucklandWarkworthNew Zealand
| | - Thorsten Stoeck
- Department of EcologyTechnische Universität KaiserslauternKaiserslauternGermany
| | - Jan Pawlowski
- Department of Genetics and EvolutionScience IIIUniversity of GenevaGenevaSwitzerland
- ID‐Gene EcodiagnosticsGenevaSwitzerland
- Institute of OceanologyPolish Academy of SciencesSopotPoland
| | - Anders Lanzén
- AZTIMarine ResearchBasque Research and Technology Alliance (BRTA)Spain
- Basque Foundation for ScienceIKERBASQUEBilbaoSpain
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17
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Loss of m 1acp 3Ψ Ribosomal RNA Modification Is a Major Feature of Cancer. Cell Rep 2021; 31:107611. [PMID: 32375039 DOI: 10.1016/j.celrep.2020.107611] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 02/03/2020] [Accepted: 04/14/2020] [Indexed: 12/22/2022] Open
Abstract
The ribosome is an RNA-protein complex that is essential for translation in all domains of life. The structural and catalytic core of the ribosome is its ribosomal RNA (rRNA). While mutations in ribosomal protein (RP) genes are known drivers of oncogenesis, oncogenic rRNA variants have remained elusive. We identify a cancer-specific single-nucleotide variation in 18S rRNA at nucleotide 1248.U in up to 45.9% of patients with colorectal carcinoma (CRC) and present across >22 cancer types. This is the site of a unique hyper-modified base, 1-methyl-3-α-amino-α-carboxyl-propyl pseudouridine (m1acp3Ψ), a >1-billion-years-conserved RNA modification at the peptidyl decoding site of the ribosome. A subset of CRC tumors we call hypo-m1acp3Ψ shows sub-stoichiometric m1acp3Ψ modification, unlike normal control tissues. An m1acp3Ψ knockout model and hypo-m1acp3Ψ patient tumors share a translational signature characterized by highly abundant ribosomal proteins. Thus, m1acp3Ψ-deficient rRNA forms an uncharacterized class of "onco-ribosome" which may serve as a chemotherapeutic target for treating cancer patients.
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18
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The occurrence of Nematoda in coastal sea ice on Svalbard (European Arctic) determined with the 18S small subunit rRNA gene. Polar Biol 2021. [DOI: 10.1007/s00300-021-02863-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
AbstractUnderstanding the diversity and functioning of Arctic sea ice ecosystems is vital to evaluate and predict the impact of current and future climate change. In the microscopic communities inhabiting the brine channels inside sea ice, nematodes often dominate numerically and act as bacterivores and herbivores. Despite nematodes great abundances and known ecological roles, molecular tools have not been applied to investigate their species diversity in sea ice. In an attempt to begin establishing a molecular baseline for species diversity of sea ice nematodes, we Sanger sequenced 74 specimens from four locations around Svalbard (European Arctic), using the 18S rRNA barcode. Currently available nucleotide reference databases are both underpopulated with representative marine nematode taxa and contain a substantial number of misidentified organisms. Together, these limitations inhibited the ability to identify marine specimens collected in this study with certainty. Nevertheless, our molecular data indicate the presence of two genera in sea ice on Svalbard—Theristus and Halomonhystera. While it is possible that the latter represents a novel ice nematode species, future studies, including morphometric analysis, are needed to verify our molecular findings. We leverage the assignment of molecular information to robustly identify nematodes and provide the first insight into the diversity of sea ice nematodes in the European Arctic. We advocate for an intensified cooperation between molecular and morphological taxonomists to expedite the establishment of baseline surveys that are required to predict biological consequences of the diminishing sea ice habitat in the future.
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19
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Jurburg SD, Keil P, Singh BK, Chase JM. All together now: Limitations and recommendations for the simultaneous analysis of all eukaryotic soil sequences. Mol Ecol Resour 2021; 21:1759-1771. [PMID: 33943001 DOI: 10.1111/1755-0998.13401] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 03/31/2021] [Accepted: 04/13/2021] [Indexed: 02/06/2023]
Abstract
The soil environment contains a large, but historically underexplored, reservoir of biodiversity. Sequencing prokaryotic marker genes has become commonplace for the discovery and characterization of soil bacteria and archaea. Increasingly, this approach is also applied to eukaryotic marker genes to characterize the diversity and distribution of soil eukaryotes. However, understanding the properties and limitations of eukaryotic marker sequences is essential for correctly analysing, interpreting, and synthesizing the resulting data. Here, we illustrate several biases from sequencing data that affect measurements of biodiversity that arise from variation in morphology, taxonomy and phylogeny between organisms, as well as from sampling designs. We recommend analytical approaches to overcome these limitations, and outline how the benchmarking and standardization of sequencing protocols may improve the comparability of the data.
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Affiliation(s)
- Stephanie D Jurburg
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.,Institute of Biology, Leipzig University, Leipzig, Germany
| | - Petr Keil
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.,Department of Computer Science, Martin Luther University, Halle-Wittenberg, Halle, Germany.,Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Praha-Suchdol, Czech Republic
| | - Brajesh K Singh
- Hawkesbury Institute for the Environment, and Global Centre for Land-Based Innovation, Western Sydney University, Penrith, NSW, Australia
| | - Jonathan M Chase
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.,Department of Computer Science, Martin Luther University, Halle-Wittenberg, Halle, Germany
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20
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The genomic structure of a human chromosome 22 nucleolar organizer region determined by TAR cloning. Sci Rep 2021; 11:2997. [PMID: 33542373 PMCID: PMC7862453 DOI: 10.1038/s41598-021-82565-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 01/18/2021] [Indexed: 12/13/2022] Open
Abstract
The rDNA clusters and flanking sequences on human chromosomes 13, 14, 15, 21 and 22 represent large gaps in the current genomic assembly. The organization and the degree of divergence of the human rDNA units within an individual nucleolar organizer region (NOR) are only partially known. To address this lacuna, we previously applied transformation-associated recombination (TAR) cloning to isolate individual rDNA units from chromosome 21. That approach revealed an unexpectedly high level of heterogeneity in human rDNA, raising the possibility of corresponding variations in ribosome dynamics. We have now applied the same strategy to analyze an entire rDNA array end-to-end from a copy of chromosome 22. Sequencing of TAR isolates provided the entire NOR sequence, including proximal and distal junctions that may be involved in nucleolar function. Comparison of the newly sequenced rDNAs to reference sequence for chromosomes 22 and 21 revealed variants that are shared in human rDNA in individuals from different ethnic groups, many of them at high frequency. Analysis infers comparable intra- and inter-individual divergence of rDNA units on the same and different chromosomes, supporting the concerted evolution of rDNA units. The results provide a route to investigate further the role of rDNA variation in nucleolar formation and in the empirical associations of nucleoli with pathology.
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21
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De Luca D, Kooistra WHCF, Sarno D, Biffali E, Piredda R. Empirical evidence for concerted evolution in the 18S rDNA region of the planktonic diatom genus Chaetoceros. Sci Rep 2021; 11:807. [PMID: 33437054 PMCID: PMC7804092 DOI: 10.1038/s41598-020-80829-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 12/28/2020] [Indexed: 11/08/2022] Open
Abstract
Concerted evolution is a process of homogenisation of repetitive sequences within a genome through unequal crossing over and gene conversion. This homogenisation is never fully achieved because mutations always create new variants. Classically, concerted evolution has been detected as "noise" in electropherograms and these variants have been characterised through cloning and sequencing of subsamples of amplified products. However, this approach limits the number of detectable variants and provides no information about the abundance of each variant. In this study, we investigated concerted evolution by using environmental time-series metabarcoding data, single strain high-throughput sequencing (HTS) and a collection of Sanger reference barcode sequences. We used six species of the marine planktonic diatom genus Chaetoceros as study system. Abundance plots obtained from environmental metabarcoding and single strain HTS showed the presence of a haplotype far more abundant than all the others (the "dominant" haplotype) and identical to the reference sequences of that species obtained with Sanger sequencing. This distribution fitted best with Zipf's law among the rank abundance/ dominance models tested. Furthermore, in each strain 99% of reads showed a similarity of 99% with the dominant haplotype, confirming the efficiency of the homogenisation mechanism of concerted evolution. We also demonstrated that minor haplotypes found in the environmental samples are not only technical artefacts, but mostly intragenomic variation generated by incomplete homogenisation. Finally, we showed that concerted evolution can be visualised inferring phylogenetic networks from environmental data. In conclusion, our study provides an important contribution to the understanding of concerted evolution and to the interpretation of DNA barcoding and metabarcoding data based on multigene family markers.
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Affiliation(s)
- Daniele De Luca
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy.
- Department of Biology, University of Naples Federico II, Botanical Garden of Naples, Via Foria 223, 80139, Naples, Italy.
| | - Wiebe H C F Kooistra
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy
| | - Diana Sarno
- Department of Research Infrastructure for Marine Biological Resources, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy
| | - Elio Biffali
- Department of Research Infrastructure for Marine Biological Resources, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy
| | - Roberta Piredda
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy.
