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Oppert B, Dossey AT, Chu FC, Šatović-Vukšić E, Plohl M, Smith TPL, Koren S, Olmstead ML, Leierer D, Ragan G, Johnston JS. The Genome of the Yellow Mealworm, Tenebrio molitor: It's Bigger Than You Think. Genes (Basel) 2023; 14:2209. [PMID: 38137031 PMCID: PMC10742464 DOI: 10.3390/genes14122209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 11/26/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023] Open
Abstract
BACKGROUND Insects are a sustainable source of protein for human food and animal feed. We present a genome assembly, CRISPR gene editing, and life stage-specific transcriptomes for the yellow mealworm, Tenebrio molitor, one of the most intensively farmed insects worldwide. METHODS Long and short reads and long-range data were obtained from a T. molitor male pupa. Sequencing transcripts from 12 T. molitor life stages resulted in 279 million reads for gene prediction and genetic engineering. A unique plasmid delivery system containing guide RNAs targeting the eye color gene vermilion flanking the muscle actin gene promoter and EGFP marker was used in CRISPR/Cas9 transformation. RESULTS The assembly is approximately 53% of the genome size of 756.8 ± 9.6 Mb, measured using flow cytometry. Assembly was complicated by a satellitome of at least 11 highly conserved satDNAs occupying 28% of the genome. The injection of the plasmid into embryos resulted in knock-out of Tm vermilion and knock-in of EGFP. CONCLUSIONS The genome of T. molitor is longer than current assemblies (including ours) due to a substantial amount (26.5%) of only one highly abundant satellite DNA sequence. Genetic sequences and transformation tools for an insect important to the food and feed industries will promote the sustainable utilization of mealworms and other farmed insects.
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Affiliation(s)
- Brenda Oppert
- USDA Agricultural Research Service, Center for Grain and Animal Health Research, 1515 College Ave., Manhattan, KS 66502, USA; (M.L.O.); (G.R.)
| | - Aaron T. Dossey
- All Things Bugs LLC, 755 Research Parkway, Suite 465, Oklahoma City, OK 73130, USA or (A.T.D.); (F.-C.C.)
- Invertebrate Studies Institute, 2211 Snapper Ln, Midwest City, OK 73130, USA
| | - Fu-Chyun Chu
- All Things Bugs LLC, 755 Research Parkway, Suite 465, Oklahoma City, OK 73130, USA or (A.T.D.); (F.-C.C.)
| | - Eva Šatović-Vukšić
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia; (E.Š.-V.); (M.P.)
| | - Miroslav Plohl
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia; (E.Š.-V.); (M.P.)
| | | | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20894, USA
| | - Morgan L. Olmstead
- USDA Agricultural Research Service, Center for Grain and Animal Health Research, 1515 College Ave., Manhattan, KS 66502, USA; (M.L.O.); (G.R.)
| | - Dewey Leierer
- Department of Molecular Biology and Biophysics, Kansas State University, Manhattan, KS 66506, USA;
| | - Gail Ragan
- USDA Agricultural Research Service, Center for Grain and Animal Health Research, 1515 College Ave., Manhattan, KS 66502, USA; (M.L.O.); (G.R.)
| | - J. Spencer Johnston
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA;
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Kaur S, Stinson SA, diCenzo GC. Whole genome assemblies of Zophobas morio and Tenebrio molitor. G3 (BETHESDA, MD.) 2023; 13:jkad079. [PMID: 37002914 PMCID: PMC10234394 DOI: 10.1093/g3journal/jkad079] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 03/29/2023] [Indexed: 01/12/2024]
Abstract
Zophobas morio (=Zophobas atratus) and Tenebrio molitor are darkling beetles with industrial importance due to their use as feeder insects and their apparent ability to biodegrade plastics. High quality genome assemblies were recently reported for both species. Here, we report additional independent Z. morio and T. molitor genome assemblies generated from Nanopore and Illumina data. Following scaffolding against the published genomes, haploid assemblies of 462 Mb (scaffold N90 of 16.8 Mb) and 258 Mb (scaffold N90 of 5.9 Mb) were produced for Z. morio and T. molitor, respectively. Gene prediction led to the prediction of 28,544 and 19,830 genes for Z. morio and T. molitor, respectively. Benchmarking Universal Single Copy Orthologs (BUSCO) analyses suggested that both assemblies have a high level of completeness; 91.5 and 89.0% of the BUSCO endopterygota marker genes were complete in the Z. morio assembly and proteome, respectively, while 99.1 and 92.8% were complete in the T. molitor assembly and proteome, respectively. Phylogenomic analyses of four genera from the family Tenebrionidae yielded phylogenies consistent with those previously constructed based on mitochondrial genomes. Synteny analyses revealed large stretches of macrosynteny across the family Tenebrionidae, as well as numerous within-chromosome rearrangements. Finally, orthogroup analysis identified ∼28,000 gene families across the family Tenebrionidae, of which 8,185 were identified in all five of the analyzed species, and 10,837 were conserved between Z. morio and T. molitor. We expect that the availability of multiple whole genome sequences for Z. morio and T. molitor will facilitate population genetics studies to identify genetic variation associated with industrially relevant phenotypes.
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Affiliation(s)
- Sabhjeet Kaur
- Department of Biology, Queen's University, 116 Barrie Street, Kingston, Ontario K7L 3N6, Canada
| | - Sydnie A Stinson
- Department of Biology, Queen's University, 116 Barrie Street, Kingston, Ontario K7L 3N6, Canada
| | - George C diCenzo
- Department of Biology, Queen's University, 116 Barrie Street, Kingston, Ontario K7L 3N6, Canada
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3
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Eleftheriou E, Aury JM, Vacherie B, Istace B, Belser C, Noel B, Moret Y, Rigaud T, Berro F, Gasparian S, Labadie-Bretheau K, Lefebvre T, Madoui MA. Chromosome-scale assembly of the yellow mealworm genome. OPEN RESEARCH EUROPE 2022; 1:94. [PMID: 37645128 PMCID: PMC10445852 DOI: 10.12688/openreseurope.13987.2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 08/30/2022] [Indexed: 03/12/2024]
Abstract
Background: The yellow mealworm beetle, Tenebrio molitor, is a promising alternative protein source for animal and human nutrition and its farming involves relatively low environmental costs. For these reasons, its industrial scale production started this century. However, to optimize and breed sustainable new T. molitor lines, the access to its genome remains essential. Methods: By combining Oxford Nanopore and Illumina Hi-C data, we constructed a high-quality chromosome-scale assembly of T. molitor. Then, we combined RNA-seq data and available coleoptera proteomes for gene prediction with GMOVE. Results: We produced a high-quality genome with a N50 = 21.9Mb with a completeness of 99.5% and predicted 21,435 genes with a median size of 1,780 bp. Gene orthology between T. molitor and Tribolium castaneum showed a highly conserved synteny between the two coleoptera and paralogs search revealed an expansion of histones in the T. molitor genome. Conclusions: The present genome will greatly help fundamental and applied research such as genetic breeding and will contribute to the sustainable production of the yellow mealworm.
