scholarly journals Landscape and evolutionary dynamics of terminal-repeat retrotransposons in miniature (TRIMs) in 48 whole plant genomes

2014 ◽  
Author(s):  
Dongying Gao ◽  
Yupeng Li ◽  
Brian Abernathy ◽  
Scott Jackson
Keyword(s):  
Evolutionary Dynamics ◽  
De Novo ◽  
Gene Evolution ◽  
Terminal Repeat ◽  
Plant Genome ◽  
Ltr Retrotransposons ◽  
Functional Roles ◽  
Whole Plant ◽  
Plant Families ◽  
Transposition Mechanism

Terminal-repeat retrotransposons in miniature (TRIMs) are structurally similar to long terminal repeat (LTR) retrotransposons except that they are extremely small and difficult to identify. Thus far, only a few TRIMs have been characterized in the euphyllophytes and the evolutionary and biological impacts and transposition mechanism of TRIMs are poorly understood. In this study, we combined de novo and homology-based methods to annotate TRIMs in 48 plant genome sequences, spanning land plants to algae. We found 156 TRIM families, 146 previously undescribed. Notably, we identified the first TRIMs in a lycophyte and non-vascular plants. The majority of the TRIM families were highly conserved and shared within and between plant families. Even though TRIMs contribute only a small fraction of any plant genome, they are enriched in or near genes and may play important roles in gene evolution. TRIMs were frequently organized into tandem arrays we called TA-TRIMs, another unique feature distinguishing them from LTR retrotransposons. Importantly, we identified putative autonomous retrotransposons that may mobilize specific TRIM elements and detected very recent transpositions of a TRIM in O. sativa. Overall, this comprehensive analysis of TRIMs across the entire plant kingdom provides insight into the evolution and conservation of TRIMs and the functional roles they may play in gene evolution.

scholarly journals Investigation of orthologous pathogen recognition gene-rich regions in solanaceous species

Genome ◽  
2017 ◽  
Vol 60 (10) ◽  
pp. 850-859 ◽  
Author(s):  
A. Di Donato ◽  
G. Andolfo ◽  
A. Ferrarini ◽  
M. Delledonne ◽  
M.R. Ercolano
Keyword(s):  
Evolutionary Dynamics ◽  
Plant Immunity ◽  
Parallel Evolution ◽  
Protein Domain ◽  
Plant Genome ◽  
Pathogen Recognition ◽  
Leading Role ◽  
The Family ◽  
Powerful Approach ◽  
Plant Families

Pathogen receptor proteins such as receptor-like protein (RLP), receptor-like kinase (RLK), and nucleotide-binding leucine-rich repeat (NLR) play a leading role in plant immunity activation. The genome architecture of such genes has been extensively investigated in several plant species. However, we still know little about their elaborate reorganization that arose during the plant speciation process. Using recently released pepper and eggplant genome sequences, we were able to identify 1097 pathogen recognition genes (PRGs) in the cultivated pepper Zunla-1 and 775 in the eggplant line Nakate-Shinkuro. The retrieved genes were analysed for their tendency to cluster, using different methods to infer the means of grouping. Orthologous relationships among clustering loci were found, and interesting reshuffling within given loci was observed for each analysed species. The information obtained was integrated into a comparative map to highlight the evolutionary dynamics in which the PRG loci were involved. Diversification of 14 selected PRG-rich regions was also explored using a DNA target-enrichment approach. A large number of gene variants were found as well as rearrangements of sequences encoding single protein domain and changes in chromosome gene order among species. Gene duplication and transposition activity have clearly influenced plant genome R-gene architecture and diversification. Our findings contribute to addressing several biological questions concerning the parallel evolution that occurred between genomes of the family Solanaceae. Moreover, the integration of different methods proved a powerful approach to reconstruct the evolutionary history in plant families and to transfer important biology findings among plant genomes.

scholarly journals New Insights into Long Terminal Repeat Retrotransposons in Mulberry Species