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22
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Sims J, Rabanal FA, Elgert C, von Haeseler A, Schlögelhofer P. It Is Just a Matter of Time: Balancing Homologous Recombination and Non-homologous End Joining at the rDNA Locus During Meiosis. FRONTIERS IN PLANT SCIENCE 2021; 12:773052. [PMID: 34777453 PMCID: PMC8580885 DOI: 10.3389/fpls.2021.773052] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 10/04/2021] [Indexed: 05/17/2023]
Abstract
Ribosomal RNA genes (rDNAs) are located in large domains of hundreds of rDNA units organized in a head-to-tail manner. The proper and stable inheritance of rDNA clusters is of paramount importance for survival. Yet, these highly repetitive elements pose a potential risk to the genome since they can undergo non-allelic exchanges. Here, we review the current knowledge of the organization of the rDNA clusters in Arabidopsis thaliana and their stability during meiosis. Recent findings suggest that during meiosis, all rDNA loci are embedded within the nucleolus favoring non-homologous end joining (NHEJ) as a repair mechanism, while DNA repair via homologous recombination (HR) appears to be a rare event. We propose a model where (1) frequent meiotic NHEJ events generate abundant single nucleotide polymorphisms and insertions/deletions within the rDNA, resulting in a heterogeneous population of rDNA units and (2) rare HR events dynamically change rDNA unit numbers, only to be observed in large populations over many generations. Based on the latest efforts to delineate the entire rDNA sequence in A. thaliana, we discuss evidence supporting this model. The results compiled so far draw a surprising picture of rDNA sequence heterogeneity between individual units. Furthermore, rDNA cluster sizes have been recognized as relatively stable when observing less than 10 generations, yet emerged as major determinant of genome size variation between different A. thaliana ecotypes. The sequencing efforts also revealed that transcripts from the diverse rDNA units yield heterogenous ribosome populations with potential functional implications. These findings strongly motivate further research to understand the mechanisms that maintain the metastable state of rDNA loci.
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Affiliation(s)
- Jason Sims
- Department of Chromosome Biology, Max Perutz Labs, University of Vienna, Vienna BioCenter, Vienna, Austria
- *Correspondence: Jason Sims,
| | - Fernando A. Rabanal
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Christiane Elgert
- Center for Integrative Bioinformatics Vienna (CIBIV), Max Perutz Labs, University of Vienna and Medical University of Vienna, Vienna BioCenter, Vienna, Austria
| | - Arndt von Haeseler
- Center for Integrative Bioinformatics Vienna (CIBIV), Max Perutz Labs, University of Vienna and Medical University of Vienna, Vienna BioCenter, Vienna, Austria
- Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria
| | - Peter Schlögelhofer
- Department of Chromosome Biology, Max Perutz Labs, University of Vienna, Vienna BioCenter, Vienna, Austria
- Peter Schlögelhofer,
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23
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Isayama K, Watanabe K, Okamoto M, Murata T, Mizukami Y. Standardization of an LNA-based TaqMan assay qPCR analysis for Aspiculuris tetraptera DNA in mouse faeces. BMC Microbiol 2020; 20:371. [PMID: 33287731 PMCID: PMC7720592 DOI: 10.1186/s12866-020-02053-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 11/26/2020] [Indexed: 11/24/2022] Open
Abstract
Background Aspiculuris tetraptera, as a parasitic pinworm, is most frequently detected in laboratory mice, and transmission is mediated by the eggs contained in the faeces of infected mice. A highly sensitive and quantitative faeces-based diagnostic tool would be useful for the early detection of A. tetraptera to inhibit the expansion of infection. In this study, we developed a quantitative assay that exhibits high sensitivity in detecting A. tetraptera in faeces using PCR techniques. Results Endpoint PCR demonstrated the detection of A. tetraptera DNA in 0.5 ng genomic DNA extracted from the faeces of infected mice. To quantitatively detect the small amount of A. tetraptera DNA, locked nucleic acid (LNA)-based primers and LNA-based TaqMan probes were used for the quantitative PCR assay (qPCR). The combination of LNA-based DNA increased detection sensitivity by more than 100-fold compared to using normal oligo DNAs. The copy number of the A. tetraptera DNA detected was positively related to the infected faeces-derived genomic DNA with a simple linearity regression in the range of 20 pg to 15 ng of the genomic DNA. To more conveniently detect infection using faeces, the LNA-based TaqMan assay was applied to the crude fraction of the faeces without DNA purification. An assay using ethanol precipitation of the faeces yielded results consistent with those of direct microscopic observation. Conclusion The LNA-TaqMan assay developed in this study quantitatively detects A. tetraptera infection in mouse faeces. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-020-02053-6.
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Affiliation(s)
- Keishiro Isayama
- Institute of Laboratory Animals, Yamaguchi University Science Research Center, Yamaguchi, 755-8505, Japan
| | - Kenji Watanabe
- Institute of Gene Research, Yamaguchi University Science Research Center, Yamaguchi, 755-8505, Japan
| | - Mariko Okamoto
- Laboratory of Veterinary Immunology, School of Veterinary Medicine, Azabu University, Sagamihara, 252-5201, Japan
| | - Tomoaki Murata
- Institute of Laboratory Animals, Yamaguchi University Science Research Center, Yamaguchi, 755-8505, Japan
| | - Yoichi Mizukami
- Institute of Gene Research, Yamaguchi University Science Research Center, Yamaguchi, 755-8505, Japan.
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24
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Piredda R, Grimm GW, Schulze ED, Denk T, Simeone MC. High-throughput sequencing of 5S-IGS in oaks: Exploring intragenomic variation and algorithms to recognize target species in pure and mixed samples. Mol Ecol Resour 2020; 21:495-510. [PMID: 32997899 DOI: 10.1111/1755-0998.13264] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 08/28/2020] [Accepted: 09/01/2020] [Indexed: 11/30/2022]
Abstract
Measuring biological diversity is a crucial but difficult undertaking, as exemplified in oaks where complex patterns of morphological, ecological, biogeographical and genetic differentiation collide with traditional taxonomy, which measures biodiversity in number of species (or higher taxa). In this pilot study, we generated high-throughput sequencing amplicon data of the intergenic spacer of the 5S nuclear ribosomal DNA cistron (5S-IGS) in oaks, using six mock samples that differ in geographical origin, species composition and pool complexity. The potential of the marker for automated genotaxonomy applications was assessed using a reference data set of 1,770 5S-IGS cloned sequences, covering the entire taxonomic breadth and distribution range of western Eurasian Quercus, and applying similarity (blast) and evolutionary approaches (maximum-likelihood trees and Evolutionary Placement Algorithm). Both methods performed equally well, allowing correct identification of species in sections Ilex and Cerris in the pure and mixed samples, and main lineages shared by species of sect. Quercus. Application of different cut-off thresholds revealed that medium- to high-abundance (>10 or 25) sequences suffice for a net species identification of samples containing one or a few individuals. Lower thresholds identify phylogenetic correspondence with all target species in highly mixed samples (analogous to environmental bulk samples) and include rare variants pointing towards reticulation, incomplete lineage sorting, pseudogenic 5S units and in situ (natural) contamination. Our pipeline is highly promising for future assessments of intraspecific and interpopulation diversity, and of the genetic resources of natural ecosystems, which are fundamental to empower fast and solid biodiversity conservation programmes worldwide.
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Affiliation(s)
| | - Guido W Grimm
- Orléans, France.,Department of Palaeontology, University of Vienna, Vienna, Austria
| | | | - Thomas Denk
- Swedish Museum of Natural History, Stockholm, Sweden
| | - Marco Cosimo Simeone
- Dipartimento di Scienze Agrarie e Forestali (DAFNE), Università degli studi della Tuscia, Viterbo, Italy
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25
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Schenk J, Höss S, Brinke M, Kleinbölting N, Brüchner-Hüttemann H, Traunspurger W. Nematodes as bioindicators of polluted sediments using metabarcoding and microscopic taxonomy. ENVIRONMENT INTERNATIONAL 2020; 143:105922. [PMID: 32663713 DOI: 10.1016/j.envint.2020.105922] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 03/04/2020] [Accepted: 06/20/2020] [Indexed: 05/19/2023]
Abstract
The use of bioindicator species is a widely applied approach to evaluate ecological conditions, and several indices have been designed for this purpose. To assess the impact of pollution, especially in sediments, a pollution-sensitive index based on nematodes, one of the most abundant and species-rich groups of metazoa, was developed. The NemaSPEAR[%] index in its original form relies on the morphological inspection of nematode species. The application of a morphologically based NemaSPEAR[%] at the genus-level was previously validated. The present study evaluated a NemaSPEAR[%] index based on metabarcoding of nematode communities and tested the potential of fragments from the 28S rDNA, 18S rDNA and cytochrome c oxidase subunit I (COI) genes. In general, molecular-based results tended to show a poorer condition than morphology-based results for the investigated sites. At the genus level, NemaSPEAR[%] values based on morphological data strongly correlated with those based on molecular data for both the 28S rDNA and the 18S rDNA gene fragments (R2 = 0.86 and R2 = 0.74, respectively). Within the dominant genera (>3%) identified by morphology, 68% were detected by at least one of the two ribosomal markers. At the species level, however, concordance was less pronounced, as there were several deviations of the molecular from the morphological data. These differences could mostly be attributed to shortcomings in the reference database used in the molecular-based assignments. Our pilot study shows that a molecularly based, genus-level NemaSPEAR[%] can be successfully applied to evaluate polluted sediment. Future studies need to validate this approach further, e.g. with bulk extractions of whole meiofaunal communities in order to circumvent time-consuming nematode isolation. Further database curation with abundant NemaSPEAR[%] species will also increase the applicability of this approach.