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Affiliation(s)
- Evangelia Eleftheriou
- Génomique Métabolique, Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Univ Evry, Université Paris-Saclay, Université Paris-Saclay, Evry, 91057, France
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Univ Evry, Université Paris-Saclay, Université Paris-Saclay, Evry, 91057, France
| | - Benoît Vacherie
- Genoscope, Institut de biologie François Jacob, CEA, Université Paris‐Saclay, Evry, 91057, France
| | - Benjamin Istace
- Génomique Métabolique, Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Univ Evry, Université Paris-Saclay, Université Paris-Saclay, Evry, 91057, France
| | - Caroline Belser
- Génomique Métabolique, Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Univ Evry, Université Paris-Saclay, Université Paris-Saclay, Evry, 91057, France
| | - Benjamin Noel
- Génomique Métabolique, Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Univ Evry, Université Paris-Saclay, Université Paris-Saclay, Evry, 91057, France
| | - Yannick Moret
- Équipe Écologie Évolutive, UMR CNRS 6282 BioGéoSciences, Université de Bourgogne Franche-Comté, Dijon, 21000, France
| | - Thierry Rigaud
- Équipe Écologie Évolutive, UMR CNRS 6282 BioGéoSciences, Université de Bourgogne Franche-Comté, Dijon, 21000, France
| | | | | | - Karine Labadie-Bretheau
- Genoscope, Institut de biologie François Jacob, CEA, Université Paris‐Saclay, Evry, 91057, France
| | | | - Mohammed-Amin Madoui
- Génomique Métabolique, Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Univ Evry, Université Paris-Saclay, Université Paris-Saclay, Evry, 91057, France
- Équipe Écologie Évolutive, UMR CNRS 6282 BioGéoSciences, Université de Bourgogne Franche-Comté, Dijon, 21000, France
- Service d’Etude des Prions et des Infections Atypiques (SEPIA), Institut François Jacob, Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA), Université Paris Saclay, Fontenay-aux-Roses, France
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4
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Eleftheriou E, Aury JM, Vacherie B, Istace B, Belser C, Noel B, Moret Y, Rigaud T, Berro F, Gasparian S, Labadie-Bretheau K, Lefebvre T, Madoui MA. Chromosome-scale assembly of the yellow mealworm genome. OPEN RESEARCH EUROPE 2022; 1:94. [PMID: 37645128 PMCID: PMC10445852 DOI: 10.12688/openreseurope.13987.3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 08/30/2022] [Indexed: 08/31/2023]
Abstract
Background: The yellow mealworm beetle, Tenebrio molitor, is a promising alternative protein source for animal and human nutrition and its farming involves relatively low environmental costs. For these reasons, its industrial scale production started this century. However, to optimize and breed sustainable new T. molitor lines, the access to its genome remains essential. Methods: By combining Oxford Nanopore and Illumina Hi-C data, we constructed a high-quality chromosome-scale assembly of T. molitor. Then, we combined RNA-seq data and available coleoptera proteomes for gene prediction with GMOVE. Results: We produced a high-quality genome with a N50 = 21.9Mb with a completeness of 99.5% and predicted 21,435 genes with a median size of 1,780 bp. Gene orthology between T. molitor and Tribolium castaneum showed a highly conserved synteny between the two coleoptera and paralogs search revealed an expansion of histones in the T. molitor genome. Conclusions: The present genome will greatly help fundamental and applied research such as genetic breeding and will contribute to the sustainable production of the yellow mealworm.
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Affiliation(s)
- Evangelia Eleftheriou
- Génomique Métabolique, Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Univ Evry, Université Paris-Saclay, Université Paris-Saclay, Evry, 91057, France
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Univ Evry, Université Paris-Saclay, Université Paris-Saclay, Evry, 91057, France
| | - Benoît Vacherie
- Genoscope, Institut de biologie François Jacob, CEA, Université Paris‐Saclay, Evry, 91057, France
| | - Benjamin Istace
- Génomique Métabolique, Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Univ Evry, Université Paris-Saclay, Université Paris-Saclay, Evry, 91057, France
| | - Caroline Belser
- Génomique Métabolique, Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Univ Evry, Université Paris-Saclay, Université Paris-Saclay, Evry, 91057, France
| | - Benjamin Noel
- Génomique Métabolique, Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Univ Evry, Université Paris-Saclay, Université Paris-Saclay, Evry, 91057, France
| | - Yannick Moret
- Équipe Écologie Évolutive, UMR CNRS 6282 BioGéoSciences, Université de Bourgogne Franche-Comté, Dijon, 21000, France
| | - Thierry Rigaud
- Équipe Écologie Évolutive, UMR CNRS 6282 BioGéoSciences, Université de Bourgogne Franche-Comté, Dijon, 21000, France
| | | | | | - Karine Labadie-Bretheau
- Genoscope, Institut de biologie François Jacob, CEA, Université Paris‐Saclay, Evry, 91057, France
| | | | - Mohammed-Amin Madoui
- Génomique Métabolique, Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Univ Evry, Université Paris-Saclay, Université Paris-Saclay, Evry, 91057, France
- Équipe Écologie Évolutive, UMR CNRS 6282 BioGéoSciences, Université de Bourgogne Franche-Comté, Dijon, 21000, France
- Service d’Etude des Prions et des Infections Atypiques (SEPIA), Institut François Jacob, Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA), Université Paris Saclay, Fontenay-aux-Roses, France
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5
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6
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Barvish Z, Davis C, Gitelman I. A wide-range, low-cost 150 bp ladder for sizing DNA fragments between 150 and 4500 bp. Electrophoresis 2007; 28:900-2. [PMID: 17309053 DOI: 10.1002/elps.200600438] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Agarose gel electrophoresis, a very routine procedure, requires molecular weight standards; these are usually manufactured from plasmid or viral DNA fragments, or more recently, from PCR products of defined sizes. We describe here the preparation of a molecular weight standard from a completely different DNA source - the uniquely organized genome of the beetle Tenebrio molitor. The standard can be used to accurately size DNAs between 150 and 4500 bp, a useful range of sizes for many agarose gel electrophoresis applications, including separation of PCR products and plasmid cloning targets. In addition, it is easy to prepare, inexpensive, and rivals the best of the commercial ladders.
