MOESM5 of Comparative genomics of 11 complete chloroplast genomes of Senecioneae (Asteraceae) species: DNA barcodes and phylogenetics

Additional file 5: Figure S2. Phylogenetic relationships of 75 species of Asteraceae inferred from a partitioned chloroplast genome multi-gene dataset using (a) Maximum Likelihood (ML) and (b) Bayesian Inference (BI) methods

Near-resonant Raman amplification in the rotational quantum wavepackets of nitrogen molecular ions generated by strong field ionization

Generation of laser-like narrow bandwidth emissions from nitrogen molecular ions generated in intense near- and mid-infrared femtosecond laser fields has aroused much interest because of the mysterious physics underlying such a phenomenon as well as the potential application of such an effect in atmospheric spectroscopic sensing. Here, we perform a pump-probe measurement on the nonlinear interaction of rotational quantum wavepackets of nitrogen molecular ions generated in mid-infrared (e.g., at a wavelength centered at 1580 nm) femtosecond laser fields with an ultrashort probe pulse whose broad spectrum overlaps both P- and R-branch rotational transition lines between the upper and lower electronic states. The results show that in the near-resonant conditions, stimulated Raman amplification can efficiently occur which converts the broad bandwidth ultrashort probe pulse into the narrow bandwidth laser-like beam. Our finding provides an insight into the physical mechanism of strong field induced lasing actions in atmospheric environment

Ultra-high-speed high-resolution laser lithography for lithium niobate integrated photonics

Photolithography assisted chemo-mechanical etching (PLACE), a technique specifically developed for fabricating highquality large-scale photonic integrated circuits (PICs) on thin-film lithium niobate (TFLN), has enabled fabrication of a series of building blocks of PICs ranging from high-quality (high-Q) microresonators and low-loss waveguides to electrooptically (EO) tunable lasers and waveguide amplifiers. Aiming at high-throughput manufacturing of the PIC devices and systems, we have developed an ultra-high-speed high-resolution laser lithography fabrication system employing a high repetition rate femtosecond laser and a high-speed polygon laser scanner, by which a lithography fabrication efficiency of 4.8 cm2/h has been achieved at a spatial resolution of 200 nm. We demonstrate wafer-scale fabrication of TFLN-based photonic structures, optical phase masks as well as color printin

MOESM4 of Comparative genomics of 11 complete chloroplast genomes of Senecioneae (Asteraceae) species: DNA barcodes and phylogenetics

Additional file 4: Figure S1. Comparison of sequence arrangement in the chloroplast genomes of five species of Senecioneae (Asteraceae), against Nicotiana tabacum as an external reference genome. Conserved orthologs are indicated by locally collinear blocks. Similar blocks among the genomes are coded in one colour and joined by a line. The genes above the line are transcribed in a clockwise direction, those below the line are transcribed towards the counter-clockwise direction

MOESM2 of Comparative genomics of 11 complete chloroplast genomes of Senecioneae (Asteraceae) species: DNA barcodes and phylogenetics

Additional file 2: Table S2. Details of Relative Synonymous Codon Usage in chloroplast genomes of 11 species of Senecioneae

MOESM1 of Comparative genomics of 11 complete chloroplast genomes of Senecioneae (Asteraceae) species: DNA barcodes and phylogenetics

Additional file 1: Table S1. Details of the Asteraceae species used in the phylogenetic analyses

MOESM3 of Comparative genomics of 11 complete chloroplast genomes of Senecioneae (Asteraceae) species: DNA barcodes and phylogenetics

Additional file 3: Table S3. Number and type of microsatellite repeat motifs in each of the 11 complete chloroplast genomes

Data_Sheet_1_Genome-wide association study of traits in sacred lotus uncovers MITE-associated variants underlying stamen petaloid and petal number variations.PDF