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Affiliation(s)
- Janina Schenk
- Department of Animal Ecology, Bielefeld University, Konsequenz 45, 33615 Bielefeld, Germany.
| | - Sebastian Höss
- Department of Animal Ecology, Bielefeld University, Konsequenz 45, 33615 Bielefeld, Germany; Ecossa, Giselastrasse 6, 82319 Starnberg, Germany.
| | - Marvin Brinke
- Federal Institute of Hydrology (BfG), Mainzer Tor 1, 56068 Koblenz, Germany.
| | - Nils Kleinbölting
- Center for Biotechnology, Bielefeld University, Universitaetsstrasse 25, 33615 Bielefeld, Germany.
| | | | - Walter Traunspurger
- Department of Animal Ecology, Bielefeld University, Konsequenz 45, 33615 Bielefeld, Germany.
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26
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Nematode Identification Techniques and Recent Advances. PLANTS 2020; 9:plants9101260. [PMID: 32987762 PMCID: PMC7598616 DOI: 10.3390/plants9101260] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 09/21/2020] [Accepted: 09/22/2020] [Indexed: 01/02/2023]
Abstract
Nematodes are among the most diverse but least studied organisms. The classic morphology-based identification has proved insufficient to the study of nematode identification and diversity, mainly for lack of sufficient morphological variations among closely related taxa. Different molecular methods have been used to supplement morphology-based methods and/or circumvent these problems with various degrees of success. These methods range from fingerprint to sequence analyses of DNA- and/or protein-based information. Image analyses techniques have also contributed towards this success. In this review, we highlight what each of these methods entail and provide examples where more recent advances of these techniques have been employed in nematode identification. Wherever possible, emphasis has been given to nematodes of agricultural significance. We show that these alternative methods have aided nematode identification and raised our understanding of nematode diversity and phylogeny. We discuss the pros and cons of these methods and conclude that no one method by itself provides all the answers; the choice of method depends on the question at hand, the nature of the samples, and the availability of resources.
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27
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Cai R, Archidona‐Yuste A, Cantalapiedra‐Navarrete C, Palomares‐Rius JE, Castillo P. New evidence of cryptic speciation in the family Longidoridae (Nematoda: Dorylaimida). J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12393] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Ruihang Cai
- Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), Avenida Menéndez Pidal s/n, Campus de Excelencia Internacional Agroalimentario, ceiA3 CSIC Córdoba Spain
- Laboratory of Plant Nematology Institute of Biotechnology College of Agriculture and Biotechnology Zhejiang University Hangzhou China
| | - Antonio Archidona‐Yuste
- Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), Avenida Menéndez Pidal s/n, Campus de Excelencia Internacional Agroalimentario, ceiA3 CSIC Córdoba Spain
- Department of Ecological Modelling Helmholtz Centre for Environmental Research ‐ UFZ Leipzig Germany
| | - Carolina Cantalapiedra‐Navarrete
- Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), Avenida Menéndez Pidal s/n, Campus de Excelencia Internacional Agroalimentario, ceiA3 CSIC Córdoba Spain
| | - Juan E. Palomares‐Rius
- Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), Avenida Menéndez Pidal s/n, Campus de Excelencia Internacional Agroalimentario, ceiA3 CSIC Córdoba Spain
| | - Pablo Castillo
- Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), Avenida Menéndez Pidal s/n, Campus de Excelencia Internacional Agroalimentario, ceiA3 CSIC Córdoba Spain
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28
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Laidoudi Y, Davoust B, Varloud M, Niang EHA, Fenollar F, Mediannikov O. Development of a multiplex qPCR-based approach for the diagnosis of Dirofilaria immitis, D. repens and Acanthocheilonema reconditum. Parasit Vectors 2020; 13:319. [PMID: 32571427 PMCID: PMC7309989 DOI: 10.1186/s13071-020-04185-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 06/13/2020] [Indexed: 12/17/2022] Open
Abstract
Background Dirofilaria immitis, D. repens and Acanthocheilonema reconditum are the main causative agents of zoonotic canine filariosis. Methods We developed a combined multiplex approach for filaria and Wolbachia detection using the 28S-based pan-filarial and 16S-based pan-Wolbachia qPCRs, respectively, involving a fast typing method of positive samples using triplex qPCR targeting A. reconditum, D. immitis and D. repens, and a duplex qPCR targeting Wolbachia of D. immitis and D. repens. The approach was complemented by a duplex qPCR for the differential diagnosis of heartworms (D. immitis and Angiostrongylus vasorum) and pan-filarial cox1 and pan-Wolbachia ftsZ PCRs to identify other filarial parasites and their Wolbachia, respectively. A total of 168 canine blood and sera samples were used to validate the approach. Spearmanʼs correlation was used to assess the association between filarial species and the strain of Wolbachia. Positive samples for both the heartworm antigen-test after heating sera and at least one DNA-positive for D. immitis and its Wolbachia were considered true positive for heartworm infection. Indeed, the presence of D. repens DNA or that of its Wolbachia as well as A. reconditum DNA indicates true positive infections. Results The detection limit for Wolbachia and filariae qPCRs ranged from 5 × 10−1 to 1.5 × 10−4 mf/ml of blood. When tested on clinical samples, 29.2% (49/168) tested positive for filariae or Wolbachia DNA. Filarial species and Wolbachia genotypes were identified by the combined multiplex approach from all positive samples. Each species of Dirofilaria was significantly associated with a specific genotype of Wolbachia. Compared to the true positives, the approach showed excellent agreement (k = 0.98–1). Unlike D. immitis DNA, no A. vasorum DNA was detected by the duplex qPCR. The immunochromatographic test for heartworm antigen showed a substantial (k = 0.6) and a weak (k = 0.15) agreements before and after thermal pre-treatment of sera, respectively. Conclusions The proposed approach is a reliable tool for the exploration and diagnosis of occult and non-occult canine filariosis. The current diagnosis of heartworm disease based on antigen detection should always be confirmed by qPCR essays. Sera heat pre-treatment is not effective and strongly discouraged.![]()
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Affiliation(s)
- Younes Laidoudi
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UMR Aix-Marseille University, IRD, APHM, IHU Méditerranée Infection, 19-21, Bd Jean Moulin, 13005, Marseille, France.,IHU Méditerranée Infection, 19-21, Bd Jean Moulin, 13005, Marseille, France
| | - Bernard Davoust
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UMR Aix-Marseille University, IRD, APHM, IHU Méditerranée Infection, 19-21, Bd Jean Moulin, 13005, Marseille, France.,IHU Méditerranée Infection, 19-21, Bd Jean Moulin, 13005, Marseille, France
| | - Marie Varloud
- Ceva Santé Animale, 10 Avenue de la Ballastière, 33500, Libourne, France
| | - El Hadji Amadou Niang
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UMR Aix-Marseille University, IRD, APHM, IHU Méditerranée Infection, 19-21, Bd Jean Moulin, 13005, Marseille, France.,IHU Méditerranée Infection, 19-21, Bd Jean Moulin, 13005, Marseille, France
| | - Florence Fenollar
- IHU Méditerranée Infection, 19-21, Bd Jean Moulin, 13005, Marseille, France.,VITROME, UMR Aix-Marseille University, IRD, SSA, APHM, IHU Méditerranée Infection, 19-21, Bd Jean Moulin, 13005, Marseille, France
| | - Oleg Mediannikov
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UMR Aix-Marseille University, IRD, APHM, IHU Méditerranée Infection, 19-21, Bd Jean Moulin, 13005, Marseille, France. .,IHU Méditerranée Infection, 19-21, Bd Jean Moulin, 13005, Marseille, France.
