scholarly journals Genome-wide characterization of Mariner Like transposons and their derived MITEs in the Whitefly Bemisia tabaci (Hemiptera: Aleyrodidae)

2021 ◽  
Author(s):  
Marwa Zidi ◽  
Françoise Denis ◽  
Khouloud Klai ◽  
Benoît Chénais ◽  
Aurore Caruso ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Bemisia Tabaci ◽  
Insect Pest ◽  
Chemical Compounds ◽  
Inverted Repeats ◽  
Vegetable Crops ◽  
Genomic Plasticity ◽  
Genome Wide ◽  
Almost All

Abstract The whitefly, Bemisia tabaci is a hemipteran pest of vegetable crops vectoring a broad category of viruses. Currently, this insect pest showed a high adaptability and resistance to almost all the chemical compounds commonly used for its control. In many cases, Transposable Elements (TEs) contributed to the evolution of host genomic plasticity. This study focuses on the annotation of Mariner Like Elements (MLEs) and their derived Miniature Inverted repeat Transposable Elements (MITEs) in the genome of B. tabaci. Two full-length MLEs belonging to mauritiana and irritans subfamilies were detected and named Btmar1.1 and Btmar2.1, respectively. Additionally, 548 defective MLE sequences clustering mainly into 19 different Mariner lineages of mauritiana and irritans subfamilies were identified. Each subfamily showed a significant variation in MLE copy number and size. Furthermore, 71 MITEs were identified as MLEs derivatives that could be mobilized via the potentially active transposases encoded by Btmar 1.1 and Btmar2.1. The vast majority of sequences detected in the whitefly genome present unusual Terminal Inverted Repeats (TIRs) of up to 400 bp in length. However, some exceptions are sequences without TIRs. This feature of the MLEs and their derived MITEs in B. tabaci genome that distinguishes them from all the other MLEs so far described in insects, which have TIRs size ranging from 20 to 40 bp. Overall, our study provides an overview of MLEs, especially those with large TIRs, and their related MITEs, as well as diversity of their families, which will provide a better understanding of the evolution and adaptation of the whitefly genome.

scholarly journals Characterization of a Class II Defective Transposon Carrying Two Haloacetate Dehalogenase Genes from Delftia acidovorans Plasmid pUO1

2002 ◽  
Vol 68 (5) ◽  
pp. 2307-2315 ◽  
Author(s):  
Masahiro Sota ◽  
Masahiro Endo ◽  
Keiji Nitta ◽  
Haruhiko Kawasaki ◽  
Masataka Tsuda
Keyword(s):  
Transposable Elements ◽  
Class Ii ◽  
Class I ◽  
Inverted Repeats ◽  
High Homology ◽  
Terminal Inverted Repeats ◽  
Delftia Acidovorans

ABSTRACT The two haloacetate dehalogenase genes, dehH1 and dehH2, on the 65-kb plasmid pUO1 from Delftia acidovorans strain B were found to be located on transposable elements. The dehH2 gene was carried on an 8.9-kb class I composite transposon (TnHad1) that was flanked by two directly repeated copies of IS1071, IS1071L and IS1071R. The dehH1 gene was also flanked by IS1071L and a truncated version of IS1071 (IS1071N). TnHad1, dehH1, and IS1071N were located on a 15.6-kb class II transposon (TnHad2) whose terminal inverted repeats and res site showed high homology with those of the Tn21-related transposons. TnHad2 was defective in transposition because of its lacking the transposase and resolvase genes. TnHad2 could transpose when the Tn21-encoded transposase and resolvase were supplied in trans. These results demonstrated that Tn Had2 is a defective Tn21-related transposon carrying another class I catabolic transposon.

scholarly journals Cloning of the Mutator transposable element MuA2, a putative regulator of somatic mutability of the a1-Mum2 allele in maize.

