Supplementary data for: Chromosome-scale genome assemblies of aphids reveal extensively rearranged autosomes and long-term conservation of the X chromosome
Creators
- 1. John Innes Centre, Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
- 2. Earlham Institute, Norwich Research Park, Norwich, NR4 7UH, UK
- 3. School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
Description
Myzus persicae clone O v2 frozen release
Genome assembly: Myzus_persicae_O_v2.0.scaffolds.fa.gz
BRAKER2 gene models: Myzus_persicae_O_v2.0.scaffolds.braker2.gff3
List of gene models containing internal stop codons (removed from the protein and cds fasta files): Myzus_persicae_O_v2.0.scaffolds.braker2.bad_genes.lst
BRAKER2 protein sequences: Myzus_persicae_O_v2.0.scaffolds.braker2.gff3.filtered.aa.fa
BRAKER2 protein sequences (longest transcript per gene only): Myzus_persicae_O_v2.0.scaffolds.braker2.gff3.filtered.aa.LTPG.fa
BRAKER2 coding sequences: Myzus_persicae_O_v2.0.scaffolds.braker2.gff3.filtered.cds.fa
BRAKER2 coding sequences (longest transcript per gene only): Myzus_persicae_O_v2.0.scaffolds.braker2.gff3.filtered.cds.LTPG.fa
De novo repeat library (ReapeatModeler merged with repbase insecta): Myzus_persicae_O_v2.0_repeat_lib.repeatmodeler_merged_repbase_insecta.fa
RepeatMasker transposable element annotation using the M. persicae de novo repeat library: Myzus_persicae_O_v2.0.scaffolds.repeatmodeler_merged_repbase_insecta.repeatmasker.gff.out
RepeatMasker transposable element annotation using the M. persicae de novo repeat library (gff format): Myzus_persicae_O_v2.0.scaffolds.repeatmodeler_merged_repbase_insecta.repeatmasker.gff
Acyrthosiphon pisum clone JIC1 v1 frozen release
Genome assembly: Acyrthosiphon_pisum_JIC1_v1.0.scaffolds.fa.gz
BRAKER2 gene models: Acyrthosiphon_pisum_JIC1_v1.0.scaffolds.braker2.gff
List of gene models containing internal stop codons (removed from the protein and cds fasta files): Acyrthosiphon_pisum_JIC1_v1.0.scaffolds.braker2.bad_genes.lst
BRAKER2 protein sequences: Acyrthosiphon_pisum_JIC1_v1.0.scaffolds.braker2.gff.filtered.aa.fa
BRAKER2 protein sequences (longest transcript per gene only): Acyrthosiphon_pisum_JIC1_v1.0.scaffolds.braker2.gff.filtered.aa.LTPG.fa
BRAKER2 coding sequences: Acyrthosiphon_pisum_JIC1_v1.0.scaffolds.braker2.gff.filtered.cds.fa
BRAKER2 coding sequences (longest transcript per gene only): Acyrthosiphon_pisum_JIC1_v1.0.scaffolds.braker2.gff.filtered.cds.LTPG.fa
De novo repeat library (ReapeatModeler merged with repbase insecta): Acyrthosiphon_pisum_JIC1_repeat_lib.repeatmodeler_merged_repbase_insecta.fa
RepeatMasker transposable element annotation using the A. pisum de novo repeat library: Acyrthosiphon_pisum_JIC1_v1.0.scaffolds.repeatmodeler_merged_repbase_insecta.repeatmasker.out
RepeatMasker transposable element annotation using the A. pisum de novo repeat library (gff format): Acyrthosiphon_pisum_JIC1_v1.0.scaffolds.repeatmodeler_merged_repbase_insecta.repeatmasker.gff