Understanding the genetic variants responsible for floral trait diversity is important for the molecular breeding of ornamental flowers. Widely used in water gardening for thousands of years, the sacred lotus exhibits a wide range of diversity in floral organs. Nevertheless, the genetic variations underlying various morphological characteristics in lotus remain largely unclear. Here, we performed a genome-wide association study of sacred lotus for 12 well-recorded ornamental traits. Given a moderate linkage disequilibrium level of 32.9 kb, we successfully identified 149 candidate genes responsible for seven flower traits and plant size variations, including many pleiotropic genes affecting multiple floral-organ-related traits, such as NnKUP2. Notably, we found a 2.75-kb presence-and-absence genomic fragment significantly associated with stamen petaloid and petal number variations, which was further confirmed by re-examining another independent population dataset with petal number records. Intriguingly, this fragment carries MITE transposons bound by siRNAs and is related to the expression differentiation of a nearby candidate gene between few-petalled and double-petalled lotuses. Overall, these genetic variations and candidate genes responsible for diverse lotus traits revealed by our GWAS highlight the role of transposon variations, particularly MITEs, in shaping floral trait diversity.</p

Data_Sheet_2_Genome-wide association study of traits in sacred lotus uncovers MITE-associated variants underlying stamen petaloid and petal number variations.xlsx

Understanding the genetic variants responsible for floral trait diversity is important for the molecular breeding of ornamental flowers. Widely used in water gardening for thousands of years, the sacred lotus exhibits a wide range of diversity in floral organs. Nevertheless, the genetic variations underlying various morphological characteristics in lotus remain largely unclear. Here, we performed a genome-wide association study of sacred lotus for 12 well-recorded ornamental traits. Given a moderate linkage disequilibrium level of 32.9 kb, we successfully identified 149 candidate genes responsible for seven flower traits and plant size variations, including many pleiotropic genes affecting multiple floral-organ-related traits, such as NnKUP2. Notably, we found a 2.75-kb presence-and-absence genomic fragment significantly associated with stamen petaloid and petal number variations, which was further confirmed by re-examining another independent population dataset with petal number records. Intriguingly, this fragment carries MITE transposons bound by siRNAs and is related to the expression differentiation of a nearby candidate gene between few-petalled and double-petalled lotuses. Overall, these genetic variations and candidate genes responsible for diverse lotus traits revealed by our GWAS highlight the role of transposon variations, particularly MITEs, in shaping floral trait diversity.</p

Table1_Multi-Media Occurrence of Antibiotics and Antibiotic Resistance Genes in East Dongting Lake.DOCX

With the extensive use of antibiotics, antibiotics and their induced resistance genes (ARGs) have become new types of pollutants widely distributed in a variety of environmental media. The contamination of antibiotics and ARGs occurring in important living and agricultural regions has aroused wide concern worldwide, especially in lake basins. The Dongting Lake basin is one of the important aquaculture and livestock areas in China, which is accompanied by a large amount of antibiotic use and discharge. However, the occurrence characteristics of antibiotics and ARGs in a multi-environment medium are still unclear. In this study, surface water and sediment samples in East Dongting Lake were collected by season, antibiotics and ARGs were quantitatively analyzed, and the risk quotient method was used to evaluate the ecological risk of antibiotics in surface water. 1) The concentration of antibiotics in the surface water of East Dongting Lake ranged from ND to 943.49 ng/L, with the maximum average concentration of 20.92 ng/L in spring. The concentration of antibiotics in sediments ranged from ND to 177.43 ng/g, with the maximum average concentration of 16.38 ng/g in fall. Ofloxacin (OFL) and sulfamethoxazole (SMX) were the main antibiotic pollutants in East Dongting Lake Basin. 2) sul1 and sul2 were the dominant ARGs in East Dongting Lake Basin. For spatial change, the total abundance of ARGs upstream was higher than that downstream. For seasonal change, the surface water and sediment were characterized by spring > summer > fall. 3) OFL and sulfamethoxazole might pose a significant high risk to aquatic organisms both in three seasons, and the ecological risk of antibiotics in East Dongting Lake is more significant at low temperatures than high. This study could provide important data information of the occurrence and concentration of antibiotics and ARGs in East Dongting Lake Basin.</p