Genetics ◽  
1991 ◽  
Vol 129 (3) ◽  
pp. 845-854 ◽  
Author(s):  
M M Qin ◽  
D S Robertson ◽  
A H Ellingboe
Keyword(s):  
Transposable Elements ◽  
Transposable Element ◽  
Copy Number ◽  
Inverted Repeats ◽  
Terminal Inverted Repeats ◽  
Somatic Instability ◽  
Mutator Activity ◽  
Element System ◽  
Lines Of Evidence

Abstract The identification of the autonomous or transposase-encoding element of the Mutator (Mu) transposable element system of maize is necessary to the characterization of the system. We reported previously that a transcript homologous to the internal region of the MuA element is associated with activity of the Mutator system. We describe here the cloning of another Mu element, designated MuA2, that cosegregates with Mutator activity as assayed by somatic instability of the a1-Mum2 allele. The MuA2 element has features typical of the transposable elements of the Mutator family, including the 210-bp terminal inverted repeats. Several lines of evidence suggest that MuA2 is an autonomous or transposase-encoding element of the Mu family: (1) MuA2 cosegregates with a genetically defined element that regulates somatic mutability of the a1-Mum2 allele; (2) MuA2 is hypomethylated while most other MuA2-hybridizing sequences in the genome are extensively methylated; (3) the increase of the copy number of MuA2 is concomitant with the increase of regulator elements; (4) MuA2-like elements are found in Mutator lines but not in non-Mutator inbreds. We propose that autonomous or transposase-encoding elements of the Mu family may be structurally conserved and MuA2-like.

Infestation by Bemisia tabaci (Hemiptera: Aleyrodidae) and incidence of whitefly-transmitted viruses after the application of four biorational insecticides in some crops in Egypt

2015 ◽  
Vol 35 (03) ◽  
pp. 132-136 ◽  
Author(s):  
Shaaban Abd-Rabou ◽  
Alvin M. Simmons
Keyword(s):  
Bemisia Tabaci ◽  
Insect Pest ◽  
Plant Viruses ◽  
Vegetable Crops ◽  
Row Crops ◽  
Squash Leaf Curl Virus ◽  
Virus Incidence ◽  
Leaf Curl Virus ◽  
Treated Plot ◽  
Leaf Curl

Bemisia tabaci(Gennadius) is a global insect pest that transmits many important plant viruses. A field study was conducted on infestation byB. tabaciand incidence of whitefly-transmitted viruses after the application of selected foliar and seed-treated biorational insecticides in seven vegetable and row crops in Egypt. Three foliar insecticides (Actara, Biofly and Neemix) and a treated check (Actellic) were assayed across three weeks on seedlings and mature plants, and two seed-treated insecticides (Actara and Gaucho) and a treated check (Aldicarb) were assayed on seedlings. All of the foliar insecticides led to 60–100% reductions in whitefly infestations in each crop. Biofly and Neemix were the least efficacious insecticides. Incidences of whitefly-transmitted viruses were reduced in each insecticide-treated plot with seedlings of four crops; however, no effect on virus incidence was observed in the experiment with mature plants. Crops of cucumber, eggplant, squash and tomato displayed symptoms characteristic ofCucumber vein yellowing virus,Squash leaf curl virusorTomato yellow leaf curl virus; however, no symptoms of whitefly-transmitted viruses were observed in green bean, potato or sugar beet. The results show that several biorational insecticides may suppress whitefly populations in seedlings to delay whitefly-transmitted viruses in some vegetable crops in Egypt.

scholarly journals Characterization of Mariner transposons in seven species of Rhus gall aphids

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Aftab Ahmad ◽  
Gabriel Luz Wallau ◽  
Zhumei Ren
Keyword(s):  
Transposable Elements ◽  
Present Report ◽  
Wide Distribution ◽  
Inverted Repeats ◽  
Genomic Evolution ◽  
Reading Frame ◽  
Jumping Genes ◽  
First Time ◽  
Intact Open Reading Frame

