scholarly journals Genome-Wide Analysis of mariner-Like Transposable Elements in Rice Reveals Complex Relationships With Stowaway Miniature Inverted Repeat Transposable Elements (MITEs)

Genetics ◽  
2003 ◽  
Vol 163 (2) ◽  
pp. 747-758 ◽  
Author(s):  
Cédric Feschotte ◽  
Lakshmi Swamy ◽  
Susan R Wessler
Keyword(s):  
Transposable Elements ◽  
Inverted Repeat ◽  
Sequence Similarity ◽  
Inverted Repeats ◽  
Single Plant ◽  
Genome Sequences ◽  
Sequence Comparisons ◽  
Genome Wide ◽  
Complex Relationships ◽  
Autonomous Elements

Abstract Stowaway is a superfamily of miniature inverted repeat transposable elements (MITEs) that is widespread and abundant in plant genomes. Like other MITEs, however, its origin and mode of amplification are poorly understood. Several lines of evidence point to plant mariner-like elements (MLEs) as the autonomous partners of the nonautonomous Stowaway MITEs. To better understand this relationship, we have taken advantage of the nearly complete genome sequences of two rice subspecies to generate the first inventory of virtually all MLEs and Stowaway families coexisting in a single plant species. Thirty-four different MLEs were found to group into three major clades and 25 families. More than 22,000 Stowaway MITEs were identified and classified into 36 families. On the basis of detailed sequence comparisons, MLEs were confirmed to be the best candidate autonomous elements for Stowaway MITEs. Surprisingly, however, sequence similarity between MLE and Stowaway families was restricted to the terminal inverted repeats (TIRs) and, in a few cases, to adjacent subterminal sequences. These data suggest a model whereby most of the Stowaway MITEs in rice were cross-mobilized by MLE transposases encoded by distantly related elements.

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.

Genome-wide characterization and evolution analysis of miniature inverted-repeat transposable elements (MITEs) in moso bamboo (Phyllostachys heterocycla)

Planta ◽  
2016 ◽  
Vol 244 (4) ◽  
pp. 775-787 ◽  
Author(s):  
Mingbing Zhou ◽  
Guiyun Tao ◽  
Peiyao Pi ◽  
Yihang Zhu ◽  
Youhuang Bai ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Inverted Repeat ◽  
Moso Bamboo ◽  
Evolution Analysis ◽  
Genome Wide ◽  
Phyllostachys Heterocycla

scholarly journals A Global Landscape of Miniature Inverted-Repeat Transposable Elements in the Carrot Genome

Genes ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 859
Author(s):  
Alicja Macko-Podgórni ◽  
Gabriela Machaj ◽  
Dariusz Grzebelus
Keyword(s):  
Transposable Elements ◽  
Inverted Repeat ◽  
Splice Variants ◽  
Untranslated Regions ◽  
Plant Genomes ◽  
Bioinformatic Tools ◽  
Genome Wide ◽  
Gene Structure And Expression ◽  
Coding Capacity ◽  
Reference Genomes

Miniature inverted-repeat transposable elements (MITEs) are the most abundant group of Class II mobile elements in plant genomes. Their presence in genic regions may alter gene structure and expression, providing a new source of functional diversity. Owing to their small size and lack of coding capacity, the identification of MITEs has been demanding. However, the increasing availability of reference genomes and bioinformatic tools provides better means for the genome-wide identification and analysis of MITEs and for the elucidation of their contribution to the evolution of plant genomes. We mined MITEs in the carrot reference genome DH1 using MITE-hunter and developed a curated carrot MITE repository comprising 428 families. Of the 31,025 MITE copies spanning 10.34 Mbp of the carrot genome, 54% were positioned in genic regions. Stowaways and Tourists were frequently present in the vicinity of genes, while Mutator-like MITEs were relatively more enriched in introns. hAT-like MITEs were relatively more frequently associated with transcribed regions, including untranslated regions (UTRs). Some carrot MITE families were shared with other Apiaceae species. We showed that hAT-like MITEs were involved in the formation of new splice variants of insertion-harboring genes. Thus, carrot MITEs contributed to the accretion of new diversity by altering transcripts and possibly affecting the regulation of many genes.

scholarly journals iMITEdb: the genome-wide landscape of miniature inverted-repeat transposable elements in insects