Genes ◽  
2019 ◽  
Vol 10 (4) ◽  
pp. 285 ◽  
Author(s):  
Bi Ma ◽  
Lulu Kuang ◽  
Youchao Xin ◽  
Ningjia He
Keyword(s):  
Long Terminal Repeat ◽  
Life Histories ◽  
Evolutionary Dynamics ◽  
Long Terminal Repeat Retrotransposons ◽  
Terminal Repeat ◽  
Ltr Retrotransposons ◽  
Positive Selection Pressure ◽  
Insertion And Deletion ◽  
Mulberry Tree ◽  
Dominant Influence

The evolutionary dynamics of long terminal repeat (LTR) retrotransposons in tree genomes has remained largely unknown. The availability of the complete genome sequences of the mulberry tree (Morus notabilis) has offered an unprecedented opportunity for us to characterize these retrotransposon elements. We investigated 202 and 114 families of Copia and Gypsy superfamilies, respectively, comprising 2916 intact elements in the mulberry genome. The tRNAMet was the most frequently used type of tRNA in both superfamilies. Phylogenetic analysis suggested that Copia and Gypsy from mulberry can be grouped into eight and six lineages, respectively. All previously characterized families of such elements could also be found in the mulberry genome. About 95% of the identified Copia and Gypsy full elements were estimated to have been inserted into the mulberry genome within the past 2–3 million years. Meanwhile, the estimated insertion times of members of the three most abundant families of the Copia superfamily (908 members from the three most abundant families) and Gypsy superfamily (783 members from the three most abundant families) revealed divergent life histories. Compared with the situation in Gypsy elements, three families of Copia elements are under positive selection pressure, which suggested that Copia elements may have a dominant influence in the evolution of mulberry genes. Analysis of insertion and deletion dynamics suggested that Copia and Gypsy elements exhibited a very long half-life in the mulberry genome. The present work provides new insights into the insertion and deletion dynamics of LTR retrotransposons, and it will greatly improve our understanding of the important roles transposable elements play in the architecture of the mulberry genome.

scholarly journals De novo activated transcription of newborn coding sequences is inheritable in the plant genome

2020 ◽  
Author(s):  
Takayuki Hata ◽  
Naoto Takada ◽  
Chihiro Hayakawa ◽  
Mei Kazama ◽  
Tomohiro Uchikoba ◽  
...  
Keyword(s):  
Cultured Cells ◽  
De Novo ◽  
Gene Evolution ◽  
Firefly Luciferase ◽  
Plant Genome ◽  
Experimental Scheme ◽  
Transgenic Lines ◽  
Endogenous Genes ◽  
The Individual ◽  
Comparison Of The Results

ABSTRACTThe manner in which newborn genes become transcriptionally activated and fixed in the plant genome is poorly understood. To examine such processes of gene evolution, we performed an artificial evolutionary experiment in Arabidopsis thaliana. As a model of gene-birth events, we introduced a promoterless coding sequence of the firefly luciferase (LUC) gene and established 386 T2-generation transgenic lines. Among them, we determined the individual LUC insertion loci in 76 lines and found that one-third of them were transcribed de novo even in the intergenic or inherently unexpressed regions. In the transcribed lines, transcription-related epigenetic marks were detected across the newly activated transcribed regions. These results agreed with our previous findings in A. thaliana cultured cells under a similar experimental scheme. The comparison of the results of the T2-plant and cultured cell experiments revealed that the de novo-activated transcription caused by local chromatin remodelling was inheritable. During one-generation inheritance, it seems likely that the transcription activities of the LUC inserts trapped by the endogenous genes/transcripts became stronger, while those of de novo transcription in the intergenic/untranscribed regions became weaker. These findings may offer a clue for the elucidation of the mechanism via which newborn genes become transcriptionally activated and fixed in the plant genome.

scholarly journals Kozak sequence acts as a negative regulator for de novo transcription initiation of newborn coding sequences in the plant genome

2020 ◽  
Author(s):  
Takayuki Hata ◽  
Soichirou Satoh ◽  
Naoto Takada ◽  
Mitsuhiro Matsuo ◽  
Junichi Obokata
Keyword(s):  
Transcription Initiation ◽  
Cultured Cells ◽  
De Novo ◽  
Gene Evolution ◽  
Firefly Luciferase ◽  
Open Reading Frames ◽  
Negative Regulator ◽  
Plant Genome ◽  
Coding Sequences ◽  
Precise Position