AbstractTransposable elements (TEs), also known as jumping genes, are widely spread in the genomes of insects and play a considerable role in genomic evolution. Mariner/DD34D family belongs to class II transposable elements which is widely spread in the genomes of insects and have considerable role in genomic evolution. Mariner like elements (MLEs) were searched in the genomes of seven species of Rhus gall aphids belonging to six genera. In total, 121 MLEs were detected in the genomes of the seven investigated species of Rhus gall aphids, which showed a wide distribution in both close and distant related species. The sequences of MLEs ranged from 1 to 1.4 kb in length and the structural analysis of the MLEs showed that only five copies were potentially active with intact open reading frame (ORF) and terminal inverted repeats (TIRs). Phylogenetic analysis showed that all the 121 MLE sequences belonged to four subfamilies, i.e., Mauritiana, Drosophila, Vertumana and Irritans, among which Drosophila and Vertumana subfamilies were reported in aphids for the first time. Our present report revealed the diversity and distribution of MLEs in Rhus gall aphid genomes and expanded our understandings on the characterization of transposable elements in aphid genomes, which might be useful as genetic markers and tools and would play an important role in genomic evolution and adaptation of aphids.

scholarly journals Recent amplification of microsatellite-associated miniature inverted-repeat transposable elements in the pineapple genome

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Lianyu Lin ◽  
Anupma Sharma ◽  
Qingyi Yu
Keyword(s):  
Transposable Elements ◽  
Inverted Repeat ◽  
Sequence Similarity ◽  
Genome Structure ◽  
Terminal Inverted Repeat ◽  
Essential Information ◽  
Dna Transposon ◽  
Genome Wide ◽  
Identification And Characterization

Abstract Background Miniature inverted-repeat transposable elements (MITEs) are non-autonomous DNA transposable elements that play important roles in genome organization and evolution. Genome-wide identification and characterization of MITEs provide essential information for understanding genome structure and evolution. Results We performed genome-wide identification and characterization of MITEs in the pineapple genome. The top two MITE families, accounting for 29.39% of the total MITEs and 3.86% of the pineapple genome, have insertion preference in (TA) n dinucleotide microsatellite regions. We therefore named these MITEs A. comosus microsatellite-associated MITEs (Ac-mMITEs). The two Ac-mMITE families, Ac-mMITE-1 and Ac-mMITE-2, shared sequence similarity in the terminal inverted repeat (TIR) regions, suggesting that these two Ac-mMITE families might be derived from a common or closely related autonomous elements. The Ac-mMITEs are frequently clustered via adjacent insertions. Among the 21,994 full-length Ac-mMITEs, 46.1% of them were present in clusters. By analyzing the Ac-mMITEs without (TA) n microsatellite flanking sequences, we found that Ac-mMITEs were likely derived from Mutator-like DNA transposon. Ac-MITEs showed highly polymorphic insertion sites between cultivated pineapples and their wild relatives. To better understand the evolutionary history of Ac-mMITEs, we filtered and performed comparative analysis on the two distinct groups of Ac-mMITEs, microsatellite-targeting MITEs (mt-MITEs) that are flanked by dinucleotide microsatellites on both sides and mutator-like MITEs (ml-MITEs) that contain 9/10 bp TSDs. Epigenetic analysis revealed a lower level of host-induced silencing on the mt-MITEs in comparison to the ml-MITEs, which partially explained the significantly higher abundance of mt-MITEs in pineapple genome. The mt-MITEs and ml-MITEs exhibited differential insertion preference to gene-related regions and RNA-seq analysis revealed their differential influences on expression regulation of nearby genes. Conclusions Ac-mMITEs are the most abundant MITEs in the pineapple genome and they were likely derived from Mutator-like DNA transposon. Preferential insertion in (TA) n microsatellite regions of Ac-mMITEs occurred recently and is likely the result of damage-limiting strategy adapted by Ac-mMITEs during co-evolution with their host. Insertion in (TA) n microsatellite regions might also have promoted the amplification of mt-MITEs. In addition, mt-MITEs showed no or negligible impact on nearby gene expression, which may help them escape genome control and lead to their amplification.

