Chromosome-level Assemblies of Three Candidatus Liberibacter solanacearum Vectors: Dyspersa apicalis (Förster, 1848), Dyspersa pallida (Burckhardt, 1986), and Trioza urticae (Linnaeus, 1758) (Hemiptera: Psylloidea)
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2024-09-27, 2024-09-27
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Heaven, Thomas
Mathers, Thomas C
Mugford, Sam T
Jordan, Anna
Lethmayer, Christa
Nissinen, Anne I
Høgetveit, Lars-Arne
Highet, Fiona
Soria-Carrasco, Victor
Sumner-Kalkun, Jason
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dataset
dataset
dataset
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Description
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)