Published March 16, 2020 | Version v1
Dataset Open

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

This work was funded by a BBSRC Future Leader Fellowship (BB/R01227X/1) awarded to TCM, the BBSRC Industrial Partnership Award (IPA) with Syngenta Ltd (BB/L002108/1 and BB/R009481/1) awarded to SAH, DS and CvO and BBSRC PhD fellowship of RW. Additional support was received from the BBSRC Institute Strategy Programme (BB/P012574/1) and the John Innes Foundation.

Files

Orthogroups.GeneCount.csv

Files (1.9 GB)

Name Size Download all
md5:c51c4e76a76e36941b500c677ed8fffc
23.2 MB Download
md5:ef50f273b89a4c1c4b1a38e8f153ebad
23.3 kB Download
md5:83a7b8a6d6baa2af9c9c1687df04b269
4.7 kB Download
md5:84d7f5377eab2e240c98220f0d29a09a
72.9 MB Download
md5:fe3b6ae449ef5b1fedb7bb47347b8f26
16.8 MB Download
md5:c0a8a01b796e081903b7a99e83ea6bb7
14.8 MB Download
md5:acf09b1f2d3b8067261bfa5dfe1f2a26
50.8 MB Download
md5:556a78b72593fae7eeea5cc402b62def
43.8 MB Download
md5:51bd025a924df51b5c34b292aa66a70e
158.1 MB Download
md5:4c4142dcb072d7fa7d11ffc5196ec34e
69.4 MB Download
md5:684918cd3b0245d12e33552c05ff7679
96.7 MB Download
md5:7bfb098f45b6848b2eb48600fb2d8a09
2.2 kB Download
md5:cff6f6acdde0992d869280f0278e5520
46.3 MB Download
md5:9009bb1f94b6ee5303cb30b178c83582
16.7 MB Download
md5:edc4dc82865cc786eda5ca22e6e7353f
14.1 MB Download
md5:b8572cb10d7212ff573e85299e7c50bd
50.1 MB Download
md5:1441fd40ee7df12dde042bccfab8eb7a
41.7 MB Download
md5:3e3cc523e645b63b50a87b7268f7f4d3
118.9 MB Download
md5:dce4f9b50f8c88bf30083184f59a05db
34.2 MB Download
md5:5afd79f089863dcc2b06f508bae97f6b
48.2 MB Download
md5:225f5f607f036e59b44cdb835fce79b3
22.6 MB Download
md5:99dd8885c5cafd6a4fd57f415c1c26c1
964.0 kB Preview Download
md5:fff32d50cf8dbf455f060c3aedfb54a0
6.6 MB Preview Download
md5:f4f834391e020c6cf6d1170f3c51d383
78.6 MB Download
md5:4e1a04896af5e766e745859c3f65c4c3
385 Bytes Download
md5:1ddd09faa4c847608ddac98513715b71
680.3 MB Download
md5:9632d228bce299bf00964bcc771a0715
7.9 kB Preview Download
md5:2351d73c55987356236a9e62b449b00c
995 Bytes Download
md5:7c258cf7e08552bda5c35caf1c3337bb
16.0 MB Download
md5:9fdff6a40ff93d8c0930a38d5b62e0e8
41.8 MB Download
md5:e906a0b4e74c24c68dd700948646a768
10.0 MB Download
md5:08bc7730054427c5a35a1890e5c700fc
9.7 MB Download
md5:22133b315c1b2a83e660d48aeeffe03b
29.6 MB Download
md5:02d394841fca174da1fb3689374adc19
46.1 MB Download

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