Genome-wide characterization and expression analysis of the growth-regulating factor family in Mikania micrantha.

Background: Growth-regulating factors (GRFs) are plant-specific transcription factors involved in growth, development, and stress responses. Mikania micrantha, a highly invasive weed, displays rapid growth and adaptability, yet the GRF gene family in this species remains largely unexplored.

Results: We identified and characterized 16 GRF genes in M.

Genomic insights on Mikania micrantha invasiveness: gene family expansion, transposable elements, gene expression, and population structure.

Mikania micrantha is an aggressive climbing vine that poses significant threats to ecosystems and causes severe agricultural and economic losses. However, the molecular mechanisms underlying its adaptive evolution and invasion dynamics remain unclear. Comprehensive genomics and resequencing analyses were conducted to unravel the factors driving the adaptive evolution and invasion dynamics of M.

Epigenetic regulation of organ-specific functions in Mikania micrantha and Mikania cordata: insights from DNA methylation and siRNA integration.

Background: DNA methylation is a crucial epigenetic mechanism that regulates gene expression during plant growth and development. However, the role of DNA methylation in regulating the organ-specific functions of the invasive weed Mikania micrantha remains unknown.

Results: Here, we generated DNA methylation profiles for M.

Passer, a highly active transposon from a fish genome, as a potential new robust genetic manipulation tool.

The discovery of new, active DNA transposons can expand the range of genetic tools and provide more options for genomic manipulation. In this study, a bioinformatics analysis suggested that Passer (PS) transposons, which are members of the pogo superfamily, show signs of recent and current activity in animals and may be active in some species. Cell-based transposition assays revealed that the native PS transposases from Gasterosteus aculeatus and Danio rerio displayed very high activity in human cells relative to the Sleeping Beauty transposon.

Revisiting the Transposon Evolution Revealing Extensive Involvement in the Shaping of Mammal Genomes.

The data of this study revealed that was found in a wide variety of animal genomes, including 180 species from 36 orders of invertebrates and 145 species from 29 orders of vertebrates. An extensive invasion of was observed in mammals, with a high copy number. Almost 61% of those species contain more than 50 copies of ; however, 46% harbor intact elements, although the number of these intact elements is very low.

The IS630/Tc1/mariner transposons in three ctenophore genomes.

Transposable elements (TEs) exert a significant effect on the structure and functioning of the genomes and also serve as a source of the new genes. The study of the TE diversity and evolution in different taxa is indispensable for the fundamental understanding of their roles in the genomes. IS630/Tc1/mariner (ITm) transposable elements represent the most prevalent and diverse group of DNA transposons.

Evolution and domestication of transposons in the genome of African coelacanth ().

Here, we comprehensively analysed the abundance, diversity, and activity of transposons in African coelacanth (). Fifteen autonomous transposons were identified and grouped into six clades: DD34E/, DD34D/, DD35D, DD31D/, DD30-31D/-like, and DD32-36D/, belonging to three known families: DD34E/, DD34D/, and DD×D/ (DD35D/, DD31D/, DD30-31D/-like, and DD32-36D/). Thirty-one miniature inverted-repeat transposable element (MITE) transposons of were also identified, and 20 of them display similarity to the identified autonomous transposons.

, a DD36E family of transposons newly discovered in animals.

Background: The superfamily might represent the most diverse and widely distributed group of DNA transposons. Several families have been identified; however, exploring the diversity of this superfamily and updating its classification is still ongoing in the life sciences.

Results: Here we identified a new family of transposons, named (), which is close to, but distinct from the known family DD34E.

Development of enhancer-trapping and -detection vectors mediated by the transposon in zebrafish.

Enhancers are key transcriptional drivers of gene expression. The identification of enhancers in the genome is central for understanding gene-expression programs. Although transposon-mediated enhancer trapping (ET) is a powerful approach to the identification of enhancers in zebrafish, its efficiency varies considerably.

Enhancer Trapping and Annotation in Zebrafish Mediated with Sleeping Beauty, piggyBac and Tol2 Transposons.

Although transposon-mediated enhancer trapping (ET) is successfully applied in diverse models, the efficiency of various transposon systems varies significantly, and little information is available regarding efficiency of enhancer trapping by various transposons in zebrafish. Most potential enhancers (Ens) still lack evidence of actual En activity. Here, we compared the differences in ET efficiency between (), () and transposons.

[Enhancer trapping nearby rps26 gene in zebrafish mediated by the Tol2 transposon and it's annotation].

With the completion of large-scale genome sequencing of human beings and other organisms, understanding the expression of control elements on the genome has become an important research task in the post-genome era. The enhancer trapping technology is an effective method for identifying enhancer elements in the genome and understanding its mechanism for gene expression regulation. In this study, we selected the stable enhancer trapping line TK4 (head and trunk specific GFP expression), which is generated with the mediation of Tol2 transposon system, and analyzed the trapped enhancers with the techniques of Splinkerette PCR (sp-PCR), in situ hybridization and comparative genomics.