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Sandberg TOM, Yahalomi D, Bracha N, Haddas-Sasson M, Pupko T, Atkinson SD, Bartholomew JL, Zhang JY, Huchon D. Evolution of myxozoan mitochondrial genomes: insights from myxobolids. BMC Genomics 2024; 25:388. [PMID: 38649808 PMCID: PMC11034133 DOI: 10.1186/s12864-024-10254-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Accepted: 03/26/2024] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND Myxozoa is a class of cnidarian parasites that encompasses over 2,400 species. Phylogenetic relationships among myxozoans remain highly debated, owing to both a lack of informative morphological characters and a shortage of molecular markers. Mitochondrial (mt) genomes are a common marker in phylogeny and biogeography. However, only five complete myxozoan mt genomes have been sequenced: four belonging to two closely related genera, Enteromyxum and Kudoa, and one from the genus Myxobolus. Interestingly, while cytochrome oxidase genes could be identified in Enteromyxum and Kudoa, no such genes were found in Myxobolus squamalis, and another member of the Myxobolidae (Henneguya salminicola) was found to have lost its entire mt genome. To evaluate the utility of mt genomes to reconstruct myxozoan relationships and to understand if the loss of cytochrome oxidase genes is a characteristic of myxobolids, we sequenced the mt genome of five myxozoans (Myxobolus wulii, M. honghuensis, M. shantungensis, Thelohanellus kitauei and, Sphaeromyxa zaharoni) using Illumina and Oxford Nanopore platforms. RESULTS Unlike Enteromyxum, which possesses a partitioned mt genome, the five mt genomes were encoded on single circular chromosomes. An mt plasmid was found in M. wulii, as described previously in Kudoa iwatai. In all new myxozoan genomes, five protein-coding genes (cob, cox1, cox2, nad1, and nad5) and two rRNAs (rnl and rns) were recognized, but no tRNA. We found that Myxobolus and Thelohanellus species shared unidentified reading frames, supporting the view that these mt open reading frames are functional. Our phylogenetic reconstructions based on the five conserved mt genes agree with previously published trees based on the 18S rRNA gene. CONCLUSIONS Our results suggest that the loss of cytochrome oxidase genes is not a characteristic of all myxobolids, the ancestral myxozoan mt genome was likely encoded on a single circular chromosome, and mt plasmids exist in a few lineages. Our findings indicate that myxozoan mt sequences are poor markers for reconstructing myxozoan phylogenetic relationships because of their fast-evolutionary rates and the abundance of repeated elements, which complicates assembly.
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Affiliation(s)
| | - Dayana Yahalomi
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Noam Bracha
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Michal Haddas-Sasson
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Tal Pupko
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Stephen D Atkinson
- Department of Microbiology, Oregon State University, 97331, Corvallis, OR, USA
| | - Jerri L Bartholomew
- Department of Microbiology, Oregon State University, 97331, Corvallis, OR, USA
| | - Jin Yong Zhang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Dorothée Huchon
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 6997801, Tel Aviv, Israel.
- The Steinhardt Museum of Natural History and National Research Center, Tel Aviv University, 6997801, Tel Aviv, Israel.
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Lau MML, Lim LWK, Chung HH, Gan HM. The first draft genome assembly and data analysis of the Malaysian mahseer (Tor tambroides). Aquaculture and Fisheries 2022. [DOI: 10.1016/j.aaf.2022.05.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Attix H, George A, Panchal H, Cortez A, Cho M, Zarilla K, Hastie E. Wild Caught Nematode Identification and Early Embryo Development: An accessible undergraduate research experience. MicroPubl Biol 2021; 2021. [PMID: 34414363 PMCID: PMC8369341 DOI: 10.17912/micropub.biology.000447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/06/2021] [Accepted: 08/10/2021] [Indexed: 11/06/2022]
Abstract
Ample evidence suggests that participation in undergraduate research in community college is critical for stimulating interest and retention in STEM careers. Guided skill development and practice in a collaborative lab setting allows students to be competitive when applying to future research opportunities. The goals of this undergraduate research experience (URE) was for student-driven discovery with unknown outcomes including: introduction to primary literature, developmental biology, developing hypotheses, learning worm maintenance, microscopy, PCR, and sequencing analysis. The use of C. elegans and wild caught nematodes facilitated an exciting and affordable project that can be built on in future UREs.
