Transferability of Nikita and Sukkula retrotransposons in domestic goose (Anser anser domesticus) genome.

This article aimed to detect the existence of barley-specific Nikita and Sukkula retrotransposons in domestic geese samples and to evaluate the evolutionary relationships between these and other transposons belonging to the family Anatidae. Inter-retrotransposonamplified polymorphism-polymerase chain reaction (IRAP-PCR) method was performed for these retrotransposons movements in three diverse domestic goose populations (Chinese x Embden crossbred, Turkish White, and Turkish Multicolor). Polymorphism ratios were between 0 and 33% in all samples for Nikita and 0-73% in all samples for Sukkula. In addition, intrapopulation genetic polymorphism rates were also 0-15% in Chinese x Embden crossbred, 0-25% in Turkish White, 0-25% in Turkish Multicolor for Nikita; while 0-27% in Chinese x Embden, and 0-50% in Turkish Multicolor for Sukkula. There was no polymorphism for Sukkula among Turkish White samples. Moreover, the neighbour-joining method was used for phylogenetic tree construction using 38 sequences of different ducks, geese, and swans. In silico analyses supported the transitions of retrotransposons in the family Anatidae. It is concluded that transposon mobility among the phylogenetically distant species may lead to understanding evolutionary relationships. This report is one of the first studies investigating retrotransposon movements in domestic geese, revealing a new perspective on the goose genome regarding mobile genetic elements.

The power of retrotransposons in high-throughput genotyping and sequencing.

The use of molecular markers has become an essential part of molecular genetics through their application in numerous fields, which includes identification of genes associated with targeted traits, operation of backcrossing programs, modern plant breeding, genetic characterization, and marker-assisted selection. Transposable elements are a core component of all eukaryotic genomes, making them suitable as molecular markers. Most of the large plant genomes consist primarily of transposable elements; variations in their abundance contribute to most of the variation in genome size. Retrotransposons are widely present throughout plant genomes, and replicative transposition enables them to insert into the genome without removing the original elements. Various applications of molecular markers have been developed that exploit the fact that these genetic elements are present everywhere and their ability to stably integrate into dispersed chromosomal localities that are polymorphic within a species. The ongoing development of molecular marker technologies is directly related to the deployment of high-throughput genotype sequencing platforms, and this research is of considerable significance. In this review, the practical application to molecular markers, which is a use of technology of interspersed repeats in the plant genome were examined using genomic sources from the past to the present. Prospects and possibilities are also presented.

Antibacterial activity of Calendula officinalis and Echinacea purpurea extracts against the causal agent of tomatoes' bacterial canker: Clavibacter michiganensis subsp. michiganensis / Actividad antibacteriana de los extractos de Calendula officinalis y Echinacea purpurea contra el agente causal del cancro bacteriano del tomate: Clavibacter michiganensis subsp. Michiganensis

We aimed to investigate the effects of Calendula officinalis and Echinacea purpurea extracts in terms of growth parameters, antibacterial activity and phenolic profile in tomato infected by Clavibacter michiganensis subsp. michiganensis (CmmT7). A significant difference was observed in E. purpuraextract, indicating the highest effects on plant height (27.25 cm), fresh plant weight (28.45 cm), root length (24.42 cm), and root weight (6.74 g) (p<0.05). Moreover, Calendula officinalis and Echinacea purpurea extracts showed significant inhibitory activity against CmmT7 (p<0.05). Among phenolic compounds, the only chlorogenic acid amounts were varied in the tomato seedlings leaves with C. officinalis extract (K3) + CmmT7, E. purpurea extract (E3) + CmmT7 and CmmT7 (p<0.01). Moreover, chlorogenic acid amount was approximately 9 times higher than in CmmT7-treated leaves when compared to control. The results showed that application of the extracts of these plants had a significant influence on bacterial canker and growth parameters.

Nuestro objetivo fue investigar los efectos de los extractos de Calendula officinalis y Echinacea purpurea en términos de parámetros de crecimiento, actividad antibacteriana y perfil fenólico en tomate infectado por Clavibacter michiganensis subsp. michiganensis (CmmT7). Se observó una diferencia significativa en el extracto de E. purpura, que indica los mayores efectos sobre la altura de la planta (27,25 cm), el peso de la planta fresca(28,45 cm), la longitud de la raíz (24,42 cm) y el peso de la raíz (6,74 g) (p<0,05). Además, los extractos de Calendula officinalis y Echinacea purpurea mostraron una actividad inhibidora significativa contra CmmT7 (p<0,05). Entre los compuestos fenólicos, las únicas cantidades de ácido clorogénico se variaron en las hojas de las plántulas de tomate con extracto de C. officinalis (K3) CmmT7, extracto de E. purpurea(E3) CmmT7 y CmmT7 (p<0.01). Además, la cantidad de ácido clorogénico fue aproximadamente 9 veces mayor que en las hojas tratadas con CmmT7 en comparación con el control. Los resultados mostraron que la aplicación de los extractos de estas plantas tuvo una influencia significativa sobre el cancro bacteriano y los parámetros de crecimiento.

In silico determination of transposon-derived miRNAs and targets in Aegilops species.