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Affiliation(s)
- Zeev Barvish
- Department of Virology and Developmental Genetics, Faculty of Health Sciences, Ben Gurion University of Negev, Beer Sheva, Israel
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7
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Bruvo B, Plohl M, Ugarković D. Uniform distribution of satellite DNA variants on the chromosomes of tenebrionid species Alphitobius diaperinus and Tenebrio molitor. Hereditas 2004; 123:69-75. [PMID: 8598348 DOI: 10.1111/j.1601-5223.1995.00069.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The chromosomes of tenebrionid species Alphitobius diaperinus contain large blocks of pericentromerically located constitutive heterochromatin, as revealed by C-banding procedure. As previously reported, satellite DNA of this species is composed of two related monomeric units organized in three satellite subfamilies. In order to analyze the chromosomal location of the satellite DNA and the distribution of monomeric variants within it, and compare it with the distribution of monomer variants in Tenebrio molitor satellite DNA, the methods of in situ hybridization and restriction enzyme/nick translation were performed. Fluorescent in situ hybridization with the entire satellite DNA reveals the pericentromerically located signals on all chromosomes of the complement, coinciding with heterochromatic blocks. Results of fluorescent in situ hybridization with particular monomeric variants and of in situ restriction enzyme/nick translation show that monomeric variants are homogeneously dispersed within the entire satellite DNA. The spreading of satellite monomeric variants of the related species T. molitor within the pericentromeric heterochromatin of the entire complement, is demonstrated using the method of in situ restriction enzyme/nick translation. Although the complexity of organization of satellite DNAs is quite distinct in these two species, obtained results suggest similar efficiency of mechanisms of spreading and homogenization resulting in random chromosomal distribution of their satellite variants.
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Affiliation(s)
- B Bruvo
- Department of Molecular Genetics, Ruder Bosković Institute, Zagreb, Croatia
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8
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Pons J, Petitpierre E, Juan C. Characterization of the heterochromatin of the darkling beetle Misolampus goudoti: cloning of two satellite DNA families and digestion of chromosomes with restriction enzymes. Hereditas 2004; 119:179-85. [PMID: 8106263 DOI: 10.1111/j.1601-5223.1993.00179.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The darkling beetle Misolampus goudoti Er. has 58% of C-banded chromosome material. In this paper we deal with the study of the heterochromatin of this insect both by molecular and cytogenetical methods. Two different satellite DNA families have been characterized in Misolampus goudoti by agarose gel electrophoresis of EcoRI and PstI restriction fragments, respectively. The EcoRI family is composed of a monomeric unit of 196 bp (64.3% A-T rich) DNA sequence, representing about 120,000 copies per haploid genome. The presence of frequent intermediate-size satellite variants and an internal direct repetition of 61 bp in the EcoRI repetitive main monomer suggest that the evolution of this satellite proceeded by unequal crossing-over, occurring both within and between the 196 bp unit. Another highly repetitive sequence, defined by digestion of genomic DNA with PstI, has a more complex unit of 1.2 kb with about 70,000 copies per haploid genome. In situ digestion of M. goudoti chromosomes with restriction enzymes shows a non-specific chromosome DNA extraction from pericentromeric positions with EcoRI and chromosome specific extraction of DNA with PstI and HinfI. This is discussed in relation to the chromosomal location of both satellites.
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Affiliation(s)
- J Pons
- Departament de Biologia Ambiental, Universitat de les Illes Balears, Palma de Mallorca, Spain
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9
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Gallin J, Vogler AP. Evolutionary dynamics of a satellite DNA in the tiger beetle species pair Cicindela campestris and C. maroccana. Genome 2003; 46:213-23. [PMID: 12723037 DOI: 10.1139/g02-126] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Satellite repeat elements are an abundant component of eukaryotic genomes, but not enough is known about their evolutionary dynamics and their involvement in karyotype and species differentiation. We report the nucleotide sequence, chromosomal localization, and evolutionary dynamics of a repetitive DNA element of the tiger beetle species pair Cicindela maroccana and Cicindela campestris. The element was detected after restriction digest of C. maroccana total genomic DNA with EcoRI as a single band and its multimers on agarose gels. Cloning and sequencing of several isolates revealed a consensus sequence of 383 bp with no internal repeat structure and no detectable similarity to any entry in GenBank. Hybridization of the satellite unit to C. maroccana mitotic and meiotic chromosomes revealed the presence of this repetitive DNA in the centromeres of all chromosomes except the Y chromosome, which exhibited only a very weak signal in its short arm. PCR-based tests for this satellite in related species revealed its presence in the sister species C. campestris, but not in other closely related species. Phylogenetic analysis of PCR products revealed well-supported clades that generally separate copies from each species. Because both species exhibit the multiple X chromosome karyotypic system common to Cicindela, but differ in their X chromosome numbers (four in C. maroccana vs. three in C. campestris), structural differences could also be investigated with regard to the position of satellites in a newly arisen X chromosome. We find the satellite in a centromeric position in all X chromosomes of C. maroccana, suggesting that the origin of the additional X chromosome involves multiple karyotypic rearrangements.
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Affiliation(s)
- José Gallin
- Departamento de Zoología y Antropología Física, Facultad de Veterinaria, 3a Planta, Universidad de Murcia, Apdo. 4021, Murcia, 30071, Spain.