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Nyaku ST, Sripathi VR, Lawrence K, Sharma G. Characterizing Repeats in Two Whole-Genome Amplification Methods in the Reniform Nematode Genome. Int J Genomics 2021; 2021:5532885. [PMID: 33748264 DOI: 10.1155/2021/5532885] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 02/26/2021] [Indexed: 11/17/2022] Open
Abstract
One of the major problems in the U.S. and global cotton production is the damage caused by the reniform nematode, Rotylenchulus reniformis. Amplification of DNA from single nematodes for further molecular analysis can be challenging sometimes. In this research, two whole-genome amplification (WGA) methods were evaluated for their efficiencies in DNA amplification from a single reniform nematode. The WGA was carried out using both REPLI-g Mini and Midi kits, and the GenomePlex single cell whole-genome amplification kit. Sequence analysis produced 4 Mb and 12 Mb of genomic sequences for the reniform nematode using REPLI-g and SIGMA libraries. These sequences were assembled into 28,784 and 24,508 contigs, respectively, for REPLI-g and SIGMA libraries. The highest repeats in both libraries were of low complexity, and the lowest for the REPLI-g library were for satellites and for the SIGMA library, RTE/BOV-B. The same kind of repeats were observed for both libraries; however, the SIGMA library had four other repeat elements (Penelope (long interspersed nucleotide element (LINE)), RTE/BOV-B (LINE), PiggyBac, and Mirage/P-element/Transib), which were not seen in the REPLI-g library. DNA transposons were also found in both libraries. Both reniform nematode 18S rRNA variants (RN_VAR1 and RN_VAR2) could easily be identified in both libraries. This research has therefore demonstrated the ability of using both WGA methods, in amplification of gDNA isolated from single reniform nematodes.
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Singh PR, Kashando BE, Couvreur M, Karssen G, Bert W. Plant-parasitic nematodes associated with sugarcane in Kilimanjaro, Tanzania. J Nematol 2020; 52:1-17. [PMID: 32628825 PMCID: PMC7366841 DOI: 10.21307/jofnem-2020-059] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Indexed: 11/11/2022] Open
Abstract
Morphological and molecular analyses of plant-parasitic nematodes (PPN) from 12 sugarcane plantation sites of Tanganyika Planting Company (TPC) Limited in Kilimanjaro region of Tanzania revealed the presence of six PPN genera, i.e. Helicotylenchus, Hemicycliophora, Pratylenchus, Rotylenchulus, Scutellonema, and Tylenchorhynchus. The genera with the highest densities and present in virtually all samples were Pratylenchus and Rotylenchulus, and the most important species appeared to be R. parvus, P. zeae, T. crassicaudatus, and T. ventrosignatus. A total sequences of 11 partial ITS, 15 D2-D3 of 28S, and 6 partial 18S of rRNA gene, and 7 partial COI gene of mtDNA of these species were obtained in this study. Morphology and molecular data comparisons between the Tanzanian R. parvus and the South African R. parvus indicated that R. parvus is a cryptic species complex. Based on the results of morphological and molecular analyses of T. crassicaudatus and T. agri from China, Haiti, Indonesia, Iran, Niger and the USA, T. agri syn. n. is proposed as a junior synonym of T. crassicaudatus.