ABSTRACTThe manner in which newborn coding sequences and their transcriptional competency emerge during the process of gene evolution remains unclear. Here, we experimentally simulated eukaryotic gene origination processes by mimicking horizontal gene transfer events in the plant genome. We mapped the precise position of the transcription start sites (TSSs) of hundreds of newly introduced promoterless firefly luciferase (LUC) coding sequences in the genome of Arabidopsis thaliana cultured cells. The systematic characterization of the LUC-TSSs revealed that 80% of them occurred under the influence of endogenous promoters, while the remainder underwent de novo activation in the intergenic regions, starting from pyrimidine-purine dinucleotides. These de novo TSSs obeyed unexpected rules; they predominantly occurred ~100 bp upstream of the LUC inserts and did not overlap with Kozak-containing putative open reading frames (ORFs). These features were the output of the immediate responses to the sequence insertions, rather than a bias in the screening of the LUC gene function. Regarding the wild-type genic TSSs, they appeared to have evolved to lack any ORFs in their vicinities. Therefore, the repulsion by the de novo TSSs of Kozak-containing ORFs described above might be the first selection gate for the occurrence and evolution of TSSs in the plant genome. Based on these results, we characterized the de novo type of TSS identified in the plant genome and discuss its significance in genome evolution.

scholarly journals De novo activated transcription of inserted foreign coding sequences is inheritable in the plant genome

PLoS ONE ◽  
2021 ◽  
Vol 16 (6) ◽  
pp. e0252674
Author(s):  
Takayuki Hata ◽  
Naoto Takada ◽  
Chihiro Hayakawa ◽  
Mei Kazama ◽  
Tomohiro Uchikoba ◽  
...  
Keyword(s):  
Cultured Cells ◽  
De Novo ◽  
Gene Evolution ◽  
Firefly Luciferase ◽  
Plant Genome ◽  
Coding Sequences ◽  
Experimental Scheme ◽  
Transgenic Lines ◽  
The Individual ◽  
Comparison Of The Results

The manner in which inserted foreign coding sequences become transcriptionally activated and fixed in the plant genome is poorly understood. To examine such processes of gene evolution, we performed an artificial evolutionary experiment in Arabidopsis thaliana. As a model of gene-birth events, we introduced a promoterless coding sequence of the firefly luciferase (LUC) gene and established 386 T2-generation transgenic lines. Among them, we determined the individual LUC insertion loci in 76 lines and found that one-third of them were transcribed de novo even in the intergenic or inherently unexpressed regions. In the transcribed lines, transcription-related chromatin marks were detected across the newly activated transcribed regions. These results agreed with our previous findings in A. thaliana cultured cells under a similar experimental scheme. A comparison of the results of the T2-plant and cultured cell experiments revealed that the de novo-activated transcription concomitant with local chromatin remodelling was inheritable. During one-generation inheritance, it seems likely that the transcription activities of the LUC inserts trapped by the endogenous genes/transcripts became stronger, while those of de novo transcription in the intergenic/untranscribed regions became weaker. These findings may offer a clue for the elucidation of the mechanism by which inserted foreign coding sequences become transcriptionally activated and fixed in the plant genome.

scholarly journals Kozak sequence acts as a negative regulator for de novo transcription initiation of newborn coding sequences in the plant genome

2021 ◽  
Author(s):  
Takayuki Hata ◽  
Soichirou Satoh ◽  
Naoto Takada ◽  
Mitsuhiro Matsuo ◽  
Junichi Obokata
Keyword(s):  
Transcription Initiation ◽  
Cultured Cells ◽  
De Novo ◽  
Gene Evolution ◽  
Firefly Luciferase ◽  
Open Reading Frames ◽  
Negative Regulator ◽  
Plant Genome ◽  
Coding Sequences ◽  
Precise Position

