Metadata

Name

Supplementary data for: Chromosome-scale genome assemblies of aphids reveal extensively rearranged autosomes and long-term conservation of the X chromosome

Repository

ZENODO

Identifier

doi:10.5281/zenodo.3712089

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

Data or Study Types

multiple

Source Organization

Unknown

Access Conditions

available

Year

2020

Access Hyperlink

https://doi.org/10.5281/zenodo.3712089

Distributions

• Encoding Format: HTML ; URL: https://doi.org/10.5281/zenodo.3712089