Next-generation sequencing (NGS) technology applications like RNA-sequencing (RNA-seq) have dramatically expanded the potential for novel genomics discoveries, but the proliferation of various platforms and protocols for RNA-seq has created a need for reference data sets to help gauge the performance characteristics of these disparate methods. Here we describe the results of the ABRF-NGS Study on RNA-seq, which leverages replicate experiments across multiple sites using two reference RNA standards tested with four protocols (polyA selected, ribo-depleted, size selected, and degraded RNA), and examined across five NGS platforms (IlluminaM-bM-^@M-^Ys HiSeqs, Life TechnologiesM-bM-^@M-^Y Personal Genome Machine and Proton, Roche 454 GS FLX, and Pacific Biosciences RS). These results show high (R2 >0.9) intra-platform consistency across test sites, high inter-platform concordance (R2 >0.8) for transcriptome profiling, and a large set of novel splice junctions observed across all platforms. Also, we observe that protocols using ribosomal RNA depletion can both salvage degraded RNA samples and also be readily compared to polyA-enriched fractions. These data provide a broad foundation for standardization, evaluation and improvement of RNA-seq methods. Two reference RNA standards tested with four protocols (polyA selected, ribo-depleted, size selected, and degraded RNA), and examined across five NGS platforms (IlluminaM-bM-^@M-^Ys HiSeqs, Life TechnologiesM-bM-^@M-^Y Personal Genome Machine and Proton, Roche 454 GS FLX, and Pacific Biosciences RS). Please note that the samples were named following the ABRF-Platform-Site-Sample-Replicate# format. For example, ABRF-454-CNL-A-1 means Sample A was run on 454 platform at Cornell and this is the first replicate, and ABRF-454-CNL-A-2 means the same exact sample was ran with same machine at same location and is 2nd replicate.

National Data Buoy Center SOS

This station provides the following variables: Winds

Selection of 6 samples, with 6 Forward (R1) and 6 Reverse (R2) files, including primers. R1 and R2 reads are ca. 300 bp long, and were obtained from Illumina MiSeq technologies, at the FEM facility sequencing platform. The files refer to the18S rRNA gene reads obtained from the analyses carried out on the samples collected and filtered (Sterivex^TM 0.22 µm) in different areas and depths of Lake Garda on September, 2018 (see EAW_2018_FASTQ_18S_description.docx).

Sampling and analyses were carried out in the framework of the project Eco-AlpsWater (ASP569), funded by the Interreg Alpine Space program.

A bioinformatic protocol for analyzing these data using DADA2 is available in Zenodo:

https://doi.org/10.5281/zenodo.5233527

The corresponding 16S rRNA gene reads, obtained from the same eDNA extracts, are saved in https://doi.org/10.5281/zenodo.5215815

Polyploidy or whole-genome duplication (WGD) is a significant evolutionary force, especially in angiosperms. However, the underlying mechanisms governing polyploid genome evolution remain unclear, limited largely by a lack of functional analysis tools in organisms that best exemplify the earliest stages of WGD. Tragopogon (Asteraceae) includes an evolutionary model system for studying the immediate consequences of polyploidy. In this study, we significantly improved the genetic transformation of Tragopogon and obtained genome-edited T. porrifolius (2x) and T. mirus (4x) primary generation (T0) individuals. Using CRISPR/Cas9, we knocked out the dihydroflavonol 4-reductase (DFR) gene, which controls anthocyanin synthesis, in both T. porrifolius and T. mirus. All transgenic allotetraploid T. mirus individuals had at least one mutant DFR allele and 71.4% of the plants had all four DFR alleles (from both homeologs) edited, indicating a high efficiency of the CRISPR system in polyploid Tragopogon. The anticipated absence of the anthocyanin was observed in both leaf and floral tissues from T. porrifolius and T. mirus mutants. In addition, the mutations were inherited in the T1 generation. This study demonstrates a highly efficient CRISPR platform producing genome-edited Tragopogon individuals that have successfully completed their life cycle. The approaches used and challenges faced in building the CRISPR system in Tragopogon provide a framework for building similar systems in other nongenetic models. Genome editing in Tragopogon paves the way for novel functional biology studies of polyploid genome evolution and the consequences of WGD on complex traits, which holds enormous potential for both basic and applied research. Methods This dataset contains the sequencing results of the DFR gene in CRISPR-mediated Tragopogon mutants. To genotype T. porrifolius, primers TragDFR-F1 and TragDFR-R2 were used to amplify a fragment (containing the CRISPR target sites) from TpoDFR. One microliter of genomic DNA (20-100 ng) was added into a 20‐μl PCR (1× Phusion HF Buffer [New England Biolabs, Ipswich, MA, USA], 200 μM dNTPs, 0.5 μM of each primer, 0.02 U/μl Phusion DNA polymerase [New England Biolabs, Ipswich, MA, USA]). The PCR conditions were as follows: one cycle of denaturation at 98°C for 30 s; 32 cycles at 98°C for 10 s, 59.5°C annealing for 30 s and 72°C extension for 1min 15 s; one cycle at 72°C for 10 min; and hold at 4°C. The PCR product was accessed via gel electrophoresis; the band with the expected size (~1.7 kb) was excised from the gel and purified using the Wizard Plus SV Minipreps DNA Purification System (Promega, Madison, WI, USA). PCR products were then sequenced at Eurofins Genomics (Louisville, KY, USA). For T. mirus, we genotyped one homeolog at a time. Utilizing the SNP and indel information between the two homeologs of TragDFR in T. mirus, GSP (Wang et al., 2016) was used to design homeolog-specific primers: Tdu-sub_DFR_F1 and Tdu-sub_DFR_R1 were used to amplify the T. dubius homeolog (amplicon size: 992 bp), and Tpo-sub_DFR_F1 and Tpo-sub_DFR_R1 were used to amplify the T. porrifolius homeolog (amplicon size: 851 bp). To amplify each homeolog in T. mirus, the PCR conditions were the same as described above (genotyping T. porrifolius) except for the annealing temperature and extension time. For both sets of primers, the annealing temperature was 61.5°C and the PCR extension time was 45 s. PCR products were then purified and sequenced as described above.