Rhodnius prolixus DNA zoo chromosome-scale genome assembly annotation
R. prolixus chromosome-scale genome assembly was obtained here: https://www.dnazoo.org/assemblies/Rhodnius_prolixus.
Genome assembly: Rhodnius_prolixus-3.0.3_HiC.fasta
BRAKER2 gene models: Rhodnius_prolixus-3.0.3_HiC.braker2.gff
BRAKER2 protein sequences: Rhodnius_prolixus-3.0.3_HiC.braker2.gff.aa.fa
BRAKER2 protein sequences (longest transcript per gene only): Rhodnius_prolixus-3.0.3_HiC.braker2.gff.aa.LTPG.fa
BRAKER2 coding sequences: Rhodnius_prolixus-3.0.3_HiC.braker2.gff.cds.fa
Triatoma rubrofasciata chromosome-scale genome assembly annotation
T. rubrofasciata chromosome-scale genome assembly was obtained here: http://dx.doi.org/10.5524/100614
Genome assembly: zhuichun_assembly.fasta
BRAKER2 gene models: zhuichun_assembly.braker2.gff
BRAKER2 protein sequences: zhuichun_assembly.braker2.gff.aa.fa
BRAKER2 protein sequences (longest transcript per gene only): zhuichun_assembly.braker2.gff.aa.LTPG.fa
BRAKER2 coding sequences: zhuichun_assembly.braker2.gff.cds.fa
Hemiptera orthogroups and species tree
OrthoFinder was used to cluster proteomes of 14 Hemiptera into orthogroups for phylogenomic analysis. All proteomes were reduced to the longest transcript per gene. See here for full details:
Species included, taxon IDs and data source:
Mcer = Myzus cerasi v1.1 (https://bipaa.genouest.org/sp/myzus_cerasi/)
MperO = Myzus persicae clone O v2 (This study)
Dnox = Diuraphis noxia Thorpe et. al. gene predictions (https://bipaa.genouest.org/sp/diuraphis_noxia/)
Apis = Acyrthosiphon pisum JIC1 v1 (This study)
Pnig = Pentalonia nigronervosa (This study)
Rmai = Rhopalosiphum maidis v0.1 (http://gigadb.org/dataset/100572)
Rpad = Rhopalosiphum padi v1.0 (https://bipaa.genouest.org/sp/rhopalosiphum_padi/)
Agly = Aphis glycines biotype 4 v2.1 (https://zenodo.org/record/3453468#.XnpL5JOgLRY)
BtabMEAM1 = Bemissia tabacci MEAM1 v1.2 (http://www.whiteflygenomics.org/cgi-bin/bta/index.cgi)
Trub = Triatoma rubrofasciata (This study)
Rpro = Rhodnius prolixus (This study)
Ofas = Oncopeltus fasciatus OGS v1.0 (https://i5k.nal.usda.gov/Oncopeltus_fasciatus)
Sfuc = Sogatella furcifera v1 (http://dx.doi.org/10.5524/100255)
Nlug = Nilaparvata lugens (https://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0521-0#Sec42)
Files:
Proteomes included in the analysis: proteomes.tar.gz
Orthogroups: Orthogroups.txt
Gene counts per orthogroup, per species: Orthogroups.GeneCount.csv
Single copy conserved orthogroups used for species tree: SingleCopyOrthogroups.txt
Species tree alignment: SpeciesTreeAlignment.fa
r8s configuration file (includes time calibrations and OrthoFinder ML species tree with branch lengths): species_tree_rooted.r8s.nex
r8s time calibrated species tree: r8s_tree.nwk
Notes
Files
Orthogroups.GeneCount.csv
Files
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Additional details
Related works
- Is cited by
- Preprint: 10.1101/2020.03.24.006411 (DOI)
Funding
- Evolutionary genomics of host range expansion in aphid crop pests BB/R01227X/1
- UK Research and Innovation
- Functional Genomics of Aphid Adaptation to Plant Species BB/L002108/1
- UK Research and Innovation
- Resistance: DNA methylation and the evolution of pesticide-resistance genes in aphids BB/R009481/1
- UK Research and Innovation