Abstract The manner in which newborn coding sequences and their transcriptional competency emerge during the process of gene evolution remains unclear. Here, we experimentally simulated eukaryotic gene origination processes by mimicking horizontal gene transfer events in the plant genome. We mapped the precise position of the transcription start sites (TSSs) of hundreds of newly introduced promoterless firefly luciferase (LUC) coding sequences in the genome of Arabidopsis thaliana cultured cells. The systematic characterization of the LUC-TSSs revealed that 80% of them occurred under the influence of endogenous promoters, while the remainder underwent de novo activation in the intergenic regions, starting from pyrimidine-purine dinucleotides. These de novo TSSs obeyed unexpected rules; they predominantly occurred ∼100 bp upstream of the LUC inserts and did not overlap with Kozak-containing putative open reading frames (ORFs). These features were the output of the immediate responses to the sequence insertions, rather than a bias in the screening of the LUC gene function. Regarding the wild-type genic TSSs, they appeared to have evolved to lack any ORFs in their vicinities. Therefore, the repulsion by the de novo TSSs of Kozak-containing ORFs described above might be the first selection gate for the occurrence and evolution of TSSs in the plant genome. Based on these results, we characterized the de novo type of TSS identified in the plant genome and discuss its significance in genome evolution.

scholarly journals A comprehensive annotation dataset of intact LTR retrotransposons of 300 plant genomes

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Shan-Shan Zhou ◽  
Xue-Mei Yan ◽  
Kai-Fu Zhang ◽  
Hui Liu ◽  
Jie Xu ◽  
...  
Keyword(s):  
Evolutionary Dynamics ◽  
Age Determination ◽  
Genome Plasticity ◽  
Ltr Retrotransposons ◽  
Functional Variation ◽  
Plant Genomes ◽  
Sequencing Technologies ◽  
Plant Groups ◽  
Functional Implications ◽  
Classification Information

AbstractLTR retrotransposons (LTR-RTs) are ubiquitous and represent the dominant repeat element in plant genomes, playing important roles in functional variation, genome plasticity and evolution. With the advent of new sequencing technologies, a growing number of whole-genome sequences have been made publicly available, making it possible to carry out systematic analyses of LTR-RTs. However, a comprehensive and unified annotation of LTR-RTs in plant groups is still lacking. Here, we constructed a plant intact LTR-RTs dataset, which is designed to classify and annotate intact LTR-RTs with a standardized procedure. The dataset currently comprises a total of 2,593,685 intact LTR-RTs from genomes of 300 plant species representing 93 families of 46 orders. The dataset is accompanied by sequence, diverse structural and functional annotation, age determination and classification information associated with the LTR-RTs. This dataset will contribute valuable resources for investigating the evolutionary dynamics and functional implications of LTR-RTs in plant genomes.

scholarly journals Glycosylation of Cancer Extracellular Vesicles: Capture Strategies, Functional Roles and Potential Clinical Applications

Cells ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 109
Author(s):  
Álvaro M. Martins ◽  
Cátia C. Ramos ◽  
Daniela Freitas ◽  
Celso A. Reis
Keyword(s):  
Extracellular Vesicles ◽  
Biomarker Discovery ◽  
De Novo ◽  
Recipient Cell ◽  
Cell Communication ◽  
Cancer Biomarkers ◽  
Functional Roles ◽  
Molecular Information ◽  
Glycosylation Pathway ◽  
Organ Tropism

Glycans are major constituents of extracellular vesicles (EVs). Alterations in the glycosylation pathway are a common feature of cancer cells, which gives rise to de novo or increased synthesis of particular glycans. Therefore, glycans and glycoproteins have been widely used in the clinic as both stratification and prognosis cancer biomarkers. Interestingly, several of the known tumor-associated glycans have already been identified in cancer EVs, highlighting EV glycosylation as a potential source of circulating cancer biomarkers. These particles are crucial vehicles of cell–cell communication, being able to transfer molecular information and to modulate the recipient cell behavior. The presence of particular glycoconjugates has been described to be important for EV protein sorting, uptake and organ-tropism. Furthermore, specific EV glycans or glycoproteins have been described to be able to distinguish tumor EVs from benign EVs. In this review, the application of EV glycosylation in the development of novel EV detection and capture methodologies is discussed. In addition, we highlight the potential of EV glycosylation in the clinical setting for both cancer biomarker discovery and EV therapeutic delivery strategies.

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