Table3_TRcaller: a novel tool for precise and ultrafast tandem repeat variant genotyping in massively parallel sequencing reads.XLSX

Calling tandem repeat (TR) variants from DNA sequences is of both theoretical and practical significance. Some bioinformatics tools have been developed for detecting or genotyping TRs. However, little study has been done to genotyping TR alleles from long-read sequencing data, and the accuracy of genotyping TR alleles from next-generation sequencing data still needs to be improved. Herein, a novel algorithm is described to retrieve TR regions from sequence alignment, and a software program TRcaller has been developed and integrated into a web portal to call TR alleles from both short- and long-read sequences, both whole genome and targeted sequences generated from multiple sequencing platforms. All TR alleles are genotyped as haplotypes and the robust alleles will be reported, even multiple alleles in a DNA mixture. TRcaller could provide substantially higher accuracy (>99% in 289 human individuals) in detecting TR alleles with magnitudes faster (e.g., ∼2 s for 300x human sequence data) than the mainstream software tools. The web portal preselected 119 TR loci from forensics, genealogy, and disease related TR loci. TRcaller is validated to be scalable in various applications, such as DNA forensics and disease diagnosis, which can be expanded into other fields like breeding programs. Availability: TRcaller is available at https://www.trcaller.com/SignIn.aspx.</p

Table2_TRcaller: a novel tool for precise and ultrafast tandem repeat variant genotyping in massively parallel sequencing reads.XLSX

Calling tandem repeat (TR) variants from DNA sequences is of both theoretical and practical significance. Some bioinformatics tools have been developed for detecting or genotyping TRs. However, little study has been done to genotyping TR alleles from long-read sequencing data, and the accuracy of genotyping TR alleles from next-generation sequencing data still needs to be improved. Herein, a novel algorithm is described to retrieve TR regions from sequence alignment, and a software program TRcaller has been developed and integrated into a web portal to call TR alleles from both short- and long-read sequences, both whole genome and targeted sequences generated from multiple sequencing platforms. All TR alleles are genotyped as haplotypes and the robust alleles will be reported, even multiple alleles in a DNA mixture. TRcaller could provide substantially higher accuracy (>99% in 289 human individuals) in detecting TR alleles with magnitudes faster (e.g., ∼2 s for 300x human sequence data) than the mainstream software tools. The web portal preselected 119 TR loci from forensics, genealogy, and disease related TR loci. TRcaller is validated to be scalable in various applications, such as DNA forensics and disease diagnosis, which can be expanded into other fields like breeding programs. Availability: TRcaller is available at https://www.trcaller.com/SignIn.aspx.</p

Table1_TRcaller: a novel tool for precise and ultrafast tandem repeat variant genotyping in massively parallel sequencing reads.DOCX

Calling tandem repeat (TR) variants from DNA sequences is of both theoretical and practical significance. Some bioinformatics tools have been developed for detecting or genotyping TRs. However, little study has been done to genotyping TR alleles from long-read sequencing data, and the accuracy of genotyping TR alleles from next-generation sequencing data still needs to be improved. Herein, a novel algorithm is described to retrieve TR regions from sequence alignment, and a software program TRcaller has been developed and integrated into a web portal to call TR alleles from both short- and long-read sequences, both whole genome and targeted sequences generated from multiple sequencing platforms. All TR alleles are genotyped as haplotypes and the robust alleles will be reported, even multiple alleles in a DNA mixture. TRcaller could provide substantially higher accuracy (>99% in 289 human individuals) in detecting TR alleles with magnitudes faster (e.g., ∼2 s for 300x human sequence data) than the mainstream software tools. The web portal preselected 119 TR loci from forensics, genealogy, and disease related TR loci. TRcaller is validated to be scalable in various applications, such as DNA forensics and disease diagnosis, which can be expanded into other fields like breeding programs. Availability: TRcaller is available at https://www.trcaller.com/SignIn.aspx.</p

DataSheet_1_Genetic dissection of the soybean dwarf mutant dm with integrated genomic, transcriptomic and methylomic analyses.docx

