Genome-wide development of transposable elements-based markers in foxtail millet and construction of an integrated database

Abstract Background With the expansion of high throughput sequencing, we now have access to a larger number of genome-wide studies analyzing the Transposable elements (TEs) composition in a wide variety of organisms. However, genomic analyses often remain too limited in number and diversity of species investigated to study in depth the dynamics and evolutionary success of the different types of TEs among metazoans. Therefore, we chose to investigate the use of transcriptomes to describe the diversity of TEs in phylogenetically related species by conducting the first comparative analysis of TEs in two groups of polychaetes and evaluate the diversity of TEs that might impact genomic evolution as a result of their mobility. Results We present a detailed analysis of TEs distribution in transcriptomes extracted from 15 polychaetes depending on the number of reads used during assembly, and also compare these results with additional TE scans on associated low-coverage genomes. We then characterized the clades defined by 1021 LTR-retrotransposon families identified in 26 species. Clade richness was highly dependent on the considered superfamily. Copia elements appear rare and are equally distributed in only three clades, GalEa, Hydra and CoMol. Among the eight BEL/Pao clades identified in annelids, two small clades within the Sailor lineage are new for science. We characterized 17 Gypsy clades of which only 4 are new; the C-clade largely dominates with a quarter of the families. Finally, all species also expressed for the majority two distinct transcripts encoding PIWI proteins, known to be involved in control of TEs mobilities. Conclusions This study shows that the use of transcriptomes assembled from 40 million reads was sufficient to access to the diversity and proportion of the transposable elements compared to those obtained by low coverage sequencing. Among LTR-retrotransposons Gypsy elements were unequivocally dominant but results suggest that the number of Gypsy clades, although high, may be more limited than previously thought in metazoans. For BEL/Pao elements, the organization of clades within the Sailor lineage appears more difficult to establish clearly. The Copia elements remain rare and result from the evolutionary consistent success of the same three clades.

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Genome-wide identification and in silico characterization of chitinase gene family in Foxtail millet (Setaria italica)

Journal of Applied Biology & Biotechnology ◽

10.7324/jabb.2021.9403 ◽

2020 ◽

Author(s):

Motukuri S. R. Krishna ◽

Nerella Dheeraj ◽

Bathuru Jayasree ◽

Chodisetty Bhavya ◽

Nallamothu Jaswanthi

Keyword(s):

Gene Family ◽

In Silico ◽

Foxtail Millet ◽

Chitinase Gene ◽

Setaria Italica ◽

Genome Wide ◽

In Silico Characterization

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The Genomic Ecosystem of Transposable Elements in Maize

10.1101/559922 ◽

2019 ◽

Cited By ~ 18

Author(s):

Michelle C. Stitzer ◽

Sarah N. Anderson ◽

Nathan M. Springer ◽

Jeffrey Ross-Ibarra

Keyword(s):

Transposable Elements ◽

Evolutionary Dynamics ◽

Phenotypic Diversity ◽

Flowering Plant ◽

Genome Wide ◽

Family Level ◽

Genomic Environment ◽

Single Category ◽

The Impact

Transposable elements (TEs) constitute the majority of flowering plant DNA, reflecting their tremendous success in subverting, avoiding, and surviving the defenses of their host genomes to ensure their selfish replication. More than 85% of the sequence of the maize genome can be ascribed to past transposition, providing a major contribution to the structure of the genome. Evidence from individual loci has informed our understanding of how transposition has shaped the genome, and a number of individual TE insertions have been causally linked to dramatic phenotypic changes. But genome-wide analyses in maize and other taxa have frequently represented TEs as a relatively homogeneous class of fragmentary relics of past transposition, obscuring their evolutionary history and interaction with their host genome. Using an updated annotation of structurally intact TEs in the maize reference genome, we investigate the family-level ecological and evolutionary dynamics of TEs in maize. Integrating a variety of data, from descriptors of individual TEs like coding capacity, expression, and methylation, as well as similar features of the sequence they inserted into, we model the relationship between these attributes of the genomic environment and the survival of TE copies and families. Our analyses reveal a diversity of ecological strategies of TE families, each representing the evolution of a distinct ecological niche allowing survival of the TE family. In contrast to the wholesale relegation of all TEs to a single category of junk DNA, these differences generate a rich ecology of the genome, suggesting families of TEs that coexist in time and space compete and cooperate with each other. We conclude that while the impact of transposition is highly family- and context-dependent, a family-level understanding of the ecology of TEs in the genome can refine our ability to predict the role of TEs in generating genetic and phenotypic diversity.‘Lumping our beautiful collection of transposons into a single category is a crime’-Michael R. Freeling, Mar. 10, 2017

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Low temperature triggers genome-wide hypermethylation of transposable elements and centromeres in maize

10.1101/573915 ◽

2019 ◽

Cited By ~ 1

Author(s):

Zeineb Achour ◽

Johann Joets ◽

Martine Leguilloux ◽

Hélène Sellier ◽

Jean-Philippe Pichon ◽

...

Keyword(s):

Dna Methylation ◽

Transposable Elements ◽

Transcriptional Activation ◽

Gene Expression Regulation ◽

Environmental Cues ◽

Specific Response ◽

Genome Wide ◽

A Genome ◽

Response To Stress ◽

Context Specific

ABSTRACTCharacterizing the molecular processes developed by plants to respond to environmental cues is a major task to better understand local adaptation. DNA methylation is a chromatin mark involved in the transcriptional silencing of transposable elements (TEs) and gene expression regulation. While the molecular bases of DNA methylation regulation are now well described, involvement of DNA methylation in plant response to environmental cues remains poorly characterized. Here, using the TE-rich maize genome and analyzing methylome response to prolonged cold at the chromosome and feature scales, we investigate how genomic architecture affects methylome response to stress in a cold-sensitive genotype. Interestingly, we show that cold stress induces a genome-wide methylation increase through the hypermethylation of TE sequences and centromeres. Our work highlights a cytosine context-specific response of TE methylation that depends on TE types, chromosomal location and proximity to genes. The patterns observed can be explained by the parallel transcriptional activation of multiple DNA methylation pathways that methylate TEs in the various chromatin locations where they reside. Our results open new insights into the possible role of genome-wide DNA methylation in phenotypic response to stress.

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Genome-wide identification of MITE-derived microRNAs and their targets in bread wheat

10.21203/rs.3.rs-236927/v1 ◽

2021 ◽

Author(s):

Juan Manuel Crescente ◽

Diego Zavallo ◽

Mariana del Vas ◽

Sebastian Asurmendi ◽

Marcelo Helguera ◽

...

Keyword(s):

Gene Expression ◽

Triticum Aestivum ◽

Transposable Elements ◽

Small Rna ◽

Translational Repression ◽

High Homology ◽

Genome Wide ◽

Target Sites ◽

The Common ◽

Non Coding Rnas

Abstract Plant microRNAs (miRNAs) are a class of small non-coding RNAs that are 20–24 nucleotides length and can repress gene expression at post-transcriptional levels by target degradation or translational repression. There is increasing evidence that some microRNAs can be derived from a group of non-autonomous class II transposable elements called Miniature Inverted-repeat Transposable Elements (MITEs) in plants. We used public small RNA, degradome libraries and the common wheat (Triticum aestivum) genome to screen miRNAs production and target sites. We also created a comprehensive wheat MITE database using known and identifying novel elements. We found high homology between MITEs and 14% of all the miRNAs production sites in wheat. Furthermore, we show that MITE-derived miRNAs have preference for target degradation sites with MITE insertions in 3' UTR regions in wheat.

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