scholarly journals Molecular characterization of mariner-like elements in Bruchus pisorum and Bruchus rufimanus (Coleoptera: Bruchidae)

2017 ◽  
Vol 69 (2) ◽  
pp. 353-360 ◽  
Author(s):  
Salma Djebbi ◽  
Amara Ben ◽  
Hanem Makni ◽  
Mohamed Makni ◽  
Maha Mezghani-Khemakhem
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Transposable Elements ◽  
Inverted Repeats ◽  
Terminal Inverted Repeats ◽  
Transfer Genes ◽  
Recent Origin ◽  
Bruchus Pisorum ◽  
Respective Host

Mariner-like elements (MLEs) are Class-II transposons that are widely present in diverse organisms and encode a D,D34D transposase motif. MLE sequences from two coleopteran species, Bruchuspisorum and B. rufimanus were obtained using the terminal-inverted repeats (TIRs) of mariner elements belonging to the mauritiana subfamily as primer. The characterized elements were between 1073 and 1302 bp in length and are likely to be inactive, based on the presence of multiple stop codons and/or frameshifts. A single consensus of MLE was detected in B. pisorum and was named Bpmar1. This element exhibited several conserved amino acid blocks as well as the specific D,D(34)D signature. As for B. rufimanus, two MLE consensuses, designated Brmar1 and Brmar2, were isolated, both containing deletions overlapping the internal region of the transposase. Structural and phylogenetic analysis of these sequences suggested a relatively recent origin of Bpmar1 versus a more ancient invasion of Brmar1 and Brmar2 in their respective host genomes. Given that MLEs are potential mediators of insect resistance and have been used as vectors to transfer genes into host genomes, the MLEs characterized in this study will have valuable implications for selecting appropriate transposable elements in transgenesis.

scholarly journals Genome-wide analysis of gibberellin-dioxygenases gene family and their responses to GA applications in maize

PLoS ONE ◽  
2021 ◽  
Vol 16 (5) ◽  
pp. e0250349
Author(s):  
Jiabin Ci ◽  
Xingyang Wang ◽  
Qi Wang ◽  
Fuxing Zhao ◽  
Wei Yang ◽  
...  
Keyword(s):  
Gene Family ◽  
Plant Development ◽  
Functional Characterization ◽  
Tissue Expression ◽  
Leaf Sheath ◽  
Solid Base ◽  
Specific Expression ◽  
Genome Wide ◽  
Almost All

Gibberellin-dioxygenases genes plays important roles in the regulating plant development. However, Gibberellin-dioxygenases genes are rarely reported in maize, especially response to gibberellin (GA). In present study, 27 Gibberellin-dioxygenases genes were identified in the maize and they were classified into seven subfamilies (I-VII) based on phylogenetic analysis. This result was also further confirmed by their gene structure and conserved motif characteristics. And gibberellin-dioxygenases genes only occurred segmental duplication that occurs most frequently in plants. Furthermore, the gibberellin-dioxygenases genes showed different tissue expression pattern in different tissues and most of the gibberellin-dioxygenases genes showed tissue specific expression. Moreover, almost all the gibberellin-dioxygenases genes were significantly elevated in response to GA except for ZmGA2ox2 and ZmGA20ox10 of 15 gibberellin-dioxygenases genes normally expressed in leaves while 10 and 11 gibberellin-dioxygenases genes showed up and down regulated under GA treatment than that under normal condition in leaf sheath. In addition, we found that ZmGA2ox1, ZmGA2ox4, ZmGA20ox7, ZmGA3ox1 and ZmGA3ox3 might be potential genes for regulating balance of GAs which play essential roles in plant development. These findings will increase our understanding of Gibberellin-dioxygenases gene family in response to GA and will provide a solid base for further functional characterization of Gibberellin-dioxygenases genes in maize.