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Landais I, Chavigny P, Castagnone C, Pizzol J, Abad P, Vanlerberghe-Masutti F. Characterization of a highly conserved satellite DNA from the parasitoid wasp Trichogramma brassicae. Gene 2000; 255:65-73. [PMID: 10974566 DOI: 10.1016/s0378-1119(00)00318-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An EcoRI satellite DNA has been isolated, cloned and sequenced from Trichogramma brassicae, a minute parasitic wasp. This repeated family represents 16% of the genome. The monomer is 385 base pairs (bp) long and has an A+T content of 64.5%. The average nucleotide sequence variability among 12 randomly chosen monomers is extremely low (0.5%), suggesting that the amplification of the monomer into a high-copy-number family occurred recently. An EcoRI satellite DNA probe has been developed and used, at high stringency, as an identification tool to unambiguously discriminate T. brassicae from nine other Trichogramma species. However, at a lower stringency, a hybridization signal can be detected in two closely related Trichogramma species, and, using PCR assay, the presence of the T. brassicae EcoRI monomer has been detected in several other species of Trichogramma. These results argue in favor of the 'library' model of satellite DNA evolution that predicts that related species share a number of low-copy satellite sequences, some of which could be amplified into a major satellite family in each of the species. Furthermore, this T. brassicae EcoRI satellite DNA sequence exhibits particular internal features such as a long inverted repeat that can form a dyad structure. Such sequence motifs seem to be a common characteristic of satellite DNAs, suggesting that they could result from selective forces acting on repetitive DNA.
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Affiliation(s)
- I Landais
- Institut National de la Recherche Agronomique, Unité Santé Végétale et Environnement, Antibes, France
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11
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Castagnone-Sereno P, Leroy F, Abad P. Cloning and characterization of an extremely conserved satellite DNA family from the root-knot nematode Meloidogyne arenaria. Genome 2000; 43:346-53. [PMID: 10791824 DOI: 10.1139/g00-007] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A new satellite DNA family, named pMaE, has been cloned from the genome of the phytoparasitic nematode, Meloidogyne arenaria (Nematoda: Tylenchida). It is represented as tandemly repeated sequences with a monomeric unit of 172 bp. The monomers are present at approximately 15700 copies per haploid genome, and represent about 5.3% of the total genomic DNA. Twenty-seven independent monomers have been cloned and sequenced. The deduced consensus sequence is 70.9% A + T rich, with frequent stretches of A and (or) T. Several direct or inverted sub-repeats are present in the sequence, which may allow the formation of a dyad structure, suggesting some potential role of this repetitive sequence in heterochromatin condensation. The monomers are very homogeneous in sequence, showing on average 1.8% divergence from their consensus sequence. Moreover, Southern blot experiments and sequence analysis of homologous monomers from the genome of geographically distinct M. arenaria populations have shown that this satellite DNA is uniformly distributed and highly conserved within the species. Therefore, it is hypothesized that this unusually low level of variability, either within the genome of a given population or between populations, could be achieved as the result of some highly effective homogenization mechanism acting upon the nematode genome.
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Affiliation(s)
- P Castagnone-Sereno
- Institut National de la Recherche Agronomique (INRA), Unité Santé Végétale et Environnement, Antibes, France.
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González LM, Montero E, Harrison LJ, Parkhouse RM, Garate T. Differential diagnosis of Taenia saginata and Taenia solium infection by PCR. J Clin Microbiol 2000; 38:737-44. [PMID: 10655377 PMCID: PMC86191 DOI: 10.1128/jcm.38.2.737-744.2000] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We have designed species-specific oligonucleotides which permit the differential detection of two species of cestodes, Taenia saginata and Taenia solium. The oligonucleotides contain sequences established for two previously reported, noncoding DNA fragments cloned from a genomic library of T. saginata. The first, which is T. saginata specific (fragment HDP1), is a repetitive sequence with a 53-bp monomeric unit repeated 24 times in direct tandem along the 1, 272-bp fragment. From this sequence the two oligonucleotides that were selected (oligonucleotides PTs4F1 and PTs4R1) specifically amplified genomic DNA (gDNA) from T. saginata but not T. solium or other related cestodes and had a sensitivity down to 10 pg of T. saginata gDNA. The second DNA fragment (fragment HDP2; 3,954 bp) hybridized to both T. saginata and T. solium DNAs and was not a repetitive sequence. Three oligonucleotides (oligonucleotides PTs7S35F1, PTs7S35F2, and PTs7S35R1) designed from the sequence of HDP2 allowed the differential amplification of gDNAs from T. saginata, T. solium, and Echinococcus granulosus in a multiplex PCR, which exhibits a sensitivity of 10 pg.
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Affiliation(s)
- L M González
- Ministerio de Sanidad y Consumo, Instituto de Salud Carlos III, Centro Nacional de Microbiologia, 28220 Majadahonda, Madrid, Spain
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Braquart C, Royer V, Bouhin H. DEC: a new miniature inverted-repeat transposable element from the genome of the beetle Tenebrio molitor. INSECT MOLECULAR BIOLOGY 1999; 8:571-574. [PMID: 10620054 DOI: 10.1046/j.1365-2583.1999.00144.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
In this paper we describe a novel family of miniature inverted-repeat transposable elements (MITEs), named DEC, isolated from the genome of the beetle Tenebrio molitor. These elements are highly reiterated and their number is estimated to be around 3500 per haploid genome. Two of them have been isolated and the two sequences are 84% identical. Like other MITEs, they are characterized by their small size, their A + T richness, the presence of terminal inverted repeats and the absence of open reading frames. These data suggest that MITEs are probably widely distributed in arthropods.
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Affiliation(s)
- C Braquart
- UMR CNRS 5548, 'Développement et communication chimique', Faculté des Sciences, Dijon, France
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14
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Lorite P, García MF, Palomeque T. Satellite DNA in the ant Messor structor (Hymenoptera, Formicidae). Genome 1999; 42:881-6. [PMID: 10584309 DOI: 10.1139/g99-018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
This paper is the first record of the satellite DNA of Formicidae. The satellite DNA of the ant Messor structor is organized in a tandem repeat of monomers of 79 bp. Like satellite DNAs of other insects, it is AT rich and presents direct and inverted internal repeats. Restriction analysis of the total DNA with methylation-sensitive enzymes strongly suggests that this DNA is undermethylated. The presence of this repetitive DNA in other species of the genus Messor is also tested.
