Gene models for protein-coding genes in the genome of the rice coral Montipora capitata, Hawaii Island. Annotation was performed with Augustus v3.3.1, using RNA-seq data as extrinsic evidence. Gene structures (.gff), coding sequences (_cds.fas), and amino acid sequences (_aa.fas) are provided.
This Official Gene Set is an integration (NCBI Cephus cinctus Annotation Release 101) from NCBI's eukaryotic annotation pipeline v8.0 with manual annotations by the research community (done via the Apollo manual annotation software). QC and Merge of the dataset was performed using the GFF3toolkit software (https://github.com/NAL-i5K/GFF3toolkit).
Watermelon (Citrullus lanatus) and other cucurbits are important crops grown in Guatemala for local consumption and export. Four samplings of crowns, peduncles, and/or leaves of symptomatic plants were made in March and April 2015. Total RNA was extracted from symptomatic plant tissue and tested by RT-PCR for SqVYV, CYSDV, PRSV, and/or begomoviruses. This is the first report of SqVYV infecting watermelon in Central America.
Data from: Genome Sequence of the Thermotolerant Foodborne Pathogen Salmonella enterica Serovar Senftenberg ATCC 43845 and Phylogenetic Analysis of Loci Encoding Increased Protein Quality Control Mechanisms
Salmonella enterica subsp. enterica bacteria are important foodborne pathogens with major economic impact. Some isolates exhibit increased heat tolerance, a concern for food safety. Analysis of a finished-quality genome sequence of an isolate commonly used in heat resistance studies, S. enterica subsp. enterica serovar Senftenberg…
To study the impact of wheat streak mosaic virus on global gene expression in wheat curl mite, we generated a de novo transcriptome assembly using 50 x 50 paired end reads from the Illumina HiSeq 2500. Reads were assembled using Trinity (version 2.0.6) and contigs greater than 200 nt were retained. All assembled transcripts were annotated using the Trinotate pipeline using blastp searches against the Swiss-prot/Uni-Prot database, blastx searches against the Swiss-prot/Uni-Prot databases, HMM searches against the Pfam-A database, blastp searches against the non-redundant protein database, and signalP and tmHMM predictions. To reduce noise from low abundance transcripts not well supported by the data, we filtered the assembly to retain only those transcripts with TPM values >=0.5.
Transcriptomes were assembled de novo from pools of adult aphids that were feeding on sorghum and switchgrass. Reads from all replicates were pooled, normalized in silico to 25X coverage, and assembled using Trinity. Only the most abundant isoform for each unigene was retained for annotation and unigenes with transcripts per million mapped reads (TPM) less than 0.5 were removed from the dataset. The remaining unigenes were annotated using Trinotate with BLASTP comparisons against the Swiss-Prot/UniProt database. In addition, Pfam-A assignments were computed using hmmer, signal peptide predictions were performed using SignalP, and transmembrane domain predictions were performed using tmHMM. Gene ontology (GO assignments) were retrieved from Trinotate using the highest scoring BLASTp matches as queries.