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Affiliation(s)
| | - Beatrice E Kashando
- Nematology Research Unit, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium ; Tanzania Agricultural Research Institute (TARI), P.O. Box 30031, Tumbi Road, Kibaha Coast region, Tanzania
| | - Marjolein Couvreur
- Nematology Research Unit, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Gerrit Karssen
- Nematology Research Unit, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium ; National Plant Protection Organization, Wageningen Nematode Collection, P.O. Box 9102, 6700 HC Wageningen, The Netherlands
| | - Wim Bert
- Nematology Research Unit, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
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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: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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7
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García-Martín JM, Zamora JC, Lado C. 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] [What about the content of this article? (0)] [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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Viviani A, Bernardi R, Cavallini A, Rossi E. Genotypic Characterization of Torymus sinensis (Hymenoptera: Torymidae) After Its Introduction in Tuscany (Italy) for the Biological Control of Dryocosmus kuriphilus (Hymenoptera: Cynipidae). J Insect Sci 2019; 19:5550985. [PMID: 31422419 PMCID: PMC6698180 DOI: 10.1093/jisesa/iez080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Indexed: 06/10/2023]
Abstract
Torymus sinensis Kamijo (Hymenoptera: Torymidae) is an alien parasitoid that is used in many areas of the world for biological control the Asian chestnut gall wasp, Dryocosmus kuriphilus Yasumatsu (Hymenoptera: Cynipidae). In Italy, this parasitoid was imported from Japan in 2003 and subsequently multiplied and released throughout the country. In this study, a phylogenetic investigation was carried out on insects from three different sites in northern Tuscany (Italy). Moreover, the possible hybridization between T. sinensis and some native Torymus species was evaluated. The conserved region 18S rRNA gene and the hypervariable ITS2 (Internal Transcribed Spacer 2) region of the ribosomal cistrone were selected as molecular markers. Sequencing the amplified products, after cloning, ruled out any hybridization between T. sinensis and the native Torymus species, and also confirmed the presence of two haplotypes for the Tuscan population of T. sinensis both for the region of the 18S rRNA gene as well as for the ITS2 region. These results confirm that the environmental impact of the alien parasitoid T. sinensis in the study site is acceptable, although an extensive and repeated monitoring would be desirable.
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Affiliation(s)
- Ambra Viviani
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto, Pisa, Italy
| | - Rodolfo Bernardi
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto, Pisa, Italy
| | - Andrea Cavallini
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto, Pisa, Italy
| | - Elisabetta Rossi
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto, Pisa, Italy
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10
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Zhou S, Fu X, Pei P, Kucka M, Liu J, Tang L, Zhan T, He S, Chan YF, Rödelsperger C, Liu D, Streit A. Characterization of a non-sexual population of Strongyloides stercoralis with hybrid 18S rDNA haplotypes in Guangxi, Southern China. PLoS Negl Trop Dis 2019; 13:e0007396. [PMID: 31059500 PMCID: PMC6522072 DOI: 10.1371/journal.pntd.0007396] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 05/16/2019] [Accepted: 04/16/2019] [Indexed: 11/18/2022] Open
Abstract
Strongyloidiasis is a much-neglected but sometimes fatal soil born helminthiasis. The causing agent, the small intestinal parasitic nematode Strongyloides stercoralis can reproduce sexually through the indirect/heterogonic life cycle, or asexually through the auto-infective or the direct/homogonic life cycles. Usually, among the progeny of the parasitic females both, parthenogenetic parasitic (females only) and sexual free-living (females and males) individuals, are present simultaneously. We isolated S. stercoralis from people living in a village with a high incidence of parasitic helminths, in particular liver flukes (Clonorchis sinensis) and hookworms, in the southern Chinese province Guangxi. We determined nuclear and mitochondrial DNA sequences of individual S. stercoralis isolated from this village and from close by hospitals and we compared these S. stercoralis among themselves and with selected published S. stercoralis from other geographic locations. For comparison, we also analyzed the hookworms present in the same location. We found that, compared to earlier studies of S. stercoralis populations in South East Asia, all S. stercoralis sampled in our study area were very closely related, suggesting a recent common source of infection for all patients. In contrast, the hookworms from the same location, while all belonging to the species Necator americanus, showed rather extensive genetic diversity even within host individuals. Different from earlier studies conducted in other geographic locations, almost all S. stercoralis in this study appeared heterozygous for different sequence variants of the 18S rDNA hypervariable regions (HVR) I and IV. In contrast to earlier investigations, except for three males, all S. stercoralis we isolated in this study were infective larvae, suggesting that the sampled population reproduces predominantly, if not exclusively through the clonal life cycles. Consistently, whole genome sequencing of individual worms revealed higher heterozygosity than reported earlier for likely sexual populations of S. stercoralis. Elevated heterozygosity is frequently associated with asexual clonal reproduction.