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29
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Schenk J, Geisen S, Kleinboelting N, Traunspurger W. Metabarcoding data allow for reliable biomass estimates in the most abundant animals on earth. METABARCODING AND METAGENOMICS 2019. [DOI: 10.3897/mbmg.3.46704] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Microscopic organisms are the dominant and most diverse organisms on Earth. Nematodes, as part of this microscopic diversity, are by far the most abundant animals and their diversity is equally high. Molecular metabarcoding is often applied to study the diversity of microorganisms, but has yet to become the standard to determine nematode communities. As such, the information metabarcoding provides, such as in terms of species coverage, taxonomic resolution and especially if sequence reads can be linked to the abundance or biomass of nematodes in a sample, has yet to be determined. Here, we applied metabarcoding using three primer sets located within ribosomal rRNA gene regions to target assembled mock-communities consisting of 18 different nematode species that we established in 9 different compositions. We determined abundances and biomass of all species added to examine if relative sequence abundance or biomass can be linked to relative sequence reads. We found that nematode communities are not equally represented by the three different primer sets and we found that relative read abundances almost perfectly correlated positively with relative species biomass for two of the primer sets. This strong biomass-read number correlation suggests that metabarcoding reads can reveal biomass information even amongst more complex nematode communities as present in the environment and possibly can be transferred to better study other groups of organisms. This biomass-read link is of particular importance for more reliably assessing nutrient flow through food-webs, as well as adjusting biogeochemical models through user-friendly and easily obtainable metabarcoding data.
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30
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Qing X, Bik H, Yergaliyev TM, Gu J, Fonderie P, Brown-Miyara S, Szitenberg A, Bert W. Widespread prevalence but contrasting patterns of intragenomic rRNA polymorphisms in nematodes: Implications for phylogeny, species delimitation and life history inference. Mol Ecol Resour 2019; 20:318-332. [PMID: 31721426 DOI: 10.1111/1755-0998.13118] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 10/26/2019] [Accepted: 11/07/2019] [Indexed: 01/15/2023]
Abstract
Ribosomal RNA genes have long been a favoured locus in phylogenetic and metabarcoding studies. Within a genome, rRNA loci are organized as tandem repeated arrays and the copies are homogenized through the process of concerted evolution. However, some level of rRNA variation (intragenomic polymorphism) is known to persist and be maintained in the genomes of many species. In nematode worms, the extent of rRNA polymorphism (RP) across species and the evolutionary and life history factors that contribute to the maintenance of intragenomic RP is largely unknown. Here, we present an extensive analysis across 30 terrestrial nematode species representing a range of free-living and parasitic taxa isolated worldwide. Our results indicate that RP is common and widespread, ribosome function appears to be maintained despite mutational changes, and intragenomic variants are stable in the genome and neutrally evolving. However, levels of variation were varied widely across rRNA locus and species, with some taxa observed to lack RP entirely. Higher levels of RP were significantly correlated with shorter generation time and high reproductive rates, and population-level factors may play a role in the geographic and phylogenetic structuring of rRNA variants observed in genera such as Rotylenchulus and Pratylenchus. Although RP did not dramatically impact the clustering and recovery of taxa in mock metabarcoding analyses, the present study has significant implications for global biodiversity estimates of nematode species derived from environmental rRNA amplicon studies, as well as our understanding of the evolutionary and ecological factors shaping genetic diversity across the nematode Tree of Life.
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Affiliation(s)
- Xue Qing
- Nematology Research Unit, Department of Biology, Ghent University, Ghent, Belgium.,Department of Entomology, Nematology and Chemistry Units, Agricultural Research Organization (ARO), Volcani Center, Rishon LeZion, Israel
| | - Holly Bik
- Department of Nematology, University of California-Riverside, Riverside, CA, USA
| | - Timur M Yergaliyev
- Dead Sea and Arava Science Center, Dead Sea Branch, Masada National Park, Tamar Regional Council, Tel Aviv, Israel.,A. Baitursynov Kostanay State University, Kostanay, Kazakhstan
| | - Jianfeng Gu
- Technical Center of Ningbo Customs (Ningbo Inspection and Quarantine Science Technology Academy), Ningbo, China
| | - Pamela Fonderie
- Nematology Research Unit, Department of Biology, Ghent University, Ghent, Belgium
| | - Sigal Brown-Miyara
- Department of Entomology, Nematology and Chemistry Units, Agricultural Research Organization (ARO), Volcani Center, Rishon LeZion, Israel
| | - Amir Szitenberg
- Dead Sea and Arava Science Center, Dead Sea Branch, Masada National Park, Tamar Regional Council, Tel Aviv, Israel
| | - Wim Bert
- Nematology Research Unit, Department of Biology, Ghent University, Ghent, Belgium
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31
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Evidence of Intra-individual SSU Polymorphisms in Dark-spored Myxomycetes (Amoebozoa). Protist 2019; 170:125681. [PMID: 31586669 DOI: 10.1016/j.protis.2019.125681] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 08/21/2019] [Accepted: 08/27/2019] [Indexed: 11/24/2022]
Abstract
The nuclear small subunit rRNA gene (SSU or 18S) is a marker frequently used in phylogenetic and barcoding studies in Amoebozoa, including Myxomycetes. Despite its common usage and the confirmed existence of divergent copies of ribosomal genes in other protists, the potential presence of intra-individual SSU variability in Myxomycetes has never been studied before. Here we investigated the pattern of nucleotide polymorphism in the 5' end fragment of SSU by cloning and sequencing a total of 238 variants from eight specimens, each representing a species of the dark-spored orders Stemonitidales and Physarales. After excluding singletons, a relatively low SSU intra-individual variability was found but our data indicate that this might be a widely distributed phenomenon in Myxomycetes as all samples analyzed possessed various ribotypes. To determine if the occurrence of multiple SSU variants within a single specimen has a negative effect on the circumscription of species boundaries, we conducted phylogenetic analyses that revealed that clone variation may be detrimental for inferring phylogenetic relationships among some of the specimens analyzed. Despite that intra-individual variability should be assessed in additional taxa, our results indicate that special care should be taken for species identification when working with closely related species.
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32
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Grant JR, Pilotte N, Williams SA. A Case for Using Genomics and a Bioinformatics Pipeline to Develop Sensitive and Species-Specific PCR-Based Diagnostics for Soil-Transmitted Helminths. Front Genet 2019; 10:883. [PMID: 31608116 PMCID: PMC6768101 DOI: 10.3389/fgene.2019.00883] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 08/21/2019] [Indexed: 12/22/2022] Open
Abstract
The balance of expense and ease of use vs. specificity and sensitivity in diagnostic assays for helminth disease is an important consideration, with expense and ease often winning out in endemic areas where funds and sophisticated equipment may be scarce. In this review, we argue that molecular diagnostics, specifically new assays that have been developed with the aid of next-generation sequence data and robust bioinformatic tools, more than make up for their expense with the benefit of a clear and precise assessment of the situation on the ground. Elimination efforts associated with the London Declaration and the World Health Organization (WHO) 2020 Roadmap have resulted in areas of low disease incidence and reduced infection burdens. An accurate assessment of infection levels is critical for determining where and when the programs can be successfully ended. Thus, more sensitive assays are needed in locations where elimination efforts are approaching a successful conclusion. Although microscopy or more general PCR targets have a role to play, they can mislead and cause study results to be confounded. Hyper-specific qPCR assays enable a more definitive assessment of the situation in the field, as well as of shifting dynamics and emerging diseases.
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Affiliation(s)
- Jessica R. Grant
- Department of Biological Sciences, Smith College, Northampton, MA, United States
| | - Nils Pilotte
- Department of Biological Sciences, Smith College, Northampton, MA, United States
- Molecular and Cellular Biology Program, University of Massachusetts, Amherst, MA, United States
| | - Steven A. Williams
- Department of Biological Sciences, Smith College, Northampton, MA, United States
- Molecular and Cellular Biology Program, University of Massachusetts, Amherst, MA, United States
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Stracke K, Clarke N, Awburn CV, Vaz Nery S, Khieu V, Traub RJ, Jex AR. Development and validation of a multiplexed-tandem qPCR tool for diagnostics of human soil-transmitted helminth infections. PLoS Negl Trop Dis 2019; 13:e0007363. [PMID: 31206520 PMCID: PMC6597125 DOI: 10.1371/journal.pntd.0007363] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 06/27/2019] [Accepted: 04/05/2019] [Indexed: 11/30/2022] Open
Abstract
Soil-transmitted helminths (STH) are a major cause of morbidity in tropical developing countries with a global infection prevalence of more than one billion people and disease burden of around 3.4 million disability adjusted life years. Infection prevalence directly correlates to inadequate sanitation, impoverished conditions and limited access to public health systems. Underestimation of infection prevalence using traditional microscopy-based diagnostic techniques is common, specifically in populations with access to benzimidazole mass treatment programs and a predominance of low intensity infections. In this study, we developed a multiplexed-tandem qPCR (MT-PCR) tool to identify and quantify STH eggs in stool samples. We have assessed this assay by measuring infection prevalence and intensity in field samples of two cohorts of participants from Timor-Leste and Cambodia, which were collected as part of earlier epidemiological studies. MT-PCR diagnostic parameters were compared to a previously published multiplexed qPCR for STH detection. The MT-PCR assay agreed strongly with qPCR data and showed a diagnostic specificity of 99.60-100.00% (sensitivity of 83.33-100.00%) compared to qPCR and kappa agreement exceeding 0.85 in all tests. In addition, the MT-PCR has the added advantage of distinguishing Ancylostoma spp. species, namely Ancylostoma duodenale and Ancylostoma ceylanicum. This semi-automated platform uses a standardized, manufactured reagent kit, shows excellent run-to-run consistency/repeatability and supports high-throughput detection and quantitation at a moderate cost.
