Chromosome-level Assemblies of Three Candidatus Liberibacter solanacearum Vectors: Dyspersa apicalis (Förster, 1848), Dyspersa pallida (Burckhardt, 1986), and Trioza urticae (Linnaeus, 1758) (Hemiptera: Psylloidea)
<p>Genomic datasets generated from three species of psyllid insect (Hemiptera: Psylloidea). This repository includes chromosome-scale genomic assemblies, mitochondrial genomes, co-assembled bacterial genomes, coding sequence annotations, transposable element annotations, and called SNPs, as well as files related to comparative genomics analyses. </p>
<p><strong>Dataset contains:</strong><br><strong>From Trioza urticae genome assembly:</strong><br> - Genome assembly (fasta)<br> - Suspected contaminant seqeunces removed from the genome assembly (fasta)<br> - T. urticae derived Candidatus Carsonella ruddii primary endosymbiont co-assembled genome (fasta)<br> - Transposable element annotations from EarlgreyTE:<br> - - Transpoable element library (fasta)<br> - - Predicted TEs (bed and gff)<br> - - Figures (pdf)<br> - Gene predictions from braker3+ :<br> - - Braker gene predictions (gft and aa) <br> - - Longest isoforms (faa)<br> - - - Interproscan annotation of gene predicitions (tsv)</p>
<p><strong>From Dyspersa pallida (Trioza anthrisci) genome assembly:</strong><br> - Genome assembly (fasta)<br> - Suspected contaminant seqeunces removed from the genome assembly (fasta)<br> - D. pallida mitochondrial genome assembly (fasta)<br> - D. pallida derived Candidatus Carsonella ruddii primary endosymbiont co-assembled genome (fasta)<br> - Transposable element annotations from EarlgreyTE:<br> - - Transpoable element library (fasta)<br> - - Predicted TEs (bed and gff)<br> - - Figures (pdf)<br> - Gene predictions from braker3+ :<br> - - Braker gene predictions (gft and aa) <br> - - Longest isoforms (faa)<br> - - - Interproscan annotation of gene predicitions (tsv)</p>
<p><strong>From Dyspersa apicalis (Trioza apicalis) genome assembly:</strong><br> - Genome assembly (fasta)<br> - Suspected contaminant seqeunces removed from the genome assembly (fasta)<br> - D. apicalis mitochondrial genome assembly (fasta)<br> - D. apicalis derived Candidatus Carsonella ruddii primary endosymbiont co-assembled genome (fasta)<br> - Transposable element annotations from EarlgreyTE:<br> - - Transpoable element library (fasta)<br> - - Predicted TEs (bed and gff)<br> - - Figures (pdf)<br> - Gene predictions from braker3+ :<br> - - Braker gene predictions (gft and aa) <br> - - Longest isoforms (faa)<br> - - - Interproscan annotation of gene predicitions (tsv)</p>
<p><strong>From comparative genomics analysis:</strong><br> - Orthofinder analysis<br> - - Output of orthofinder analysis comparing protein predictions from de novo psyllid assemblies with other hemiptera proteomes (tsv and fasta)<br> - Cafe5 analysis<br> - - Output of cafe analysis comparing protein predictions from de novo psyllid assemblies with other hemiptera proteomes (excel, png, tab)<br> - - Enrichment analysis of GO and KO terms associated with expanded/contracted gene families at the Dyspersa taxonomic node (excel and tiff)<br> - - Enrichment analysis of GO and KO terms associated with expanded/contracted gene families at the D. pallida taxonomic node (excel and tiff)<br> - - Enrichment analysis of GO and KO terms associated with expanded/contracted gene families at the D. apicalis taxonomic node (excel and tiff)<br> - - - Plots showing expansion/contraction of different orthogroups across the hemiptera phylogeny (png)<br> - Time calibrated phylogenetic tree of hemiptera including psyllids produced by iqtree2 (txt)<br> - Time calibrated phylogenetic tree of hemiptera including psyllids produced by astral (txt)<br> - C. Ca ruddii primary endosymbiont phylogenetic tree (txt)</p>
<p><strong>From psyllid population resequencing:</strong><br> - Resequencing data<br> - - High confidence biallelic SNPs from D. pallida resequenced samples called against the de novo D. pallida genome assembly (vcf)<br> - - High confidence biallelic SNPs from D. apicalis resequenced samples called against the de novo D. apicalis genome assembly (vcf)<br> - - High confidence biallelic SNPs from resequenced samples called against the reference C. Ca ruddi endosymbiont genome assembly (vcf)<br> - - For suspected contanimant contigs removed from the D. pallida genome assembly; predicted identity, and coverage in each resequenced D. pallida sample (txt)<br> - - For suspected contanimant contigs removed from the D. apicalis genome assembly; predicted identity, and coverage in each resequenced D. apicalis sample (txt)<br> - - - Qualimap evaluation of resequencing data aligned to de novo psyllid genome for each resequenced sample (pdf)<br><br><br></p>
opencc-by-4.0Sep 2024View details →