Genome-wide screening and characterization of transposable elements and their distribution analysis in the silkworm, Bombyx mori

2008 ◽  
Vol 38 (12) ◽  
pp. 1046-1057 ◽  
Author(s):  
Mizuko Osanai-Futahashi ◽  
Yoshitaka Suetsugu ◽  
Kazuei Mita ◽  
Haruhiko Fujiwara
Keyword(s):  
Transposable Elements ◽  
Bombyx Mori ◽  
Distribution Analysis ◽  
Genome Wide ◽  
Silkworm Bombyx Mori

scholarly journals On the Trail of Tetu1: Genome-Wide Discovery of CACTA Transposable Elements in Sunflower Genome

2020 ◽  
Vol 21 (6) ◽  
pp. 2021
Author(s):  
Maria Ventimiglia ◽  
Claudio Pugliesi ◽  
Alberto Vangelisti ◽  
Gabriele Usai ◽  
Tommaso Giordani ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Coding Region ◽  
Gene Encoding ◽  
Bioinformatics Analyses ◽  
Repeat Sequences ◽  
Genome Wide ◽  
Sunflower Mutant ◽  
Sunflower Genome ◽  
Identification And Characterization

Much has been said about sunflower (Helianthus annuus L.) retrotransposons, representing the majority of the sunflower’s repetitive component. By contrast, class II transposons remained poorly described within this species, as they present low sequence conservation and are mostly lacking coding domains, making the identification and characterization of these transposable elements difficult. The transposable element Tetu1, is a non-autonomous CACTA-like element that has been detected in the coding region of a CYCLOIDEA (CYC) gene of a sunflower mutant, tubular ray flower (turf). Based on our knowledge of Tetu1, the publicly available genome of sunflower was fully scanned. A combination of bioinformatics analyses led to the discovery of 707 putative CACTA sequences: 84 elements with complete ends and 623 truncated elements. A detailed characterization of the identified elements allowed further classification into three subgroups of 347 elements on the base of their terminal repeat sequences. Only 39 encode a protein similar to known transposases (TPase), with 10 TPase sequences showing signals of activation. Finally, an analysis of the proximity of CACTA transposons to sunflower genes showed that the majority of CACTA elements are close to the nearest gene, whereas a relevant fraction resides within gene-encoding sequences, likely interfering with sunflower genome functionality and organization.

scholarly journals Identification and Characterization of Transposable Elements of Paracoccus pantotrophus

2003 ◽  
Vol 185 (13) ◽  
pp. 3753-3763 ◽  
Author(s):  
Dariusz Bartosik ◽  
Marta Sochacka ◽  
Jadwiga Baj
Keyword(s):  
Comparative Analysis ◽  
Transposable Elements ◽  
Copy Number ◽  
Inverted Repeats ◽  
Insertion Sequences ◽  
Terminal Inverted Repeats ◽  
Paracoccus Pantotrophus ◽  
Different Strains ◽  
Identification And Characterization

ABSTRACT We studied diversity and distribution of transposable elements residing in different strains (DSM 11072, DSM 11073, DSM 65, and LMD 82.5) of a soil bacterium Paracoccus pantotrophus (α-Proteobacteria). With application of a shuttle entrapment vector pMEC1, several novel insertion sequences (ISs) and transposons (Tns) have been identified. They were sequenced and subjected to detailed comparative analysis, which allowed their characterization (i.e., identification of transposase genes, terminal inverted repeats, as well as target sequences) and classification into the appropriate IS or Tn families. The frequency of transposition of these elements varied and ranged from 10−6 to 10−3 depending on the strain. The copy number, localization (plasmid or chromosome), and distribution of these elements in the Paracoccus species P. pantotrophus, P. denitrificans, P. methylutens, P. solventivorans, and P. versutus were analyzed. This allowed us to distinguish elements that are common in paracocci (ISPpa2, ISPpa3—both of the IS5 family—and ISPpa5 of IS66 family) as well as strain-specific ones (ISPpa1 of the IS256 family, ISPpa4 of the IS5 family, and Tn3434 and Tn5393 of the Tn3 family), acquired by lateral transfer events. These elements will be of a great value in the design of new genetic tools for paracocci, since only one element (IS1248 of P. denitrificans) has been described so far in this genus.

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