A large set of genome-wide markers and a high-throughput genotyping platform can facilitate the genetic dissection of complex traits and accelerate molecular breeding applications. Previously, we identified about 0.9 million SNP markers by sequencing transcriptomes of 27 diverse alfalfa genotypes. From this SNP set, we developed an Illumina Infinium array containing 9,277 SNPs. Using this array, we genotyped 280 diverse alfalfa genotypes and several genotypes from related species. About 81% (7,476) of the SNPs met the criteria for quality control and showed polymorphisms. The alfalfa SNP array also showed a high level of transferability for several closely related Medicago species. Principal component analysis and model-based clustering showed clear population structure corresponding to subspecies and ploidy levels. Within cultivated tetraploid alfalfa, genotypes from dormant and nondormant cultivars were largely assigned to different clusters; genotypes from semidormant cultivars were split between the groups. The extent of linkage disequilibrium (LD) across all genotypes rapidly decayed to 26 Kbp at r2 = 0.2, but the rate varied across ploidy levels and subspecies. A high level of consistency in LD was found between and within the two subpopulations of cultivated dormant and nondormant alfalfa suggesting that genome-wide association studies (GWAS) and genomic selection (GS) could be conducted using alfalfa genotypes from throughout the fall dormancy spectrum. However, the relatively low LD levels would require a large number of markers to fully saturate the genome.

This layer shows Election Results of 2023 District Council Ordinary Election in Hong Kong. It is a set of the data made available by the Electoral Affairs Commission under the Government of Hong Kong Special Administrative Region (the "Government") at https://portal.csdi.gov.hk ("CSDI Portal"). The source data has been processed and converted into Esri File Geodatabase format and then uploaded to Esri’s ArcGIS Online platform for sharing and reference purpose. The objectives are to facilitate our Hong Kong ArcGIS Online users to use the data in a spatial ready format and save their data conversion effort.For details about the data, source format and terms of conditions of usage, please refer to the website of Hong Kong CSDI Portal at https://portal.csdi.gov.hk.

Stripe rust, caused by Puccinia striiformis f. sp. tritici, is a severe disease in wheat worldwide, including Ethiopia, causing up to 100% wheat yield loss in the worst season. The use of resistant cultivars is considered to be the most effective and durable management technique for controlling the disease. Therefore, the present study targeted the genetic architecture of adult plant resistance to yellow rust in 178 wheat association panels. The panel was phenotyped for yellow rust adult-plant resistance at three locations. Phonological, yield, yield-related, and agro-morphological traits were recorded. The association panel was fingerprinted using the genotyping-by-sequencing (GBS) platform, and a total of 6,788 polymorphic single nucleotide polymorphisms (SNPs) were used for genome-wide association analysis to identify effective yellow rust resistance genes. The marker-trait association analysis was conducted using the Genome Association and Prediction Integrated Tool (GAPIT). The broad-sense heritability for the considered traits ranged from 74.52% to 88.64%, implying the presence of promising yellow rust resistance alleles in the association panel that could be deployed to improve wheat resistance to the disease. The overall linkage disequilibrium (LD) declined within an average physical distance of 31.44 Mbp at r2 = 0.2. Marker-trait association (MTA) analysis identified 148 loci significantly (p = 0.001) associated with yellow rust adult-plant resistance. Most of the detected resistance quantitative trait loci (QTLs) were located on the same chromosomes as previously reported QTLs for yellow rust resistance and mapped on chromosomes 1A, 1B, 1D, 2A, 2B, 2D, 3A, 3B, 3D, 4A, 4B, 4D, 5A, 5B, 6A, 6B, 7A, and 7D. However, 12 of the discovered MTAs were not previously documented in the wheat literature, suggesting that they could represent novel loci for stripe rust resistance. Zooming into the QTL regions in IWGSC RefSeq Annotation v1 identified crucial disease resistance-associated genes that are key in plants’ defense mechanisms against pathogen infections. The detected QTLs will be helpful for marker-assisted breeding of wheat to increase resistance to stripe rust. Generally, the present study identified putative QTLs for field resistance to yellow rust and some important agronomic traits. Most of the discovered QTLs have been reported previously, indicating the potential to improve wheat resistance to yellow rust by deploying the QTLs discovered by marker-assisted selection.