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Affiliation(s)
- Siyu Zhou
- Department of Evolutionary Biology, Max-Planck-Institute for Developmental Biology, Tübingen, Germany
| | - Xiaoyin Fu
- Department of Parasitology, Guangxi Medical University, Nanning, China
| | - Pei Pei
- Department of Parasitology, Guangxi Medical University, Nanning, China
| | - Marek Kucka
- Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany
| | - Jing Liu
- Department of Parasitology, Guangxi Medical University, Nanning, China
| | - Lili Tang
- Department of Parasitology, Guangxi Medical University, Nanning, China
| | - Tingzheng Zhan
- Department of Parasitology, Guangxi Medical University, Nanning, China
| | - Shanshan He
- Department of Parasitology, Guangxi Medical University, Nanning, China
| | | | - Christian Rödelsperger
- Department of Evolutionary Biology, Max-Planck-Institute for Developmental Biology, Tübingen, Germany
| | - Dengyu Liu
- Department of Parasitology, Guangxi Medical University, Nanning, China
- * E-mail: (DL); (AS)
| | - Adrian Streit
- Department of Evolutionary Biology, Max-Planck-Institute for Developmental Biology, Tübingen, Germany
- * E-mail: (DL); (AS)
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Bespalaya YV, Bolotov IN, Aksenova OV, Kondakov AV, Gofarov MY, Laenko TM, Sokolova SE, Shevchenko AR, Travina OV. Aliens are moving to the Arctic frontiers: an integrative approach reveals selective expansion of androgenic hybrid Corbicula lineages towards the North of Russia. Biol Invasions 2018. [DOI: 10.1007/s10530-018-1698-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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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 Dis 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Nyaku ST, Kantety RV, Cebert E, Lawrence KS, Honger JO, Sharma GC. Principal Component Analysis and Molecular Characterization of Reniform Nematode Populations in Alabama. Plant Pathol J 2016; 32:123-35. [PMID: 27147932 PMCID: PMC4853102 DOI: 10.5423/ppj.oa.09.2015.0194] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 11/02/2015] [Accepted: 11/10/2015] [Indexed: 06/05/2023]
Abstract
U.S. cotton production is suffering from the yield loss caused by the reniform nematode (RN), Rotylenchulus reniformis. Management of this devastating pest is of utmost importance because, no upland cotton cultivar exhibits adequate resistance to RN. Nine populations of RN from distinct regions in Alabama and one population from Mississippi were studied and thirteen morphometric features were measured on 20 male and 20 female nematodes from each population. Highly correlated variables (positive) in female and male RN morphometric parameters were observed for body length (L) and distance of vulva from the lip region (V) (r = 0.7) and tail length (TL) and c' (r = 0.8), respectively. The first and second principal components for the female and male populations showed distinct clustering into three groups. These results show pattern of sub-groups within the RN populations in Alabama. A one-way ANOVA on female and male RN populations showed significant differences (p ≤ 0.05) among the variables. Multiple sequence alignment (MSA) of 18S rRNA sequences (421) showed lengths of 653 bp. Sites within the aligned sequences were conserved (53%), parsimony-informative (17%), singletons (28%), and indels (2%), respectively. Neighbor-Joining analysis showed intra and inter-nematodal variations within the populations as clone sequences from different nematodes irrespective of the sex of nematode isolate clustered together. Morphologically, the three groups (I, II and III) could not be distinctly associated with the molecular data from the 18S rRNA sequences. The three groups may be identified as being non-geographically contiguous.