Database ◽  
2016 ◽  
Vol 2016 ◽  
pp. baw148 ◽  
Author(s):  
Min-Jin Han ◽  
Qiu-Zhong Zhou ◽  
Hua-Hao Zhang ◽  
Xiaoling Tong ◽  
Cheng Lu ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Inverted Repeat ◽  
Genome Wide

scholarly journals Hybrid decay: a transgenerational epigenetic decline in vigor and viability triggered in backcross populations of teosinte with maize

2019 ◽  
Author(s):  
Wei Xue ◽  
Sarah N. Anderson ◽  
Xufeng Wang ◽  
Liyan Yang ◽  
Peter A. Crisp ◽  
...  
Keyword(s):  
Transposable Elements ◽  
De Novo ◽  
Genome Instability ◽  
Sequence Similarity ◽  
Hybrid Incompatibility ◽  
Advanced Backcross ◽  
Genome Wide ◽  
Normal Maize ◽  
Plant Phenotype ◽  
Backcross Populations

ABSTRACTIn the course of generating populations of maize with teosinte chromosomal introgressions, an unusual sickly plant phenotype was noted in individuals from crosses with two teosinte accessions collected near Valle de Bravo, Mexico. The plants of these Bravo teosinte accessions appear phenotypically normal themselves and the F1plants appear similar to typical maize x teosinte F1s. However, upon backcrossing to maize, the BC1and subsequent generations display a number of detrimental characteristics including shorter stature, reduced seed set and abnormal floral structures. This phenomenon is observed in all BC individuals and there is no chromosomal segment linked to the sickly plant phenotype in advanced backcross generations. Once the sickly phenotype appears in a lineage, normal plants are never again recovered by continued backcrossing to the normal maize parent. Whole-genome shotgun sequencing reveals a small number of genomic sequences, some with homology to transposable elements, that have increased in copy number in the backcross populations. Transcriptome analysis of seedlings, which do not have striking phenotypic abnormalities, identified segments of 18 maize genes that exhibit increased expression in sickly plants. Ade novoassembly of transcripts present in plants exhibiting the sickly phenotype identified a set of 59 up-regulated novel transcripts. These transcripts include some examples with sequence similarity to transposable elements and other sequences present in the recurrent maize parent (W22) genome as well as novel sequences not present in the W22 genome. Genome-wide profiles of gene expression, DNA methylation and sRNAs are similar between sickly plants and normal controls, although a few up-regulated transcripts and transposable elements are associated with altered sRNA or methylation profiles. This study documents hybrid incompatibility and genome instability triggered by the backcrossing of Bravo teosinte with maize. We name this phenomenon “hybrid decay” and present ideas on the mechanism that may underlie it.

scholarly journals Temporal Changes in Transcripts of MITE Transposable Elements during Rice Endosperm Development

2021 ◽  
Author(s):  
Hiroki Nagata ◽  
Akemi Ono ◽  
Kaoru Tonosaki ◽  
Taiji Kawakatsu ◽  
Kentaro Yano ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Inverted Repeat ◽  
Expression Patterns ◽  
Endosperm Development ◽  
Dna Demethylation ◽  
Binding Motif ◽  
Terminal Inverted Repeat ◽  
Rice Endosperm ◽  
Genome Wide ◽  
Host Defense System

The repression of transcription from transposable elements (TEs) by DNA methylation is necessary to maintain genome integrity and prevent harmful mutations. However, under certain circumstances, TEs are thought to escape from the host defense system and reactivate their transcription. In Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa), DNA demethylases target the sequences derived from TEs in the central cell, the progenitor cell for the endosperm in the female gametophyte. This genome-wide DNA demethylation is also observed in the endosperm after fertilization. In this study, we used a custom microarray to survey the transcripts generated from TEs during the rice endosperm development and at selected timepoints in the embryo as a control. The expression patterns of TE transcripts are dynamically up- and downregulated during endosperm development, especially for miniature inverted-repeat transposable elements (MITEs). Surprisingly, some TE transcripts were directionally controlled, while the other DNA transposons and retrotransposons were not. We also discovered the NF-Y binding motif, CCAAT, in the region near the 5′ terminal inverted repeat of Youren, one of the transcribed MITEs in the endosperm. Our results uncover dynamic changes in TE activity during endosperm development in rice.

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