Plant height affects crop production and breeding practices, while genetic control of dwarfism draws a broad interest of researchers. Dwarfism in soybean (Glycine max) is mainly unexplored. Here, we characterized a dwarf mutant dm screened from ethyl methanesulfonate (EMS) mutated seeds of the soybean cultivar Zhongpin 661(ZP). Phenotypically, dm showed shorter and thinner stems, smaller leaves, and more nodes than ZP under greenhouse conditions. Genetically, whole-genome sequencing and comparison revealed that 210K variants of SNPs and InDel in ZP relative to the soybean reference genome Williams82, and EMS mutagenesis affected 636 genes with variants predicted to have a large impact on protein function in dm. Whole-genome methylation sequencing found 704 differentially methylated regions in dm. Further whole-genome RNA-Seq based transcriptomic comparison between ZP and dm leaves revealed 687 differentially expressed genes (DEGs), including 263 up-regulated and 424 down-regulated genes. Integrated omics analyses revealed 11 genes with both differential expressions and DNA variants, one gene with differential expression and differential methylation, and three genes with differential methylation and sequence variation, worthy of future investigation. Genes in cellulose, fatty acids, and energy-associated processes could be the key candidate genes for the dwarf phenotype. This study provides genetic clues for further understanding of the genetic control of dwarfism in soybean. The genetic resources could help to inbreed new cultivars with a desirable dwarf characteristic.</p

Single-Step Laser Plasmonic Coloration of Metal Films

Utilization of structural colors produced by nanosized optical antennas is expected to revolutionize the current display technologies based on an inkjet or a pigmentation-based color printing. Meanwhile, the versatile color-mapping strategy combining the fast single-step single-substrate fabrication cycle with low-cost scalable operation is still missing. We propose lithography-free pure optical approach based on a direct local ablative reshaping of the gold film with nanojoule (nJ)-energy femtosecond laser pulses. Plasmon-color printing at a resolution up to 2.5 × 10⁴ dots per inch satisfying the current visualization demands and data storage capacity is achieved. By controlling only the applied pulse energy, wide gamut of colors in scattering regime was reproduced via tuning the size of the printed nanovoids, which have a polarization- and shape-dependent localized plasmon-mediated scattering. Additionally, brightness of a single pixel was gradually adjusted via varying of the spacing between the printed nanovoids. The presented experimental demonstration opens a new direction toward plasmon-color printing for various applications where durability is required: low-cost cryptography, security tagging, and ultracompact optical data storage

Multiple Step Growth of Single Crystalline Rutile Nanorods with the Assistance of Self-Assembled Monolayer for Dye Sensitized Solar Cells

A novel multiple step growth (MSG) process has been developed to synthesize rutile nanorods (NRs) on fluorine-doped tin oxide (FTO) glass with the assistance of a self-assembled monolayer (SAM) aiming to increase the internal surface area of the 1D materials for dye sensitized solar cell (DSSC) applications. The experimental result reveals that the SAM layer can be selectively decomposed at the tip of the nanorod, namely the rutile (001) surface, due to the anisotropic photocatalytic property of the rutile. The remaining SAM layer on the side-wall of the NRs remains intact and serves as water repellent which prevents the radial growth of the NRs during the next step hydrothermal synthesis; therefore, the spacing between the NRs and the porosity of the NR array can be retained after additional growth cycles. On the other hand, introduction of a middle layer formed via TiCl₄ solution treatment before the next growth cycle is found to be an effective way to control the diameters of the newly grown NRs. The performance of DSSC made from the rutile NRs grown using the MSG technique has been examined, and it is significantly affected by the internal surfaces of the NRs. Furthermore, the MSG combined with NR etching treatment by acid at low temperature (150 °C) leads to a significant enhancement in the solar cell performance. The gigantic wettability difference of the NRs before and after the SAM treatment as well as the MSG method could be adapted to prepare superhydrophobic and superhydrophilic nanostructured patterns for other applications

Single-Layer Single-Crystalline SnSe Nanosheets

Single-layer single-crystalline SnSe nanosheet with four-atomic thickness of ∼1.0 nm and lateral size of ∼300 nm is presented here by using a one-pot synthetic method. It is found that 1,10-phenanthroline plays an important role in determining the morphology of the SnSe product as three-dimensional SnSe nanoflowers are obtained in the absence of 1,10-phenanthroline while keeping other reaction parameters the same. The evolution process study discloses that single-crystalline nanosheets are obtained from the coalescence of the SnSe nucleus in an orientated attachment mechanism. Band gap determination and optoelectronic test based on hybrid films of SnSe and poly­(3-hexylthiophene) indicate the great potential of the ultrathin SnSe nanosheets in photodector and photovoltaic, and so forth