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Affiliation(s)
- Seloame T. Nyaku
- Department of Crop Science, College of Basic and Applied Sciences, University of Ghana, P.O. Box LG 44, Legon-Accra
- Department of Natural Resources and Environmental Sciences, Alabama A & M University, Normal-AL, 35762
| | - Ramesh V. Kantety
- Department of Natural Resources and Environmental Sciences, Alabama A & M University, Normal-AL, 35762
| | - Ernst Cebert
- Department of Natural Resources and Environmental Sciences, Alabama A & M University, Normal-AL, 35762
| | - Kathy S. Lawrence
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849
| | - Joseph O. Honger
- Soil and Irrigation Research Centre, University of Ghana, P.O. Box LG 44, Legon-Accra
| | - Govind C. Sharma
- Department of Natural Resources and Environmental Sciences, Alabama A & M University, Normal-AL, 35762
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Pereira TJ, Baldwin JG. Contrasting evolutionary patterns of 28S and ITS rRNA genes reveal high intragenomic variation in Cephalenchus (Nematoda): Implications for species delimitation. Mol Phylogenet Evol 2016; 98:244-60. [PMID: 26926945 DOI: 10.1016/j.ympev.2016.02.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 02/20/2016] [Accepted: 02/20/2016] [Indexed: 01/05/2023]
Abstract
Concerted evolution is often assumed to be the evolutionary force driving multi-family genes, including those from ribosomal DNA (rDNA) repeat, to complete homogenization within a species, although cases of non-concerted evolution have been also documented. In this study, sequence variation of 28S and ITS ribosomal RNA (rRNA) genes in the genus Cephalenchus is assessed at three different levels, intragenomic, intraspecific, and interspecific. The findings suggest that not all Cephalenchus species undergo concerted evolution. High levels of intraspecific polymorphism, mostly due to intragenomic variation, are found in Cephalenchus sp1 (BRA-01). Secondary structure analyses of both rRNA genes and across different species show a similar substitution pattern, including mostly compensatory (CBC) and semi-compensatory (SBC) base changes, thus suggesting the functionality of these rRNA copies despite the variation found in some species. This view is also supported by low sequence variation in the 5.8S gene in relation to the flanking ITS-1 and ITS-2 as well as by the existence of conserved motifs in the former gene. It is suggested that potential cross-fertilization in some Cephalenchus species, based on inspection of female reproductive system, might contribute to both intragenomic and intraspecific polymorphism of their rRNA genes. These results reinforce the potential implications of intragenomic and intraspecific genetic diversity on species delimitation, especially in biodiversity studies based solely on metagenetic approaches. Knowledge of sequence variation will be crucial for accurate species diversity estimation using molecular methods.
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Affiliation(s)
- Tiago José Pereira
- Department of Nematology, University of California, Riverside, 900 University Avenue, Riverside, CA 92521, USA.
| | - James Gordon Baldwin
- Department of Nematology, University of California, Riverside, 900 University Avenue, Riverside, CA 92521, USA.
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Van Den Berg E, Palomares-Rius JE, Vovlas N, Tiedt LR, Castillo P, Subbotin SA. Morphological and molecular characterisation of one new and several known species of the reniform nematode, Rotylenchulus Linford & Oliveira, 1940 (Hoplolaimidae: Rotylenchulinae), and a phylogeny of the genus. NEMATOLOGY 2016. [DOI: 10.1163/15685411-00002945] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The reniform nematodes of the genusRotylenchulusare semi-endoparasites of numerous herbaceous and woody plant roots and are mainly distributed in tropical and subtropical regions. In this study, we provide morphological and molecular characterisation of six out of ten presently known valid species ofRotylenchulus:R. clavicaudatus,R. leptus,R. macrodoratus,R. macrosoma,R. reniformisandR. saccharifrom South Africa, USA, Italy and Spain.Rotylenchulus parvuswas only studied morphologically. A new species,R. macrosomoidessp. n., isolated from soil and roots of sugarcane in South Africa, is described. The phylogeny ofRotylenchulus, as inferred from the analyses of D2-D3 of 28S rRNA, ITS rRNA,coxImtDNA andhsp90gene sequences, is presented. The study revealed thatR. reniformisandR. macrosomahave a sister relationship, but that relationships between otherRotylenchulusspecies remain unresolved. The phylogenetic analysis also confirmed the hypothesis that this genus originated from the Afrotropical zoogeographical region. Our study revealed thatR. reniformisandR. macrosomoidessp. n. have two distinct rRNA gene types andR. macrosomahave three rRNA gene types in their genomes. PCR with species-specific primers was developed for rapid diagnostics ofR. reniformis.