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Affiliation(s)
- P Lorite
- Departamento de Biología Experimental, Universidad de Jaén, Spain
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15
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Abadon M, Grenier E, Laumond C, Abad P. A species-specific satellite DNA from the entomopathogenic nematode Heterorhabditis indicus. Genome 1998; 41:148-53. [PMID: 9644825 DOI: 10.1139/g98-005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
An AluI satellite DNA family has been cloned from the entomopathogenic nematode Heterorhabditis indicus. This repeated sequence appears to be an unusually abundant satellite DNA, since it constitutes about 45% of the H. indicus genome. The consensus sequence is 174 nucleotides long and has an A + T content of 56%, with the presence of direct and inverted repeat clusters. DNA sequence data reveal that monomers are quite homogeneous. Such homogeneity suggests that some mechanism is acting to maintain the homogeneity of this satellite DNA, despite its abundance, or that this repeated sequence could have appeared recently in the genome of H. indicus. Hybridization analysis of genomic DNAs from different Heterorhabditis species shows that this satellite DNA sequence is specific to the H. indicus genome. Considering the species specificity and the high copy number of this AluI satellite DNA sequence, it could provide a rapid and powerful tool for identifying H. indicus strains.
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Affiliation(s)
- M Abadon
- Laboratoire de biologie des invertébrés, Insitut national de la recherche agronomique (INRA), Antibes, France.
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16
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Wolf KW. Fine structure of the kinetochores in six species of the Coleoptera. Genome 1997; 40:379-85. [PMID: 18464835 DOI: 10.1139/g97-051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Kinetochore structure was examined in a total of 6 species from 5 different families of the Coleoptera using transmission electron microscopy of ultrathin serial sections. Metaphase spermatogonia and primary and secondary spermatocytes were studied in Tenebrio molitor (Tenebrionidae) to determine whether kinetochore structure varies depending on the cell type. In all three cell types, the kinetochore microtubules (MTs) were in direct contact with the chromosomal surface, and kinetochore plates were not detectable. In the other species, only metaphase I spermatocytes were examined. As in T. molitor, distinct kinetochore plates were also absent in Adelocera murina (Elateridae), Agapanthia villosoviridescens (Cerambycidae), and Coccinella septempunctata (Coccinellidae). However, bivalents in male meiosis of two representatives of the Chrysomelidae, Agelastica alni and Chrysolina graminis, showed roughly spherical kinetochores at their poleward surfaces. Microtubules were in contact with this material. Thus, although the present survey covers only a small number of species, it is clear that at least two kinetochore types occur in the Coleoptera. The cytological findings are discussed in the context of chromosome number and genome size variability in the Coleopteran families studied. It is suggested that properties of the kinetochores could play a role in karyotype evolution in the Coleoptera.
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17
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Grenier E, Laumond C, Abad P. Molecular characterization of two species-specific tandemly repeated DNAs from entomopathogenic nematodes Steinernema and Heterorhabditis (Nematoda:Rhabditida). Mol Biochem Parasitol 1996; 83:47-56. [PMID: 9010841 DOI: 10.1016/s0166-6851(96)02747-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Two AluI tandemly repeated DNAs were cloned from two entomopathogenic nematodes: the first one from Steinernema glaseri and the second one from Heterorhabditis bacteriophora. The monomeric units of these two satellite DNAs have a repeat length of 174 and 168 bp, respectively. These AluI repeated element families appear to constitute 5.5% of the S. glaseri genome and 5% of the H. bacteriophora genome. Their A + T contents were estimated at 55% and 57%. Moreover, the monomers of these two families are quite homogeneous in sequence, showing, on average, 3.9% and 2.7% divergence from their respective consensus sequence. These results suggest that some mechanism is acting to maintain the homogeneity of these repeated DNAs despite their abundance. We have also shown that these two DNA families are species-specific and therefore could be used for the identification of Steinernema and Heterorhabditis entomopathogenic nematode species.
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Affiliation(s)
- E Grenier
- Laboratoire de Biologie des Invertébrés, INRA, BP 2078, Antibes, France
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18
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Bizzaro D, Manicardi GC, Bianchi U. Chromosomal localization of a highly repeated EcoRI DNA fragment in Megoura viciae (Homoptera, Aphididae) by nick translation and fluorescence in situ hybridization. Chromosome Res 1996; 4:392-6. [PMID: 8871828 DOI: 10.1007/bf02257275] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
To investigate the genome of the aphid Megoura viciae at molecular level, we have studied total DNA by agarose gel electrophoresis after cleavage with different restriction endonucleases. EcoRI digestion produced a highly repeated DNA fragment, about 600 pb long. The contribution of this EcoRI element to the total genome of M. viciae was estimated at about 6% by means of densitometric scanning of agarose gel photographs. The chromosomal localization of this fragment, investigated by fluorescent in situ hybridization (FISH), constantly showed one large and two narrower fluorescent bands located on the X chromosome, all corresponding to C-positive heterochromatic areas. These results are in full accordance with the data obtained by in situ nick translation experiments carried out after EcoRI digestion, and clearly demonstrate that a substantial amount of M. viciae heterochromatin consists of EcoRI fragments which are mainly located on the X chromosome. Using the EcoRI restriction fragment as a molecular probe may be a practical tool for the investigation of taxonomic and evolutionary relationships in this group of insects.
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Affiliation(s)
- D Bizzaro
- Dipartimento di Biologia Animale, Università di Modena, Italy
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19
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Petitpierre E. Molecular cytogenetics and taxonomy of insects, with particular reference to the coleoptera. ACTA ACUST UNITED AC 1996. [DOI: 10.1016/0020-7322(95)00024-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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20
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Yussa M, Alonso CE, Abdelhay E. Highly polymorphic repetitive sequences in Rhynchosciara americana genome. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 1995; 25:909-914. [PMID: 7550247 DOI: 10.1016/0965-1748(95)00026-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Rhynchosciara americana genomic DNA when digested with EcoR1 or BamH1 presents visible fragments suggestive of repetitive sequences after fractionation on EtBr stained agarose gels. The cloning and molecular analysis of some of these fragments showed a highly polymorphic family of repetitive sequences. These were mapped by in situ hybridization to telomeres and some heterochromatic regions on polytene chromosomes.