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Affiliation(s)
- Katharina Stracke
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Naomi Clarke
- Research School of Population Health, Australian National University, Canberra, Australian Capital Territory, Australia
- Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia
| | - Camille V. Awburn
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - Susana Vaz Nery
- Research School of Population Health, Australian National University, Canberra, Australian Capital Territory, Australia
- Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia
| | - Virak Khieu
- National Center for Parasitology, Entomology and Malaria Control, Ministry of Health, Phnom Penh, Cambodia
| | - Rebecca J. Traub
- Faculty for Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Aaron R. Jex
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Faculty for Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, Victoria, Australia
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Cordier T, Lanzén A, Apothéloz-Perret-Gentil L, Stoeck T, Pawlowski J. Embracing Environmental Genomics and Machine Learning for Routine Biomonitoring. Trends Microbiol 2019; 27:387-397. [DOI: 10.1016/j.tim.2018.10.012] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 10/17/2018] [Accepted: 10/30/2018] [Indexed: 01/28/2023]
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New Insights Into Nematode DNA-metabarcoding as Revealed by the Characterization of Artificial and Spiked Nematode Communities. DIVERSITY-BASEL 2019. [DOI: 10.3390/d11040052] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Nematodes are ideal biological indicators to monitor soil biodiversity and ecosystem functioning. For this reason, they have been receiving increasing attention from a broad range of scientists. The main method to characterize soil nematode communities until at least genus level is still based on microscopic observations of nematode morphology. Such an approach is time-consuming, labor-intensive, and requires specialized personnel. The first studies on the potential use of DNA-metabarcoding to characterize nematode communities showed some shortcomings: under- or overestimation of species richness caused by failure to detect a number of nematode species or caused by intraspecific sequence variants increasing the number of OTUs (operational taxonomic units) or ‘molecular’ species, and flaws in quantification. We set up experiments to optimize this metabarcoding approach. Our results provided new insights such as the drastic effect of different DNA-extraction methods on nematode species richness due to variation in lysis efficacy. Our newly designed primer set (18S rRNA gene, V4-V5 region) showed in silico an improved taxonomic coverage compared with a published primer set (18S rRNA gene, V6-V8 region). However, results of DNA-metabarcoding with the new primer set showed less taxonomic coverage, and more non-nematode reads. Thus, the new primer set might be more suitable for whole soil faunal analysis. Species-specific correction factors calculated from a mock community with equal amounts of different nematode species were applied on another mock community with different amounts of the same nematode species and on a biological sample spiked with four selected nematode species. Results showed an improved molecular quantification. In conclusion, DNA-metabarcoding of soil nematode communities is useful for monitoring shifts in nematode composition but the technique still needs further optimization to enhance its precision.
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Cenik ES, Meng X, Tang NH, Hall RN, Arribere JA, Cenik C, Jin Y, Fire A. Maternal Ribosomes Are Sufficient for Tissue Diversification during Embryonic Development in C. elegans. Dev Cell 2019; 48:811-826.e6. [PMID: 30799226 DOI: 10.1016/j.devcel.2019.01.019] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 11/06/2018] [Accepted: 01/21/2019] [Indexed: 12/20/2022]
Abstract
Caenorhabditis elegans provides an amenable system to explore whether newly composed ribosomes are required to progress through development. Despite the complex pattern of tissues that are formed during embryonic development, we found that null homozygotes lacking any of the five different ribosomal proteins (RPs) can produce fully functional first-stage larvae, with similar developmental competence seen upon complete deletion of the multi-copy ribosomal RNA locus. These animals, relying on maternal but not zygotic contribution of ribosomal components, are capable of completing embryogenesis. In the absence of new ribosomal components, the resulting animals are arrested before progression from the first larval stage and fail in two assays for postembryonic plasticity of neuronal structure. Mosaic analyses of larvae that are a mixture of ribosome-competent and non-competent cells suggest a global regulatory mechanism in which ribosomal insufficiency in a subset of cells triggers organism-wide growth arrest.
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Affiliation(s)
- Elif Sarinay Cenik
- Department of Pathology, Stanford University Medical School, Stanford, CA, USA; Department of Molecular Biosciences, University of Texas Austin, Austin, TX, USA
| | - Xuefeng Meng
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, San Diego, CA, USA
| | - Ngang Heok Tang
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, San Diego, CA, USA
| | | | - Joshua A Arribere
- Department of MCD Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Can Cenik
- Department of Molecular Biosciences, University of Texas Austin, Austin, TX, USA
| | - Yishi Jin
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, San Diego, CA, USA
| | - Andrew Fire
- Department of Pathology, Stanford University Medical School, Stanford, CA, USA.
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Carta LK, Li S. PCR amplification of a long rDNA segment with one primer pair in agriculturally important nematodes. J Nematol 2019; 51:1-8. [PMID: 31157959 PMCID: PMC6929650 DOI: 10.21307/jofnem-2019-026] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Indexed: 11/11/2022] Open
Abstract
Ribosomal DNA has been a reliable source of taxonomic and phylogenetic markers due to its high copy number in the genome and stable variation with few polymorphisms due to the homogenizing effect of concerted evolution. Typically specific regions are amplified through polymerase chain reaction (PCR) with multiple primer pairs that generate often incomplete and overlapping regions between adjacent segments of 18S, ITS1, 5.8S, ITS2, and 28S rDNA nucleotide sequences when combined in tandem. To improve the efficiency of this effort, a strategy for generating all these molecular sequences at once through PCR amplification of a large ribosomal 3.3 to 4.2 kb DNA target was developed using primer 18S-CL-F3 paired with D3B or a new alternative 28S PCR primer (28S-CL-R) and other well-positioned and ribosomal-specific sequencing primers (including novel primers 18S-CL-F7, 18S-CL-R6, 18S-CL-R7, 18S-CL-F8, 5.8S-CL-F1, 5.8S-CL-R1, 28S-CL-F1, 28S-CL-R3, 28S-CL-F3, 28S-CL-R1, and 28S-CL-F2). The D1 region between ITS2 and 28S boundaries and the flanking sequence between 18S and ITS1 boundaries were fully revealed in this large nucleotide segment. To demonstrate the value of this strategy, the long rDNA segment was amplified and directly sequenced in 17 agriculturally important nematodes from the Tylenchida, Aphelenchida, and Dorylaimida. The primers and their positions may be employed with traditional Sanger sequencing and with next-generation sequencing reagents and protocols.
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Affiliation(s)
- L K Carta
- Mycology and Nematology Genetic Diversity and Biology Laboratory, USDA, ARS, Henry A. Wallace Beltsville Agricultural Research Center , Bldg. 010A, Room 110, Beltsville, MD, 20705-2350
| | - S Li
- Mycology and Nematology Genetic Diversity and Biology Laboratory, USDA, ARS, Henry A. Wallace Beltsville Agricultural Research Center , Bldg. 010A, Room 110, Beltsville, MD, 20705-2350
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Rojas A, Dvir E, Farkas R, Sarma K, Borthakur S, Jabbar A, Markovics A, Otranto D, Baneth G. Phylogenetic analysis of Spirocerca lupi and Spirocerca vulpis reveal high genetic diversity and intra-individual variation. Parasit Vectors 2018; 11:639. [PMID: 30547850 PMCID: PMC6295112 DOI: 10.1186/s13071-018-3202-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 11/19/2018] [Indexed: 12/12/2022] Open
Abstract
Background Spirocerca lupi is a parasitic nematode of canids that can lead to a severe and potentially fatal disease. Recently, a new species, Spirocerca vulpis, was described from red foxes in Europe, suggesting a high genetic diversity of the Spirocerca spp. infecting canids. The genetic variation and phylogenetic relationships of S. lupi collected from naturally-infected domestic dogs from Australia, Hungary, Israel, Italy, India and South Africa, and S. vulpis from red foxes from Bosnia and Herzegovina, Italy and Spain, was studied using mitochondrial and rDNA markers. Results A high intra-individual variation was found in the first internal transcribed spacer (ITS1) locus in all Spirocerca spp., ranging between 0.37–2.84%, with up to six haplotypes per specimen. In addition, a combination of phylogenetic and haplotype analyses revealed a large variability between S. lupi specimens collected from different geographical locations using the ITS1 (0.37–9.33%) and the cytochrome c oxidase subunit 1 (cox1) gene (1.42–6.74%). This genetic diversity led to the identification of two S. lupi genotypes circulating among dogs (PTP support > 0.829), including genotype 1 found in S. lupi from Australia, India, Israel and South Africa, and genotype 2 represented by specimens from Hungary and Italy. These genotypes presented pairwise nucleotide distances of 0.14%, 8.06% and 6.48 ± 0.28% in the small rDNA subunit (18S), ITS1 and cox1 loci, respectively. Additionally, Nei’s genetic distance in the ITS1 showed a further subdivision of genotype 1 worms into 1A (Israel and South Africa) and 1B (Australia and India). A morphological analysis of the anterior and posterior extremities of genotype 1 and genotype 2 worms using scanning electron microscopy did not show any differences between the specimens, contrary to the morphological differences between S. lupi and S. vulpis. Conclusions These findings demonstrate the high genetic variability among Spirocerca spp. from different geographical locations, thereby expanding our understanding of the epidemiology, evolution and phylogenetic variability within the genus. Electronic supplementary material The online version of this article (10.1186/s13071-018-3202-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alicia Rojas
- Koret School of Veterinary Medicine, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Eran Dvir
- Department of Animal Sciences, Tel-Hai Academic College, Upper Galilee, Israel
| | - Róbert Farkas
- Department of Parasitology and Zoology, University of Veterinary Medicine, Budapest, Hungary
| | - Kalyan Sarma
- Department of Veterinary Medicine, College of Veterinary Sciences and Animal Husbandry, Central Agricultural University, Mizoram, India
| | - Sonjoy Borthakur
- Department of Veterinary Parasitology, College of Veterinary Sciences and Animal Husbandry, Central Agricultural University, Mizoram, India
| | - Abdul Jabbar
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Victoria, Australia
| | | | - Domenico Otranto
- Department of Veterinary Medicine, University of Bari, Valenzano, Italy
| | - Gad Baneth
- Koret School of Veterinary Medicine, The Hebrew University of Jerusalem, Rehovot, Israel.