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Affiliation(s)
- Esther Van Den Berg
- National Collection of Nematodes, Biosystematics Programme, ARC-Plant Protection Research Institute, Private Bag X 134, Queenswood 0121, South Africa
| | - Juan E. Palomares-Rius
- Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), Campus de Excelencia Internacional Agroalimentario, ceiA3, Avenida Menéndez Pidal s/n, 14004 Córdoba, Spain
| | - Nicola Vovlas
- Istituto per la Protezione Sostenibile delle Piante (IPSP), Consiglio Nazionale delle Ricerche (CNR), U.O.S. di Bari, Via G. Amendola 122/D, 70126 Bari, Italy
| | - Louwrens R. Tiedt
- Laboratory for Electron Microscopy, North West University, Potchefstroom Campus, Potchefstroom 2520, South Africa
| | - Pablo Castillo
- Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), Campus de Excelencia Internacional Agroalimentario, ceiA3, Avenida Menéndez Pidal s/n, 14004 Córdoba, Spain
| | - Sergei A. Subbotin
- Plant Pest Diagnostic Center, California Department of Food and Agriculture, 3294 Meadowview Road, Sacramento, CA 95832, USA
- Center of Parasitology of A.N. Severtsov Institute of Ecology and Evolution of the Russian Academy of Sciences, Leninskii Prospect 33, Moscow 117071, Russia
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Brown EA, Chain FJJ, Crease TJ, MacIsaac HJ, Cristescu ME. Divergence thresholds and divergent biodiversity estimates: can metabarcoding reliably describe zooplankton communities? Ecol Evol 2015; 5:2234-51. [PMID: 26078859 PMCID: PMC4461424 DOI: 10.1002/ece3.1485] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Revised: 03/19/2015] [Accepted: 03/23/2015] [Indexed: 11/25/2022] Open
Abstract
DNA metabarcoding is a promising method for describing communities and estimating biodiversity. This approach uses high-throughput sequencing of targeted markers to identify species in a complex sample. By convention, sequences are clustered at a predefined sequence divergence threshold (often 3%) into operational taxonomic units (OTUs) that serve as a proxy for species. However, variable levels of interspecific marker variation across taxonomic groups make clustering sequences from a phylogenetically diverse dataset into OTUs at a uniform threshold problematic. In this study, we use mock zooplankton communities to evaluate the accuracy of species richness estimates when following conventional protocols to cluster hypervariable sequences of the V4 region of the small subunit ribosomal RNA gene (18S) into OTUs. By including individually tagged single specimens and “populations” of various species in our communities, we examine the impact of intra- and interspecific diversity on OTU clustering. Communities consisting of single individuals per species generated a correspondence of 59–84% between OTU number and species richness at a 3% divergence threshold. However, when multiple individuals per species were included, the correspondence between OTU number and species richness dropped to 31–63%. Our results suggest that intraspecific variation in this marker can often exceed 3%, such that a single species does not always correspond to one OTU. We advocate the need to apply group-specific divergence thresholds when analyzing complex and taxonomically diverse communities, but also encourage the development of additional filtering steps that allow identification of artifactual rRNA gene sequences or pseudogenes that may generate spurious OTUs.