Transposable elements (TEs) are found almost in all living organism, shaping organisms' genomes. miRNAs are noncoding RNA types which are especially important in gene expression regulations. Many previously determined plant miRNAs are identical/homologous to transposons (TE-MIR). The aim of this study was computational characterization of novel TE-related miRNAs and their targets in Aegilops genome by using stringent criteria. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed by BLAST2GO. Seventeen novel TE-related miRNAs in Aegilops genome were identified for the first time. GO analyses indicated that 40 targets played different roles in biological processes, cellular components and molecular functions. Moreover, these genes were involved in 10 metabolic pathways such as purine metabolism, nitrogen metabolism, oxidative phosphorylation, etc. as a result of KEGG analyses. Identification of miRNAs and their targets are significant to understand miRNA-TEs relationships and even how TEs affect plant growth and development. Obtaining results of this study are expected to provide possible new insight into Aegilops and its related species, wheat, with respect to miRNAs evolution and domestication.Communicated by Ramaswamy H. Sarma.

Identification and functional analyses of new sesame miRNAs (Sesamum indicum L.) and their targets.

Plant microRNAs (miRNAs) have been commonly investigated during many years. Hundreds of miRNAs have been identified in many different plant species but there is very little information about the function of sesame (Sesamum indicum L.) miRNAs. For this purpose, in silico prediction of novel sesame miRNAs based on BLAST searches of the expressed sequence tag database was performed, using stringent criterias for miRNA annotation. The secondary structures of their precursor sequences, potential target genes of conserved and novel miRNAs were predicted and subjected to Gene Ontology (GO) annotation. mir447 and mir8140 were reported for the first time in sesame. Enrichment analysis of the GO with biological processes, cellular component and molecular functions revealed that these target genes were potentially involved in different metabolic pathways such as transcription factors, metabolism, growth and development, stress-related and even plant hormones. Results are valuable for figure out the gene regulation mechanism in sesame, using in the medicinal aspect of this plant species. Furthermore, these miRNAs and their profiled targets could provide the improvement of regulation and management, and even development of desirable traits in this plant.

Detection of HERV-K6 and HERV-K11 transpositions in the human genome.

Mobile genetic elements classed as transposons comprise an estimated 45% of the human genome, and 8% of these elements are human endogenous retroviruses (HERVs). Endogenous retroviruses are retrotransposons, containing 5' and 3' long terminal repeat sequences and encoding envelope, group-specific antigen and DNA polymerase proteins. The aim of the present study was to analyse genome integration polymorphisms of HERV type K member 6 (HERV-K6) and HERV-K11 by using the retrotransposon based molecular marker technique, inter-retrotransposon amplified polymorphism (IRAP). For this purpose, blood samples of 18 healthy individuals within the age range of 10-79 years (10 females and 8 males) were collected, genomic DNAs were isolated and IRAP-polymerase chain reaction (PCR) was performed. IRAP-PCR analyses demonstrated that there were 0-70% polymorphism rates for HERV-K6, and 0-38% polymorphism rates for HERV-K11 among all the samples. Furthermore, the polymorphism rates were 0-70% among females and 11-60% among males for HERV-K6, and 0-38% among females and 0-25% among males for HERV-K11. Age-associated polymorphism was also investigated, but no age-associated polymorphism was observed among the samples. Therefore, HERV-K6 and HERV-K11 polymorphisms may arise on an individual-specific basis. Various previous studies have investigated the associations between the expression of HERVs and cancer or other major diseases. However, few reports have analysed HERV-K movements among individuals. This is the first report to investigate HERV-K6 and HERV-K11 retrotransposon polymorphisms between the genders and different age groups.

BAGY2 retrotransposon analyses in barley calli cultures and regenerated plantlets.

The stability of aging barley calli and regenerated plantlets from those calli was investigated by the BAGY2 retrotransposon-specific IRAP technique. Mature embryos of barley (Hordeum vulgare cv. Golden Promise) were cultured in Murashige and Skoog medium supplemented with 4 mg/L dicamba and maintained on the same medium for 45 and 90 days. Two IRAP-based primers were used, and the levels of variation of DNA isolated from 45- and 90-day-old calli and regenerated plantlets were found to be increased 0-21%, depending on the mature embryo material and the age of the callus. It has been observed that culture conditions cause genetic variations and evident BAGY2 retrotransposon alterations. Internal domains of BAGY2 were also analyzed by qPCR, and copy numbers were found to be increased. These findings are expected to contribute to understanding of how retrotransposons affect features like tissue culture (especially callus tissue) formation and genetic engineering studies.

Human endogenous retrovirus-H insertion screening.

Endogenous retroviruses (ERVs) and ERV-like sequences comprise 8% of the human genome. We aimed to analyze genome integration polymorphisms of human endogenous retrovirus (HERV)-H by the inter-retrotransposon amplified polymorphism (IRAP) technique using the sequences of LTR7A (450 bp), LTR7B (445 bp) and LTR7C (471 bp). Blood samples from 20 individuals (10 females and 10 males) of diverse ethnic origins were used for the determination of integration variations at the genomic level. Isolated genomic DNA was screened using 3 pairs of primers corresponding to LTR regions of the HERV-H gene. We observed insertion polymorphism patterns between 0-87% in all subjects. The findings obtained contribute to our understanding of the effects of HERV-H on variations within the human genome.

Genetic and epigenetic effects of salinity on in vitro growth of barley.

Morphological, physiological and molecular changes were investigated in in vitro salt-stressed barley (Hordeum vulgare L. cv. Tokak). Mature embryos were cultured in Murashige and Skoog medium containing 0 (control), 50 and 100 mM NaCl for 20 days. Both concentrations inhibited shoot growth, decreased fresh weight and protein content, and increased SOD (EC 1.15.1.1) activity in a dose-dependent manner. The lower concentration increased root growth. Salinity caused nucleotide variations in roots, but did not affect shoot DNAs. The higher concentration caused methylation changes, mainly hypermethylation in shoots. This is the first study on genetic and epigenetic effects of salinity in barley.