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Rudko SP, Reimink RL, Froelich K, Gordy MA, Blankespoor CL, Hanington PC. Use of qPCR-Based Cercariometry to Assess Swimmer's Itch in Recreational Lakes. ECOHEALTH 2018; 15:827-839. [PMID: 30120669 PMCID: PMC6267424 DOI: 10.1007/s10393-018-1362-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 07/06/2018] [Accepted: 07/28/2018] [Indexed: 06/08/2023]
Abstract
Swimmer's itch (cercarial dermatitis) is a nuisance encountered by bathers and recreational water users worldwide. The condition is caused by the penetration of larval digenean trematodes (cercariae) of the family Schistosomatidae, into the skin, following their release into freshwater from pulmonate snails that serve as the intermediate hosts for these parasites. This study utilizes qPCR-based cercariometry to monitor and quantify cercariae from water samples collected at 5 lakes in northern Michigan. The resolution provided by qPCR facilitated assessment of the environmental and biological drivers of swimmer's itch-causing cercariae concentrations, allowing us to demonstrate that cercarial abundance is greatest at the top of the water column, in locations with prevailing on- and alongshore winds.
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Affiliation(s)
- Sydney P Rudko
- School of Public Health, University of Alberta, Room 3-57, South Academic Building, Edmonton, AB, T6G 2G7, Canada
| | | | | | - Michelle A Gordy
- School of Public Health, University of Alberta, Room 3-57, South Academic Building, Edmonton, AB, T6G 2G7, Canada
| | - Curtis L Blankespoor
- Jackson College, Jackson, MI, USA
- University of Michigan Biological Station, Pellston, MI, USA
| | - Patrick C Hanington
- School of Public Health, University of Alberta, Room 3-57, South Academic Building, Edmonton, AB, T6G 2G7, Canada.
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Salgado-Salazar C, LeBlanc N, Ismaiel A, Rivera Y, Warfield CY, Crouch JA. Genetic Variation of the Pathogen Causing Impatiens Downy Mildew Predating and Including Twenty-first Century Epidemics on Impatiens walleriana. PLANT DISEASE 2018; 102:2411-2420. [PMID: 30253113 DOI: 10.1094/pdis-01-18-0077-re] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Impatiens downy mildew (IDM) of cultivated Impatiens walleriana has had a significant economic impact on the ornamental horticulture industry in the United States and globally. Although recent IDM outbreaks started in 2003, downy mildews on noncultivated Impatiens species have been documented since the 1880s. To understand the relationship between the pathogen causing recent epidemics and the pathogen historically present in the United States, this work characterized genetic variation among a collection of 1,000 samples on 18 plant hosts. Samples included collections during recent IDM epidemics and historical herbarium specimens. Ten major genotypes were identified from cloned rDNA amplicon sequencing and endpoint SNP genotyping. Three genotypes accounted for >95% of the samples, with only one of these three genotypes found on samples predating recent IDM outbreaks. Based on phylogenetic analysis integrating data from three markers and the presence of individual genotypes on multiple Impatiens species, there was some evidence of pathogen-specific infection of I. noli-tangere, but the distinction between genotypes infecting I. walleriana and I. balsamina was not upheld. Overall, this work provides evidence that the majority of rDNA genotypes recovered from recent IDM epidemics are different from historical U.S. genotypes, and that these genotypes can infect Impatiens spp. other than I. walleriana.
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Affiliation(s)
- Catalina Salgado-Salazar
- U.S. Department of Agriculture, Agricultural Research Service (USDA-ARS), Mycology and Nematology Genetic Diversity and Biology Laboratory, Beltsville, MD 20705; Oak Ridge Institute for Science and Education, ARS Research Participation Program, MC-100-44, Oak Ridge, TN 37831; and Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901
| | - Nicholas LeBlanc
- USDA-ARS, Mycology and Nematology Genetic Diversity and Biology Laboratory, Beltsville, MD 20705; and Oak Ridge Institute for Science and Education, ARS Research Participation Program, MC-100-44, Oak Ridge, TN 37831
| | - Adnan Ismaiel
- USDA-ARS, Mycology and Nematology Genetic Diversity and Biology Laboratory, Beltsville, MD 20705
| | - Yazmín Rivera
- USDA-ARS, Mycology and Nematology Genetic Diversity and Biology Laboratory, Beltsville, MD 20705; and Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901
| | | | - Jo Anne Crouch
- USDA-ARS, Mycology and Nematology Genetic Diversity and Biology Laboratory, Beltsville, MD 20705
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Leasi F, Sevigny JL, Laflamme EM, Artois T, Curini-Galletti M, de Jesus Navarrete A, Di Domenico M, Goetz F, Hall JA, Hochberg R, Jörger KM, Jondelius U, Todaro MA, Wirshing HH, Norenburg JL, Thomas WK. Biodiversity estimates and ecological interpretations of meiofaunal communities are biased by the taxonomic approach. Commun Biol 2018; 1:112. [PMID: 30271992 PMCID: PMC6123632 DOI: 10.1038/s42003-018-0119-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 07/24/2018] [Indexed: 01/05/2023] Open
Abstract
Accurate assessments of biodiversity are crucial to advising ecosystem-monitoring programs and understanding ecosystem function. Nevertheless, a standard operating procedure to assess biodiversity accurately and consistently has not been established. This is especially true for meiofauna, a diverse community (>20 phyla) of small benthic invertebrates that have fundamental ecological roles. Recent studies show that metabarcoding is a cost-effective and time-effective method to estimate meiofauna biodiversity, in contrast to morphological-based taxonomy. Here, we compare biodiversity assessments of a diverse meiofaunal community derived by applying multiple taxonomic methods based on comparative morphology, molecular phylogenetic analysis, DNA barcoding of individual specimens, and metabarcoding of environmental DNA. We show that biodiversity estimates are strongly biased across taxonomic methods and phyla. Such biases affect understanding of community structures and ecological interpretations. This study supports the urgency of improving aspects of environmental high-throughput sequencing and the value of taxonomists in correctly understanding biodiversity estimates.
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Affiliation(s)
- Francesca Leasi
- Department of Biology, Geology and Environmental Science, University of Tennessee at Chattanooga, 615 McCallie Avenue, Chattanooga, TN, 37403, USA.
- Hubbard Center for Genome Studies, Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, 35 Colovos Road, Durham, NH, 03824, USA.