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Affiliation(s)
- Emily A Brown
- Department of Biology, McGill University 1205 Docteur Penfield, Montreal, Quebec, Canada, H3A 1B1 ; Great Lakes Institute for Environmental Research, University of Windsor Windsor, Ontario, Canada, N9B 3P4
| | - Frédéric J J Chain
- Department of Biology, McGill University 1205 Docteur Penfield, Montreal, Quebec, Canada, H3A 1B1
| | - Teresa J Crease
- Department of Integrative Biology, University of Guelph 50 Stone Road East, Guelph, Ontario, Canada, N1G 2W1
| | - Hugh J MacIsaac
- Great Lakes Institute for Environmental Research, University of Windsor Windsor, Ontario, Canada, N9B 3P4
| | - Melania E Cristescu
- Department of Biology, McGill University 1205 Docteur Penfield, Montreal, Quebec, Canada, H3A 1B1
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Nyaku ST, Sripathi VR, Kantety RV, Cseke SB, Buyyarapu R, Mc Ewan R, Gu YQ, Lawrence K, Senwo Z, Sripathi P, George P, Sharma GC. Characterization of the reniform nematode genome by shotgun sequencing. Genome 2014; 57:209-21. [PMID: 25036535 DOI: 10.1139/gen-2014-0019] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The reniform nematode (RN), a major agricultural pest particularly on cotton in the United States, is among the major plant-parasitic nematodes for which limited genomic information exists. In this study, over 380 Mb of sequence data were generated from pooled DNA of four adult female RNs and assembled into 67,317 contigs, including 25,904 (38.5%) predicted coding contigs and 41,413 (61.5%) noncoding contigs. Most of the characterized repeats were of low complexity (88.9%), and 0.9% of the contigs matched with 53.2% of GenBank ESTs. The most frequent Gene Ontology (GO) terms for molecular function and biological process were protein binding (32%) and embryonic development (20%). Further analysis showed that 741 (1.1%), 94 (0.1%), and 169 (0.25%) RN genomic contigs matched with 1328 (13.9%), 1480 (5.4%), and 1330 (7.4%) supercontigs of Meloidogyne incognita, Brugia malayi, and Pristionchus pacificus, respectively. Chromosome 5 of Caenorhabditis elegans had the highest number of hits to the RN contigs. Seven putative detoxification genes and three carbohydrate-active enzymes (CAZymes) involved in cell wall degradation were studied in more detail. Additionally, kinases, G protein-coupled receptors, and neuropeptides functioning in physiological, developmental, and regulatory processes were identified in the RN genome.
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Affiliation(s)
- Seloame T Nyaku
- a Department of Biological and Environmental Sciences, Alabama A&M University, Normal, AL 35762, USA
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Koshel EI, Aleshin VV, Eroshenko GA, Kutyrev VV. Phylogenetic analysis of entomoparasitic nematodes, potential control agents of flea populations in natural foci of plague. Biomed Res Int 2014; 2014:135218. [PMID: 24804197 PMCID: PMC3996313 DOI: 10.1155/2014/135218] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Revised: 06/05/2013] [Accepted: 10/22/2013] [Indexed: 11/18/2022]
Abstract
Entomoparasitic nematodes are natural control agents for many insect pests, including fleas that transmit Yersinia pestis, a causative agent of plague, in the natural foci of this extremely dangerous zoonosis. We examined the flea samples from the Volga-Ural natural focus of plague for their infestation with nematodes. Among the six flea species feeding on different rodent hosts (Citellus pygmaeus, Microtus socialis, and Allactaga major), the rate of infestation varied from 0 to 21%. The propagation rate of parasitic nematodes in the haemocoel of infected fleas was very high; in some cases, we observed up to 1,000 juveniles per flea specimen. Our study of morphology, life cycle, and rDNA sequences of these parasites revealed that they belong to three distinct species differing in the host specificity. On SSU and LSU rRNA phylogenies, these species representing three genera (Rubzovinema, Psyllotylenchus, and Spilotylenchus), constitute a monophyletic group close to Allantonema and Parasitylenchus, the type genera of the families Allantonematidae and Parasitylenchidae (Nematoda: Tylenchida). We discuss the SSU-ITS1-5.8S-LSU rDNA phylogeny of the Tylenchida with a special emphasis on the suborder Hexatylina.
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Affiliation(s)
- E. I. Koshel
- Russian Research Anti-Plague Institute “Microbe”, Saratov 410005, Russia
| | - V. V. Aleshin
- Belozersky Institute of Physical-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow 127994, Russia
- National Research Institute of Physiology, Biochemistry, and Nutrition of Farm Animals, Russian Academy of Agricultural Sciences, Kaluga Region, Borovsk 249013, Russia
| | - G. A. Eroshenko
- Russian Research Anti-Plague Institute “Microbe”, Saratov 410005, Russia
| | - V. V. Kutyrev
- Russian Research Anti-Plague Institute “Microbe”, Saratov 410005, Russia
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