Published September 23, 2022 | Version v1
Dataset Open

Supplementary data for: Hybridisation has shaped a recent radiation of grass-feeding aphids

Authors/Creators

  • 1. John Innes John Innes Centre, Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
  • 2. School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK

Description

Orthogroups and species tree

Proteomes included in the analysis: proteomes.tar.gz
Orthogroups: Orthogroups.txt
Gene counts per orthogroup, per species: Orthogroups.GeneCount.tsv
Single copy conserved orthogroups used for species tree: Orthogroups_SingleCopyOrthologues.txt
Protein alignment used for species tree reconstruction: SpeciesTreeAlignment.fa
Species tree: SpeciesTree_rooted.txt

Whole genome alignment of S. avenae, S. miscanthi, M. dirhodum and A. pisum

Cactus whole genome alignment (hal format): Siave_Simis_Medir_Acpis.hal.gz

Haplotype divergence analysis (whole genome sequences)

VCF files of HapCUT2 phased variants for S. miscanthi Langfang-1 chromosomes (Simis_v2 assembly scaffolds 1 to 9):
Langfang1.Hapcut2_PB_plus_HiC.scaffold_1.hap.phased.VCF.gz
Langfang1.Hapcut2_PB_plus_HiC.scaffold_2.hap.phased.VCF.gz
Langfang1.Hapcut2_PB_plus_HiC.scaffold_3.hap.phased.VCF.gz
Langfang1.Hapcut2_PB_plus_HiC.scaffold_4.hap.phased.VCF.gz
Langfang1.Hapcut2_PB_plus_HiC.scaffold_5.hap.phased.VCF.gz
Langfang1.Hapcut2_PB_plus_HiC.scaffold_6.hap.phased.VCF.gz
Langfang1.Hapcut2_PB_plus_HiC.scaffold_7.hap.phased.VCF.gz
Langfang1.Hapcut2_PB_plus_HiC.scaffold_8.hap.phased.VCF.gz
Langfang1.Hapcut2_PB_plus_HiC.scaffold_9.hap.phased.VCF.gz

VCF files of HapCUT2 phased variants for S. avenae JIC1 chromosomes (Siave_v2.1 assembly scaffolds 1 to 9):
JIC1.Hapcut2_IL_plus_HiC.scaffold_1.hap.phased.VCF.gz
JIC1.Hapcut2_IL_plus_HiC.scaffold_2.hap.phased.VCF.gz
JIC1.Hapcut2_IL_plus_HiC.scaffold_3.hap.phased.VCF.gz
JIC1.Hapcut2_IL_plus_HiC.scaffold_4.hap.phased.VCF.gz
JIC1.Hapcut2_IL_plus_HiC.scaffold_5.hap.phased.VCF.gz
JIC1.Hapcut2_IL_plus_HiC.scaffold_6.hap.phased.VCF.gz
JIC1.Hapcut2_IL_plus_HiC.scaffold_7.hap.phased.VCF.gz
JIC1.Hapcut2_IL_plus_HiC.scaffold_8.hap.phased.VCF.gz
JIC1.Hapcut2_IL_plus_HiC.scaffold_9.hap.phased.VCF.gz

Haplotype resolved assemblies of S. avenae JIC1 and S. miscanthi Langfang-1 based on HapCUT2 phasing results:
JIC1_H1.Hapcut2.fa
JIC1_H2.Hapcut2.fa
Langfang1_H1.Hapcut2.fa
Langfang1_H2.Hapcut2.fa

SibeliaZ whole genome alignment of S. avenae JIC1 and S. miscanthi Langfang-1 haplotypes: alignment.filtered.ordered.stranded.sorted.maf

Filtered VCF files used for population genomics analysis

S. avenae and S. miscanthi GBS samples + JIC1 and Langfang1 WGS samples variant calls: freebayes.q30_dp2_biallelic.mm_75.indv_max_30pc_missing.recode.vcf
S. avenae and S. miscanthi GBS samples + JIC1 and Langfang1 WGS samples phased variant calls: freebayes.q30_dp2_biallelic.mm_75.indv_max_30pc_missing.recode.fix_mis.beagle.vcf
S. avenae and S. miscanthi GBS samples + JIC1, Langfang1 and M. dirhodum WGS samples variant calls: with_Medir.merged.q30_dp2_biallelic.mm_90.recode.vcf
S. avenae and S. miscanthi GBS samples + JIC1, Langfang1 and M. dirhodum WGS samples phased variant calls: with_Medir.merged.q30_dp2_biallelic.mm_90.recode.fix_mis.beagle.vcf
S. miscanthi GBS samples + JIC1 and Langfang1 WGS samples variant calls: China_plus_JIC1.merged.q30_dp2_biallelic.mm_90.recode.vcf
S. miscanthi GBS samples + JIC1 and Langfang1 WGS samples variant calls: China_plus_JIC1.merged.q30_dp2_biallelic.mm_90.recode.fix_mis.beagle.vcf

SNAPP phylogenetic analysis configuration file and trees

SNAPP configuration file: snapp.xml
SNAPP log file: ut.log
SNAPP posterior sample of trees: ut.trees
SNAPP maximum clade credibility tree with 10% burn in: ut.trees.max_cred_burn_10pc

 

 

Notes

The described work was supported by a CEPAMS grant (17.03.2) awarded to S.H. and a Biotechnology and Biological Sciences Research Council (BBSRC) Future Leader Fellowship (BB/R01227X/1) awarded to T.C.M.. R.H.M.W. was funded from the BBSRC Norwich Research Park Biosciences Doctoral Training Partnership Award (BB/M011216/1). Additional support was provided by the BBSRC Institute Strategy Programs (BBS/E/J/000PR9797 and BBS/E/J/000PR9798) awarded to the John Innes Centre. The JIC is grant-aided by the John Innes Foundation. This research was supported by JIC Technology Platforms, particularly the Entomology and Insectary facilities and staff. We thank the NBI Computing Infrastructure for Science Group, which provides technical support and maintenance to the John Innes Centre's high-performance computing cluster and storage systems.

Files

Orthogroups.txt

Files (4.0 GB)

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Additional details

Related works

References
Dataset: 10.5281/zenodo.5908005 (DOI)

Funding

UK Research and Innovation
Evolutionary genomics of host range expansion in aphid crop pests BB/R01227X/1
UK Research and Innovation
Susceptibility BBS/E/J/000PR9797
UK Research and Innovation
Evolution BBS/E/J/000PR9798
UK Research and Innovation
The Norwich Research Park Biosciences Doctoral Training Partnership BB/M011216/1