| | - Joseph L Sevigny
- Hubbard Center for Genome Studies, Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, 35 Colovos Road, Durham, NH, 03824, USA
| | - Eric M Laflamme
- Department of Mathematics, Plymouth State University, MSC29, 17 High Street, Plymouth, NH, 03264, USA
| | - Tom Artois
- Centre for Environmental Sciences, Hasselt University, Campus Diepenbeek, Agoralaan Gebouw D, 3590, Diepenbeek, Belgium
| | - Marco Curini-Galletti
- Dipartimento di Medicina Veterinaria, University of Sassari, via Muroni 25, 07100, Sassari, Italy
| | - Alberto de Jesus Navarrete
- Departmento de Sistemática y Ecología Acuática, El Colegio de la Frontera Sur, Unidad Chetumal, Av. Centenario Km. 5.5 Chetumal Quintana Roo, 77014, Chetumal, Mexico
| | - Maikon Di Domenico
- Centro de Estudos do Mar, Universidade Federal do Paraná, Av. Beira-Mar, s/n, Pontal do Sul, PO Box 61, 83255-976, Pontal do Paraná, PR, Brazil
| | - Freya Goetz
- Department of Invertebrate Zoology, Smithsonian National Museum of Natural History, 10th St. & Constitution Ave NW, Washington, DC, 20560, USA
| | - Jeffrey A Hall
- Hubbard Center for Genome Studies, Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, 35 Colovos Road, Durham, NH, 03824, USA
| | - Rick Hochberg
- Department of Biological Science, University of Massachusetts Lowell, Olsen Hall 414, 198 Riverside St., Lowell, MA, 01854, USA
| | - Katharina M Jörger
- Department of Biology, Ludwig-Maximilians-University of Munich, Großhaderner Str. 2, 82152, Planegg-Martinsried, Munich, Germany
| | - Ulf Jondelius
- Swedish Museum of Natural History, POB 5007, SE-104 05, Stockholm, Sweden
| | - M Antonio Todaro
- Department of Life Sciences, University of Modena & Reggio Emilia, Via G. Campi 213/d, 41125, Modena, Italy
| | - Herman H Wirshing
- Department of Invertebrate Zoology, Smithsonian National Museum of Natural History, 10th St. & Constitution Ave NW, Washington, DC, 20560, USA
| | - Jon L Norenburg
- Department of Invertebrate Zoology, Smithsonian National Museum of Natural History, 10th St. & Constitution Ave NW, Washington, DC, 20560, USA
| | - W Kelley Thomas
- Hubbard Center for Genome Studies, Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, 35 Colovos Road, Durham, NH, 03824, USA
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Kim JH, Dilthey AT, Nagaraja R, Lee HS, Koren S, Dudekula D, Wood Iii WH, Piao Y, Ogurtsov AY, Utani K, Noskov VN, Shabalina SA, Schlessinger D, Phillippy AM, Larionov V. Variation in human chromosome 21 ribosomal RNA genes characterized by TAR cloning and long-read sequencing. Nucleic Acids Res 2018; 46:6712-6725. [PMID: 29788454 PMCID: PMC6061828 DOI: 10.1093/nar/gky442] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 05/08/2018] [Indexed: 12/31/2022] Open
Abstract
Despite the key role of the human ribosome in protein biosynthesis, little is known about the extent of sequence variation in ribosomal DNA (rDNA) or its pre-rRNA and rRNA products. We recovered ribosomal DNA segments from a single human chromosome 21 using transformation-associated recombination (TAR) cloning in yeast. Accurate long-read sequencing of 13 isolates covering ∼0.82 Mb of the chromosome 21 rDNA complement revealed substantial variation among tandem repeat rDNA copies, several palindromic structures and potential errors in the previous reference sequence. These clones revealed 101 variant positions in the 45S transcription unit and 235 in the intergenic spacer sequence. Approximately 60% of the 45S variants were confirmed in independent whole-genome or RNA-seq data, with 47 of these further observed in mature 18S/28S rRNA sequences. TAR cloning and long-read sequencing enabled the accurate reconstruction of multiple rDNA units and a new, high-quality 44 838 bp rDNA reference sequence, which we have annotated with variants detected from chromosome 21 of a single individual. The large number of variants observed reveal heterogeneity in human rDNA, opening up the possibility of corresponding variations in ribosome dynamics.
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MESH Headings
- Animals
- Cell Line
- Chromosomes, Human, Pair 21
- Cloning, Molecular
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/isolation & purification
- DNA, Ribosomal Spacer/chemistry
- Genes, rRNA
- Genetic Variation
- Humans
- Mice
- Nucleic Acid Conformation
- Nucleolus Organizer Region/chemistry
- RNA, Ribosomal/chemistry
- RNA, Ribosomal/metabolism
- Sequence Analysis, DNA
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Affiliation(s)
- Jung-Hyun Kim
- National Cancer Institute, Developmental Therapeutics Branch, Bethesda, MD 20892, USA
| | - Alexander T Dilthey
- National Human Genome Research Institute, Computational and Statistical Genomics Branch, Bethesda, MD 20892, USA
| | - Ramaiah Nagaraja
- National Institute on Aging, Laboratory of Genetics and Genomics, Baltimore, MD 21224, USA
| | - Hee-Sheung Lee
- National Cancer Institute, Developmental Therapeutics Branch, Bethesda, MD 20892, USA
| | - Sergey Koren
- National Human Genome Research Institute, Computational and Statistical Genomics Branch, Bethesda, MD 20892, USA
| | - Dawood Dudekula
- National Institute on Aging, Laboratory of Genetics and Genomics, Baltimore, MD 21224, USA
| | - William H Wood Iii
- National Institute on Aging, Laboratory of Genetics and Genomics, Baltimore, MD 21224, USA
| | - Yulan Piao
- National Institute on Aging, Laboratory of Genetics and Genomics, Baltimore, MD 21224, USA
| | - Aleksey Y Ogurtsov
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20892, USA
| | - Koichi Utani
- National Cancer Institute, Developmental Therapeutics Branch, Bethesda, MD 20892, USA
| | - Vladimir N Noskov
- National Cancer Institute, Developmental Therapeutics Branch, Bethesda, MD 20892, USA
| | - Svetlana A Shabalina
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20892, USA
| | - David Schlessinger
- National Institute on Aging, Laboratory of Genetics and Genomics, Baltimore, MD 21224, USA
| | - Adam M Phillippy
- National Human Genome Research Institute, Computational and Statistical Genomics Branch, Bethesda, MD 20892, USA
| | - Vladimir Larionov
- National Cancer Institute, Developmental Therapeutics Branch, Bethesda, MD 20892, USA
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Mutational and transcriptional landscape of spontaneous gene duplications and deletions in Caenorhabditis elegans. Proc Natl Acad Sci U S A 2018; 115:7386-7391. [PMID: 29941601 DOI: 10.1073/pnas.1801930115] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Gene duplication and deletion are pivotal processes shaping the structural and functional repertoire of genomes, with implications for disease, adaptation, and evolution. We employed a mutation accumulation (MA) framework partnered with high-throughput genomics to assess the molecular and transcriptional characteristics of newly arisen gene copy-number variants (CNVs) in Caenorhabditis elegans populations subjected to varying intensity of selection. Here, we report a direct spontaneous genome-wide rate of gene duplication of 2.9 × 10-5/gene per generation in C. elegans, the highest for any species to date. The rate of gene deletion is sixfold lower (5 × 10-6/gene per generation). Deletions of highly expressed genes are particularly deleterious, given their paucity in even the N = 1 lines with minimal efficacy of selection. The increase in average transcript abundance of new duplicates arising under minimal selection is significantly greater than twofold compared with single copies of the same gene, suggesting that genes in segmental duplications are frequently overactive at inception. The average increase in transcriptional activity of gene duplicates is greater in the N = 1 MA lines than in MA lines with larger population bottlenecks. There is an inverse relationship between the ancestral transcription levels of new gene duplicates and population size, with duplicate copies of highly expressed genes less likely to accumulate in larger populations. Our results demonstrate a fitness cost of increased transcription following duplication, which results in purifying selection against new gene duplicates. However, on average, duplications also provide a significant increase in gene expression that can facilitate adaptation to novel environmental challenges.
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Development of a multiplex quantitative PCR assay for detection and quantification of DNA from Fasciola hepatica and the intermediate snail host, Austropeplea tomentosa, in water samples. Vet Parasitol 2018; 259:17-24. [PMID: 30056979 DOI: 10.1016/j.vetpar.2018.06.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 06/09/2018] [Accepted: 06/23/2018] [Indexed: 11/23/2022]
Abstract
Liver fluke (Fasciola hepatica) infection is an increasing threat to livestock production resulting in serious economic losses to the beef, dairy and sheep industries in Australia and globally. Triclabendazole (TCBZ) is the main drug used to control liver fluke infections in Australia and the widespread emergence of TCBZ resistance in cattle and sheep threatens liver fluke control. Alternative control measures to lower exposure of livestock to fluke infection would be useful to help preserve the usefulness of current chemical flukicides. Environmental DNA (eDNA) sampling methodology and associated molecular techniques are suited to rapidly assess the presence of pathogens on farms. In the present study, we developed a water sampling method in combination with a multiplex quantitative PCR assay to detect and quantify DNA of F. hepatica and Austropeplea tomentosa (A. tomentosa), a crucial intermediate snail host for liver fluke transmission in South-east Australia. The multiplex qPCR assay allows for the independent detection of F. hepatica and A. tomentosa DNA using specific primers and a probe targeting the ITS-2 region of the liver fluke or snail. The method allows the highly specific and sensitive (minimal DNA detection levels to 14-50 fg) detection of F. hepatica or A. tomentosa. The method allows the detection of both liver fluke and snail eDNA in water samples. The effective quantification of liver fluke and snail eDNA in water samples using this assay could potentially allow researchers to both identify and monitor F. hepatica transmission zones on farming properties in South-east Australia which will better inform control strategies, with potential application of the assay worldwide.