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Affiliation(s)
- M Yussa
- Instituto de Biofĭsica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Brasil
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21
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Burrows PR, Smoker M, Grisi ME. Sequence and genomic organisation of a novel repetitive DNA element from the potato cyst nematode Globodera pallida. Mol Biochem Parasitol 1995; 73:245-8. [PMID: 8577333 DOI: 10.1016/0166-6851(95)00095-i] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- P R Burrows
- Entomology and Nematology Department, IACR-Rothamsted, Harpenden, Herts, UK
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22
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Grenier E, Laumond C, Abad P. Characterization of a species-specific satellite DNA from the entomopathogenic nematode Steinernema carpocapsae. Mol Biochem Parasitol 1995; 69:93-100. [PMID: 7723793 DOI: 10.1016/0166-6851(94)00197-u] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
An HaeIII satellite DNA family has been cloned from the entomopathogenic nematode Steinernema carpocapsae. This repeated sequence appears to be an unusually abundant satellite DNA, since it constitutes about 62% of the S. carpocapsae genome. The nucleotide sequences of 13 monomers have been determined. This satellite DNA family is represented by two sub-families: one with monomeric units of 170 bp and the other with monomeric units of 182 bp. These monomers are quite homogeneous in sequence, showing an average intermonomer variability of 6% from the consensus sequence. These results suggest that some homogenizing mechanism is acting to maintain the homogeneity of this satellite DNA. After hybridization with the genomic DNA of several other Steinernema species, this DNA sequence appears to be specific to the S. carpocapsae genome. Therefore, the species specificity and the high copy number of the HaeIII satellite DNA sequence should provide a rapid and powerful tool which could contribute to the identification of Steinernema species.
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Affiliation(s)
- E Grenier
- Laboratoire de Biologie des Invertébrés, INRA, Antibes, France
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23
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Plohl M, Ugarković D. Characterization of two abundant satellite DNAs from the mealworm Tenebrio obscurus. J Mol Evol 1994; 39:489-95. [PMID: 7807538 DOI: 10.1007/bf00173418] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Two highly abundant satellite DNAs comprise 36% of the Tenebrio obscurus (Tenebrionidae, Coleoptera) genome. They are designated as satellite I and satellite II with the monomer length of 344 and 142 base pairs (bp), respectively. Both satellites differ in their nucleotide (nt) sequences, but the frequency of point mutations, well-conserved length of monomer variants, stretches of shared mutations characteristic for the process of gene conversion, and distribution of both satellites in regions of centromeric heterochromatin of all chromosomes indicate that the same evolutionary processes act on both of them with the same, or similar, rate. While satellite I shares no sequence similarity with any other known nt sequence, satellite II is 79.7% homologous with the highly abundant satellite from closely related Tenebrio molitor. Difference in the frequency of point mutations and absence of shared mutations indicating gene conversion strongly suggest that in these two closely related species mutational processes affecting satellite DNAs seem to be changed. Retarded electrophoretic mobility, due to sequence-induced curvature of DNA helix axis, was observed for T. obscurus satellite II, but not for satellite I. Although evolutionary processes act with different rates in T. obscurus and T. molitor satellites the monomer length and sequence-induced curvature are well preserved in both 142-bp satellites, as well as in, at the nt sequence level completely divergent, Palorus ratzeburgii (Tenebrionidae) satellite, indicating potential importance of these parameters in their evolution.
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Affiliation(s)
- M Plohl
- Department of Molecular Genetics, Ruder Bosković Institute, Zagreb, Croatia
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24
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Callaghan MJ, Beh KJ. A middle-repetitive DNA sequence element in the sheep parasitic nematode, Trichostrongylus colubriformis. Parasitology 1994; 109 ( Pt 3):345-50. [PMID: 7970890 DOI: 10.1017/s0031182000078379] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
A novel repetitive DNA sequence in the sheep parasitic nematode Trichostrongylus colubriformis was cloned and sequenced. A 1.1 kb repetitive sequence (Tc15) which hybridized with DNA from T. colubriformis but not with DNA from two other parasitic nematodes, Haemonchus contortus and Ostertagia circumcincta, or sheep was further characterized. Southern blot analysis showed that the repeat hybridized to a range of fragments in restriction digested T. colubriformis DNA and existed in multiple copy number tandem arrays. However, to define clearly the repetitive monomeric unit further screening of phagemid libraries containing BamH I restriction fragments using a subclone of Tc15 as a probe was carried out. Restriction map and sequence data were compiled for 3 clones containing a 145 bp highly repetitive sequence (designated TcREP) which shared homology with the original pTc15 clone. TcREP hybridized to a tandemly repeating sequence monomer of 145 bp in T. colubriformis DNA which was cloned from various genetic environments in the T. colubriformis genome. TcREP homologous sequences were also found in the genomes of two other species of the same genus (Trichostrongylus axei and Trichostrongylus vitrinus) but not in a fourth species (Trichostrongylus rugatus).
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Affiliation(s)
- M J Callaghan
- CSIRO Division of Animal Health, McMaster Laboratory, NSW, Australia
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25
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Ugarković D, Plohl M, Petitpierre E, Lucijanić-Justić V, Juan C. Tenebrio obscurus satellite DNA is resistant to cleavage by restriction endonucleases in situ. Chromosome Res 1994; 2:217-23. [PMID: 8069465 DOI: 10.1007/bf01553322] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Satellite DNA from the mealworm beetle, Tenebrio obscurus, is composed of 344 bp long monomers of high AT content (68%), and represents 15% of the total DNA. In situ hybridization reveals the positions of the satellite on the pericentromeric heterochromatin of all T. obscurus chromosomes. To compare restriction enzyme (RE) effects with those on naked DNA, fixed chromosomes were digested with REs having recognition sites in most of the satellite monomers, and also with enzymes having target sites present only partially, or very rarely in the satellite units. All enzymes produce similar C-like banding patterns showing heterochromatin resistance to digestion regardless of the enzyme used. In situ nick translation suggests the inability of REs to cleave satellite DNA rather than the inefficient extraction of DNA fragments. DNA in heterochromatin was only extensively digested when the chromosomes were preincubated with proteinase K, indicating that accessibility of REs to DNA is increased by the removal of chromosomal proteins. This is in contrast to recently obtained results in Tenebrio molitor, where cleavage of satellite DNA is equally efficient in both fixed chromosomes and in naked DNA. The satellite DNAs of the two congeneric species differ in their AT content, and their primary and higher order structure, which could influence both heterochromatin structure and the accessibility of REs to satellite DNA.
