Chromosome-level Assemblies of Three Candidatus Liberibacter solanacearum Vectors: Dyspersa apicalis (Förster, 1848), Dyspersa pallida (Burckhardt, 1986), and Trioza urticae (Linnaeus, 1758) (Hemiptera: Psylloidea)

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. 

Dataset contains:
From Trioza urticae genome assembly:
 - Genome assembly (fasta)
 - Suspected contaminant seqeunces removed from the genome assembly (fasta)
 - T. urticae derived Candidatus Carsonella ruddii primary endosymbiont co-assembled genome (fasta)
 - Transposable element annotations from EarlgreyTE:
 - - Transpoable element library (fasta)
 - - Predicted TEs (bed and gff)
 - - Figures (pdf)
 - Gene predictions from braker3+ :
 - - Braker gene predictions (gft and aa)
 - - Longest isoforms (faa)
 - - - Interproscan annotation of gene predicitions (tsv)

From Dyspersa pallida (Trioza anthrisci) genome assembly:
 - Genome assembly (fasta)
 - Suspected contaminant seqeunces removed from the genome assembly (fasta)
 - D. pallida mitochondrial genome assembly (fasta)
 - D. pallida derived Candidatus Carsonella ruddii primary endosymbiont co-assembled genome (fasta)
 - Transposable element annotations from EarlgreyTE:
 - - Transpoable element library (fasta)
 - - Predicted TEs (bed and gff)
 - - Figures (pdf)
 - Gene predictions from braker3+ :
 - - Braker gene predictions (gft and aa)
 - - Longest isoforms (faa)
 - - - Interproscan annotation of gene predicitions (tsv)

From Dyspersa apicalis (Trioza apicalis) genome assembly:
 - Genome assembly (fasta)
 - Suspected contaminant seqeunces removed from the genome assembly (fasta)
 - D. apicalis mitochondrial genome assembly (fasta)
 - D. apicalis derived Candidatus Carsonella ruddii primary endosymbiont co-assembled genome (fasta)
 - Transposable element annotations from EarlgreyTE:
 - - Transpoable element library (fasta)
 - - Predicted TEs (bed and gff)
 - - Figures (pdf)
 - Gene predictions from braker3+ :
 - - Braker gene predictions (gft and aa)
 - - Longest isoforms (faa)
 - - - Interproscan annotation of gene predicitions (tsv)

From comparative genomics analysis:
 - Orthofinder analysis
 - - Output of orthofinder analysis comparing protein predictions from de novo psyllid assemblies with other hemiptera proteomes (tsv and fasta)
 - Cafe5 analysis
 - - Output of cafe analysis comparing protein predictions from de novo psyllid assemblies with other hemiptera proteomes (excel, png, tab)
 - - Enrichment analysis of GO and KO terms associated with expanded/contracted gene families at the Dyspersa taxonomic node (excel and tiff)
 - - Enrichment analysis of GO and KO terms associated with expanded/contracted gene families at the D. pallida taxonomic node (excel and tiff)
 - - Enrichment analysis of GO and KO terms associated with expanded/contracted gene families at the D. apicalis taxonomic node (excel and tiff)
 - - - Plots showing expansion/contraction of different orthogroups across the hemiptera phylogeny (png)
 - Time calibrated phylogenetic tree of hemiptera including psyllids produced by iqtree2 (txt)
 - Time calibrated phylogenetic tree of hemiptera including psyllids produced by astral (txt)
 - C. Ca ruddii primary endosymbiont phylogenetic tree (txt)

From psyllid population resequencing:
 - Resequencing data
 - - High confidence biallelic SNPs from D. pallida resequenced samples called against the de novo D. pallida genome assembly (vcf)
 - - High confidence biallelic SNPs from D. apicalis resequenced samples called against the de novo D. apicalis genome assembly (vcf)
 - - High confidence biallelic SNPs from resequenced samples called against the reference C. Ca ruddi endosymbiont genome assembly (vcf)
 - - For suspected contanimant contigs removed from the D. pallida genome assembly; predicted identity, and coverage in each resequenced D. pallida sample (txt)
 - - For suspected contanimant contigs removed from the D. apicalis genome assembly; predicted identity, and coverage in each resequenced D. apicalis sample (txt)
 - - - Qualimap evaluation of resequencing data aligned to de novo psyllid genome for each resequenced sample (pdf)