Image_3_The Algicidal Fungus Trametes versicolor F21a Eliminating Blue Algae via Genes Encoding Degradation Enzymes and Metabolic Pathways Revealed by Transcriptomic Analysis.JPEG

<p>The molecular mechanism underlying the elimination of algal cells by fungal mycelia has not been fully understood. Here, we applied transcriptomic analysis to investigate the gene expression and regulation at time courses of Trametes versicolor F21a during the algicidal process. The obtained results showed that a total of 193, 332, 545, and 742 differentially expressed genes were identified at 0, 6, 12, and 30 h during the algicidal process, respectively. The gene ontology terms were enriched into glucan 1,4-α-glucosidase activity, hydrolase activity, lipase activity, and endopeptidase activity. The KEGG pathways were enriched in degradation and metabolism pathways including Glycolysis/Gluconeogenesis, Pyruvate metabolism, the Biosynthesis of amino acids, etc. The total expression levels of all Carbohydrate-Active enZYmes (CAZyme) genes for the saccharide metabolism were increased by two folds relative to the control. AA5, GH18, GH5, GH79, GH128, and PL8 were the top six significantly up-regulated modules among 43 detected CAZyme modules. Four available homologous decomposition enzymes of other species could partially inhibit the growth of algal cells. The facts suggest that the algicidal mode of T. versicolor F21a might be associated with decomposition enzymes and several metabolic pathways. The obtained results provide a new candidate way to control algal bloom by application of decomposition enzymes in the future.</p

MOESM1 of Whole plastid transcriptomes reveal abundant RNA editing sites and differential editing status in Phalaenopsis aphrodite subsp. formosana

Additional file 1: Table S1. Statistics of NGS libraries mapped to reference genome. Table S2. Plastid RNA edits in Phalaenopsis orchid. Table S3. Plastid RNA edits in protein-coding transcripts among land plants. Table S4. Plastid RNA edits in rpo transcripts among 18 species of higher plants. Table S5. Comparative analysis of plastid RNA edits from flower tissue by two different bioinformatic approaches. Figure S1. The editing efficiency of plastid RNA edits in leaf and floral tissues. Figure S2. The density of RNA editing sites in protein-coding transcripts. Figure S3. RNA editing in protein-coding transcripts. Figure S4. Nearest-neighbor bias toward a U_A context immediately before and after plastid RNA edits in moth orchid. Figure S5. The prediction of RNA secondary structures formed by the unedited and edited plastid transcripts in moth orchid

Table_3_The Algicidal Fungus Trametes versicolor F21a Eliminating Blue Algae via Genes Encoding Degradation Enzymes and Metabolic Pathways Revealed by Transcriptomic Analysis.DOCX

<p>The molecular mechanism underlying the elimination of algal cells by fungal mycelia has not been fully understood. Here, we applied transcriptomic analysis to investigate the gene expression and regulation at time courses of Trametes versicolor F21a during the algicidal process. The obtained results showed that a total of 193, 332, 545, and 742 differentially expressed genes were identified at 0, 6, 12, and 30 h during the algicidal process, respectively. The gene ontology terms were enriched into glucan 1,4-α-glucosidase activity, hydrolase activity, lipase activity, and endopeptidase activity. The KEGG pathways were enriched in degradation and metabolism pathways including Glycolysis/Gluconeogenesis, Pyruvate metabolism, the Biosynthesis of amino acids, etc. The total expression levels of all Carbohydrate-Active enZYmes (CAZyme) genes for the saccharide metabolism were increased by two folds relative to the control. AA5, GH18, GH5, GH79, GH128, and PL8 were the top six significantly up-regulated modules among 43 detected CAZyme modules. Four available homologous decomposition enzymes of other species could partially inhibit the growth of algal cells. The facts suggest that the algicidal mode of T. versicolor F21a might be associated with decomposition enzymes and several metabolic pathways. The obtained results provide a new candidate way to control algal bloom by application of decomposition enzymes in the future.</p