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Affiliation(s)
- D Ugarković
- Department of Molecular Genetics, Ruder Bosković Institute, Zagreb, Croatia
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26
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Callaghan MJ, Beh KJ. Characterization of a tandemly repetitive DNA sequence from Haemonchus contortus. Int J Parasitol 1994; 24:137-41. [PMID: 8021102 DOI: 10.1016/0020-7519(94)90068-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Genomic DNA from the sheep parasitic nematode Haemonchus contortus was shotgun cloned in the plasmid vector pUC18. Recombinants which gave the strongest hybridization signals to 32P-radiolabelled genomic DNA were selected as representatives of the repetitive component of the parasite DNA. One repetitive sequence which hybridized only with DNA from H. contortus and not with DNA from two other sheep nematodes (Trichostrongylus colubriformis and Ostertagia circumcincta) was further characterized by sequencing and dot blot analysis. A related repeat was found in the closely related species Haemonchus placei. Experiments to determine the genomic organization of the repeat showed that it existed in a multi-copy number tandem array. This is the first report on the characterization of repetitive DNA in sheep parasite nematodes.
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Affiliation(s)
- M J Callaghan
- CSIRO Division of Animal Health, McMaster Laboratory, Glebe, NSW, Australia
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27
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Plohl M, Ugarković D. Analysis of divergence of Alphitobius diaperinus satellite DNA--roles of recombination, replication slippage and gene conversion. MOLECULAR & GENERAL GENETICS : MGG 1994; 242:297-304. [PMID: 8107677 DOI: 10.1007/bf00280419] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Satellite DNA is highly abundant in Alphitobius diaperinus (Tenebrionidae, Coleoptera), comprising 25% of the total genomic DNA. Sequence analysis reveals an average GC content of 50.8% and the presence of three different groups of satellite monomer variants, tH1, tH2 and tH3 with corresponding lengths of 123, 128 and 126 bp. Their mutual homologies range between 65 and 81%. Sequence comparison shows that the monomer variant tH2 has been formed by a recombination process between tH1 and tH3, which have a low average homology of only 65.15%. The longest stretch of 100% homology between the recombining units is 17 bp and is located 3' to the predicted recombination site. There is also an indication from sequence analysis that replication slippage and gene conversion play a part in the formation of satellite units and contribute to their divergence. The tH1, tH2 and tH3 monomer variants are organized in higher order repeating structures: a dimer, composed of tH1 and tH3, and a trimer containing tH1, tH2 and tH3 in series. The dimeric and trimeric repeat units furthermore create three higher order satellite subfamilies. Two of them contain either tandemly arranged dimers or trimers, while the third one is composed of both types of repeats, mutually interspersed.
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Affiliation(s)
- M Plohl
- Ruder Bosković Institute, Zagreb, Croatia
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28
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Piotte C, Castagnone-Sereno P, Bongiovanni M, Dalmasso A, Abad P. Cloning and characterization of two satellite DNAs in the low-C-value genome of the nematode Meloidogyne spp. Gene 1994; 138:175-80. [PMID: 8125299 DOI: 10.1016/0378-1119(94)90803-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Two highly reiterated StyI satellite DNAs have been cloned from two nematode species: one from Meloidogyne hapla and another from M. incognita. The monomeric units of these two satellites have a repeat length of 169 and 295 bp, respectively. These StyI repeated element families constitute 5% of the M. hapla and 2.5% of the M. incognita haploid genomes. The A + T content is elevated in both families (i.e., 68% and 77%, respectively). Nucleotide methylation and transcriptional activity are negative. No similarity was found between the two satellites, nor to other known highly repetitive elements. These StyI satellite DNAs are quite homogenous in sequence, showing on average 3% and 3.5% divergence from their respective calculated consensus sequence. An internal subrepeating unit of about 11 bp is observed in the StyI satellite monomer sequences of M. hapla, suggesting that it could have evolved from a shorter sequence. Because of the small size of the Meloidogyne genome (51 Mb) and the abundance of repeated sequences, this genus approaches a limit in terms of coding fraction.
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Affiliation(s)
- C Piotte
- Laboratoire de Biologie des Invertébrés, INRA, Antibes, France
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29
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Juan C, Pons J, Petitpierre E. Localization of tandemly repeated DNA sequences in beetle chromosomes by fluorescent in situ hybridization. Chromosome Res 1993; 1:167-74. [PMID: 8156155 DOI: 10.1007/bf00710770] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
In situ hybridization to chromosomes and nuclei of Tenebrio molitor shows the massive presence of a species-specific satellite DNA in all chromosomes and six sites of rDNA in mitotic chromosomes. These sites are located in two autosomal pairs and in the X and Y chromosomes. In a related species, Misolampus goudoti, in which two different families of highly repetitive DNA have been previously characterized, one family is located in centromeric regions of all chromosomes with the exception of chromosome Y, while the other repeated DNA family is present both in centromeric and distal regions of all chromosomes. rRNA genes in this species are present in a medium-sized autosomal pair only. These results show that molecular cytogenetics can be applied to coleopteran chromosomes and open the way for a physical mapping of DNA sequences in these organisms. The results also provide insights into the type of meiotic association of the X and Y chromosomes in Coleoptera and the distribution of repeated DNAs within the genome of these insects.
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Affiliation(s)
- C Juan
- Departament de Biologia Ambiental, Universitat de les Illes Balears, Palma de Mallorca, Spain
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30
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Tarès S, Cornuet JM, Abad P. Characterization of an unusually conserved AluI highly reiterated DNA sequence family from the honeybee, Apis mellifera. Genetics 1993; 134:1195-204. [PMID: 8104160 PMCID: PMC1205586 DOI: 10.1093/genetics/134.4.1195] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
An AluI family of highly reiterated nontranscribed sequences has been found in the genome of the honeybee Apis mellifera. This repeated sequence is shown to be present at approximately 23,000 copies per haploid genome constituting about 2% of the total genomic DNA. The nucleotide sequence of 10 monomers was determined. The consensus sequences is 176 nucleotides long and has an A + T content of 58%. There are clusters of both direct and inverted repeats. Internal subrepeating units ranging from 11 to 17 nucleotides are observed, suggesting that it could have evolved from a shorter sequence. DNA sequence data reveal that this repeat class is unusually homogeneous compared to the other class of invertebrate highly reiterated DNA sequences. The average pairwise sequence divergence between the repeats is 2.5%. In spite of this unusual homogeneity, divergence has been found in the repeated sequence hybridization ladder between four different honeybee subspecies. Therefore, the AluI highly reiterated sequences provide a new probe for fingerprinting in A. m. mellifera.