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Buonicontro DS, Roberts DM, Oliveira CMG, Blok VC, Neilson R, Oliveira RDDL. A Rapid Diagnostic for Detection of Aphelenchoides besseyi and A. fujianensis Based on Real-Time PCR. PLANT DISEASE 2018; 102:519-526. [PMID: 30673493 DOI: 10.1094/pdis-08-17-1160-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Aphelenchoides besseyi and A. fujianensis have been frequently found in mixed populations associated with forage grass seed in Brazil. The morphological similarity between both species has previously led A. fujianensis to be erroneously identified as A. besseyi. A. besseyi is a quarantine pest in many countries that import Brazilian forage seed; however, there is no current evidence suggesting that A. fujianensis is a plant-parasitic species. Two real-time polymerase chain reaction (qPCR) diagnostics were developed to detect each species and an operational envelope was established. A set of primers and hydrolysis probes for each species was designed targeting the large subunit (LSU) region. To assess their specificity, primers and probes sets were tested with samples of nontarget Aphelenchoides and Paraphelenchus sp. also frequently associated with forage seed. Experiments using dilutions of purified plasmid standards underpinned the sensitivity of the qPCR assays, which detected as few as 10 copies of target nematode ribosomal DNA. Thus, the developed diagnostics were sufficiently sensitive to detect DNA extracted from a fragment of a single target nematode. There was a positive correlation between copy number of the target species and nematode abundance, suggesting the potential of this method for quantification. Evidence of intra-individual variability among cloned sequences of the LSU region in a single A. besseyi population is also reported.
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Affiliation(s)
- Dalila Sêni Buonicontro
- Viçosa Federal University, Department of Plant Pathology, Laboratory of Nematology, 36570-900, Viçosa, MG, Brazil
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Characterization of soil nematode communities in three cropping systems through morphological and DNA metabarcoding approaches. Sci Rep 2018; 8:2004. [PMID: 29386563 PMCID: PMC5792604 DOI: 10.1038/s41598-018-20366-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 01/17/2018] [Indexed: 11/25/2022] Open
Abstract
We used complementary morphological and DNA metabarcoding approaches to characterize soil nematode communities in three cropping systems, conventional till (CT), no-till (NT) and organic (ORG), from a long-term field experiment. We hypothesized that organic inputs to the ORG system would promote a more abundant nematode community, and that the NT system would show a more structured trophic system (higher Bongers MI) than CT due to decreased soil disturbance. The abundance of Tylenchidae and Cephalobidae both showed positive correlations to soil organic carbon and nitrogen, which were highest in the ORG system. The density of omnivore-predator and bacterial-feeding nematodes was reduced in NT soils compared to CT, while some plant-parasitic taxa increased. NT soils had similar Bongers MI values to CT, suggesting they contained nematode communities associated with soils experiencing comparable levels of disturbance. Metabarcoding revealed within-family differences in nematode diversity. Shannon and Simpson’s index values for the Tylenchidae and Rhabditidae were higher in the ORG system than CT. Compared to morphological analysis, metabarcoding over- or underestimated the prevalence of several nematode families and detected some families not observed based on morphology. Discrepancies between the techniques require further investigation to establish the accuracy of metabarcoding for characterization of soil nematode communities.
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Tatonova YV, Chelomina GN, Nguyen HM. Inter-individual and intragenomic variations in the ITS region of Clonorchis sinensis (Trematoda: Opisthorchiidae) from Russia and Vietnam. INFECTION GENETICS AND EVOLUTION 2017; 55:350-357. [DOI: 10.1016/j.meegid.2017.10.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 10/06/2017] [Accepted: 10/06/2017] [Indexed: 01/18/2023]
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Peham T, Steiner FM, Schlick‐Steiner BC, Arthofer W. Are we ready to detect nematode diversity by next generation sequencing? Ecol Evol 2017; 7:4147-4151. [PMID: 28649327 PMCID: PMC5478071 DOI: 10.1002/ece3.2998] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Revised: 03/16/2017] [Accepted: 03/20/2017] [Indexed: 12/28/2022] Open
Abstract
In a Technical Advance article, Porazinska et al. (2009, Molecular Ecology Resources, 9, 1439-1450) assessed next generation sequencing (NGS) as a method for metagenomic analysis of nematode diversity. We agree that NGS has great potential here. However, it is not an easy path to the successful implementation of NGS for environmental DNA analysis of nematodes. Here, we describe the method's limitations and discuss prospective research questions. For instance, only a few direct extraction kits are suitable for nematode DNA extraction from bulk samples without adaptation. They enable the analysis of extracellular nematode DNA. The most crucial and unresolved issue remains the limited availability of suitable primers.
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Affiliation(s)
- Thomas Peham
- Molecular Ecology GroupInstitute of EcologyUniversity of InnsbruckInnsbruckAustria
| | - Florian M. Steiner
- Molecular Ecology GroupInstitute of EcologyUniversity of InnsbruckInnsbruckAustria
| | | | - Wolfgang Arthofer
- Molecular Ecology GroupInstitute of EcologyUniversity of InnsbruckInnsbruckAustria
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Rabanal FA, Nizhynska V, Mandáková T, Novikova PY, Lysak MA, Mott R, Nordborg M. Unstable Inheritance of 45S rRNA Genes in Arabidopsis thaliana. G3 (BETHESDA, MD.) 2017; 7:1201-1209. [PMID: 28188182 PMCID: PMC5386868 DOI: 10.1534/g3.117.040204] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 02/07/2017] [Indexed: 12/30/2022]
Abstract
The considerable genome size variation in Arabidopsis thaliana has been shown largely to be due to copy number variation (CNV) in 45S ribosomal RNA (rRNA) genes. Surprisingly, attempts to map this variation by means of genome-wide association studies (GWAS) failed to identify either of the two likely sources, namely the nucleolus organizer regions (NORs). Instead, GWAS implicated a trans-acting locus, as if rRNA gene CNV was a phenotype rather than a genotype. To explain these results, we investigated the inheritance and stability of rRNA gene copy number using the variety of genetic resources available in A. thaliana - F2 crosses, recombinant inbred lines, the multiparent advanced-generation inter-cross population, and mutation accumulation lines. Our results clearly show that rRNA gene CNV can be mapped to the NORs themselves, with both loci contributing equally to the variation. However, NOR size is unstably inherited, and dramatic copy number changes are visible already within tens of generations, which explains why it is not possible to map the NORs using GWAS. We did not find any evidence of trans-acting loci in crosses, which is also expected since changes due to such loci would take very many generations to manifest themselves. rRNA gene copy number is thus an interesting example of "missing heritability"-a trait that is heritable in pedigrees, but not in the general population.
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Affiliation(s)
- Fernando A Rabanal
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030, Austria
| | - Viktoria Nizhynska
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030, Austria
| | - Terezie Mandáková
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
| | - Polina Yu Novikova
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030, Austria
| | - Martin A Lysak
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
| | - Richard Mott
- University College London Genetics Institute, WC1E 6BT, UK
| | - Magnus Nordborg
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030, Austria
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Chand Dakal T, Giudici P, Solieri L. Contrasting Patterns of rDNA Homogenization within the Zygosaccharomyces rouxii Species Complex. PLoS One 2016; 11:e0160744. [PMID: 27501051 PMCID: PMC4976873 DOI: 10.1371/journal.pone.0160744] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 07/25/2016] [Indexed: 11/18/2022] Open
Abstract
Arrays of repetitive ribosomal DNA (rDNA) sequences are generally expected to evolve as a coherent family, where repeats within such a family are more similar to each other than to orthologs in related species. The continuous homogenization of repeats within individual genomes is a recombination process termed concerted evolution. Here, we investigated the extent and the direction of concerted evolution in 43 yeast strains of the Zygosaccharomyces rouxii species complex (Z. rouxii, Z. sapae, Z. mellis), by analyzing two portions of the 35S rDNA cistron, namely the D1/D2 domains at the 5’ end of the 26S rRNA gene and the segment including the internal transcribed spacers (ITS) 1 and 2 (ITS regions). We demonstrate that intra-genomic rDNA sequence variation is unusually frequent in this clade and that rDNA arrays in single genomes consist of an intermixing of Z. rouxii, Z. sapae and Z. mellis-like sequences, putatively evolved by reticulate evolutionary events that involved repeated hybridization between lineages. The levels and distribution of sequence polymorphisms vary across rDNA repeats in different individuals, reflecting four patterns of rDNA evolution: I) rDNA repeats that are homogeneous within a genome but are chimeras derived from two parental lineages via recombination: Z. rouxii in the ITS region and Z. sapae in the D1/D2 region; II) intra-genomic rDNA repeats that retain polymorphisms only in ITS regions; III) rDNA repeats that vary only in their D1/D2 domains; IV) heterogeneous rDNA arrays that have both polymorphic ITS and D1/D2 regions. We argue that an ongoing process of homogenization following allodiplodization or incomplete lineage sorting gave rise to divergent evolutionary trajectories in different strains, depending upon temporal, structural and functional constraints. We discuss the consequences of these findings for Zygosaccharomyces species delineation and, more in general, for yeast barcoding.
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Affiliation(s)
- Tikam Chand Dakal
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Amendola 2, 42122, Reggio Emilia, Italy
| | - Paolo Giudici
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Amendola 2, 42122, Reggio Emilia, Italy
| | - Lisa Solieri
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Amendola 2, 42122, Reggio Emilia, Italy
- * E-mail:
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