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Affiliation(s)
- S Tarès
- Laboratoire de Biologie des Invertébrés, Institut National de la Recherche Agronomique, Antibes, France
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31
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Tarès S, Lemontey JM, de Guiran G, Abad P. Cloning and characterization of a highly conserved satellite DNA sequence specific for the phytoparasitic nematode Bursaphelenchus xylophilus. Gene X 1993; 129:269-73. [PMID: 7686872 DOI: 10.1016/0378-1119(93)90278-b] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The phytoparasitic nematode, Bursaphelenchus xylophilus, contains an unusually abundant satellite DNA which constitutes up to 30% of its genome. It is represented as a tandemly repeated MspI-site-containing sequence with a monomeric unit of 160 bp. Thirteen monomers were cloned and sequenced. The consensus sequence is 62% A+T-rich, with the presence of direct and inverted repeat clusters. Monomers of the sequence are very similar, showing on average 3.9% divergence from the calculated consensus. The results suggest that some homogenizing mechanism is acting to maintain the homogeneity of this satellite DNA despite its abundance and that it is not transcribed.
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Affiliation(s)
- S Tarès
- Laboratoire de Biologie des Invertébrés, INRA, Antibes, France
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32
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Juan C, Vazquez P, Rubio JM, Petitpierre E, Hewitt GM. Presence of highly repetitive DNA sequences in Tribolium flour-beetles. Heredity (Edinb) 1993; 70 ( Pt 1):1-8. [PMID: 8094385 DOI: 10.1038/hdy.1993.1] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Digestion of genomic DNA from seven species of Tribolium (Coleoptera) with Sau3AI, TaqI and ClaI restriction enzymes shows the presence of remarkable amounts of highly repetitive DNA sequences in these species. In Tribolium freemani the sequences are tandemly repeated with a satellite monomer of 166 bp, A-T rich (70.5 per cent), representing 31 per cent of the total genome and located in centromeric chromosome areas as demonstrated by in situ hybridization. The sequence has the potential to form secondary structures such as stems or cruciforms due to the presence of frequent inverted repeats. Tribolium castaneum, T. anaphe and T. madens show homologous sequences to T. freemani satellite DNA but T. confusum, T. audax, T. brevicornis and other tenebrionid beetles, such as Tenebrio molitor and Misolampus goudoti, do not. A phylogenetic dendrogram, based on the homology and abundance of highly repetitive sequences deduced by dot-blot hybridization, chemotaxonomic and karyological characters, is proposed for the seven studied species of Tribolium.
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Affiliation(s)
- C Juan
- Departament de Biologia Ambiental, Universitat de les Illes Balears, Palma de Mallorca, Spain
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33
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Ugarković DL, Plohl M, Lucijanić-Justić V, Borstnik B. Detection of satellite DNA in Palorus ratzeburgii: analysis of curvature profiles and comparison with Tenebrio molitor satellite DNA. Biochimie 1992; 74:1075-82. [PMID: 1292615 DOI: 10.1016/0300-9084(92)90005-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Very abundant and homogenous satellite DNA has been found in the flour beetle Palorus ratzeburgii, representing 40% of its genome. Sequencing of 14 randomly cloned satellite monomers revealed a conserved monomer length of 142 bp and an average A+T content of 68%. Sequence variation analysis showed that base substitutions, appearing with a frequency of 2.3%, are predominant differences among satellite monomers. The satellite sequence is unique without significant direct repeats and with only two potentially stable inverted repeats. After electrophoresis of satellite monomers on native polyacrylamide gel retarded mobilities characteristic for curved DNA molecules are observed. The curvature profiles and DNA helix axis trajectory are calculated on the basis of three different algorithms. These calculations predict that P ratzeburgii satellite DNA forms a left-handed solenoid superstructure. Comparison of described features with other satellite DNAs reveals some striking similarities with satellite DNA from related species Tenebrio molitor, which belongs to the same family of Tenebrionidae. Both satellites are very abundant and homogenous with the same, highly conserved monomer length, although there is no homology at the nucleotide level. Their monomers, as well as multimers, exhibit very similar retarded electrophoretic mobilities. The calculated curvature profiles predict two bend centers in monomers of each satellite, resulting in a model of left-handed solenoid superstructures of similar appearance.
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Affiliation(s)
- D L Ugarković
- Department of Organic Chemistry and Biochemistry, Ruder Bosković Institute, Zagreb, Croatia
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34
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Plohl M, Borstnik B, Lucijanić-Justić V, Ugarković D. Evidence for random distribution of sequence variants in Tenebrio molitor satellite DNA. Genet Res (Camb) 1992; 60:7-13. [PMID: 1452016 DOI: 10.1017/s0016672300030615] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Tenebrio molitor satellite DNA has been analysed in order to study sequential organization of tandemly repeated monomers, i.e. to see whether different monomer variants are distributed randomly over the whole satellite, or clustered locally. Analysed sequence variants are products of single base substitutions in a consensus satellite sequence, producing additional restriction sites. The ladder of satellite multimers obtained after digestion with restriction enzymes was compared with theoretical calculations and revealed the distribution pattern of particular monomer variants within the satellite. A defined higher order repeating structure, indicating the existence of satellite subfamilies, could not be observed. Our results show that some sequence variants are very abundant, being present in nearly 50% of the monomers, while others are very rare (0-1% of monomers). However, the distribution of either very frequent, or very rare sequence variants in T. molitor satellite DNA is always random. Monomer variants are randomly distributed in the total satellite DNA and thus spread across all chromosomes, indicating a relatively high rate of sequence homogenization among different chromosomes. Such a distribution of monomer variants represents a transient stage in the process of sequence homogenization, indicating the high rate of spreading in comparison with the rate of sequence variant amplification.
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Affiliation(s)
- M Plohl
- Ruder Bosković Institute, Zagreb, Croatia
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Juan C, Gos�lvez J, Mezzanotte R, Petitpierre E. Cytological and biochemical characterization of the in situ endonuclease digestion of fixed Tenebrio molitor chromosomes. Chromosoma 1991. [DOI: 10.1007/bf00364553] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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36
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Improving beetle karyotype analysis: restriction endonuclease banding of Tenebrio molitor chromosomes. Heredity (Edinb) 1990. [DOI: 10.1038/hdy.1990.83] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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