Welcome to Papaver Genomic page

This is the Genomics Data resuorce of Papaver species genome

Currently, it includes Papaver somniferum (opium poppy), Papaver rhoeas (common poppy), and Papaver setigerum (troy poppy) genomic data

The raw genomic data and the genome assembly will released at National Genomics Data Center (NGDC) with accestion number of GWHAZPJ00000000, GWHAZPH00000000, and GWHAZPI00000000.

In this repository, we released the genomic annotation fie.

• Papaver_rhoeas: the Papaver rhoeas annotaion file

  • Papaver_rhoeas.gene.bed.tar.gz: the Papaver rhoeas protein-coding genes annotation in bed file
  • Papaver_rhoeas.gene.gff3.tar.gz: the Papaver rhoeas protein-coding genes annotation in gff3 file
  • Papaver_rhoeas.cds.tar.gz: the Papaver rhoeas cds sequences of annotated protein-coding genes data
  • Papaver_rhoeas.pep.tar.gz: the Papaver rhoeas protein sequences of annotated protein-coding genes data

• Papaver_setigerum: the Papaver setigerum annotaion file

  • Papaver_setigerum.gene.bed.tar.gz: the Papaver setigerum protein-coding genes annotation in bed file
  • Papaver_setigerum.gene.gff3.tar.gz: the Papaver setigerum protein-coding genes annotation in gff3 file
  • Papaver_setigerum.cds.tar.gz: the Papaver setigerum cds sequences of annotated protein-coding genes data
  • Papaver_setigerum.pep.tar.gz: the Papaver setigerum protein sequences of annotated protein-coding genes data

• Papaver_somniferum: the Papaver somniferum annotaion file

  • Papaver_somniferum.gene.bed.tar.gz: the Papaver somniferum protein-coding genes annotation in bed file
  • Papaver_somniferum.gene.gff3.tar.gz: the Papaver somniferum protein-coding genes annotation in gff3 file
  • Papaver_somniferum.cds.tar.gz: the Papaver somniferum cds sequences of annotated protein-coding genes data
  • Papaver_somniferum.pep.tar.gz: the Papaver somniferum protein sequences of annotated protein-coding genes data

If you want to use these data, please contact Xiaofei Yang, xfyang@xjtu.edu.cn or Kai Ye, kaiye@xjtu.edu.cn

The analysis_scripts folder includes the scripts used in our research work

• The files in the analysis_scripts as following:
  • nextdenovo_run.pbs : the script used to assembly P. setigerum and P. rhoeas gneome based on Nanopore sequencing data by NextDenovo
  • scaffHic_breakhic_run.sh : the script used to break the contigs with missing assembly based on Hi-C data by scaffHic
  • 3d-DNA-whole_pipeline.sh : the script used to scaffold genomes based on Hi-C data by 3d-DNA
  • purge_dups-whole-pipeline.sh : the script used to purge duplications in P. rhoease genome by purge_dups
  • P. rohoeas-Purge_dups-cutoffs : the cutoffs parameters used in P. rhoeas genome purge_dups
  • busco3_evaluation.sh : busco evaluation of the genome assembly
  • repetmolder_run.sh : script used to construt own repeat library by RepeatMolder
  • maker_anno.sh : Annotation genomes by MAKER pipeline
    • maker_bopts.ctl : MAKER control file
    • maker_exe.ctl : MAKER control file
    • maker_opts.ctl : MAKER control file
  • kaks_calculator_run.sh : Ks calculation by Kaks_calculator
  • mcscanx_run.sh : McscanX analysis of genome by Mcscanx
  • trinity_run.pbs : script used to assembly transcripts based on RNA-seq data by trinity
  • RNA-seq_analysis.sh : script used to calculate TPM based on RNA-seq data by hisat2, stringtie and ballgown

Citation

Yang, X., Gao, S., Guo, L. et al. Three chromosome-scale Papaver genomes reveal punctuated patchwork evolution of the morphinan and noscapine biosynthesis pathway. Nat Commun 12, 6030 (2021). https://doi.org/10.1038/s41467-021-26330-8

The 2018 version of Papaver somniferum genome citation

Guo L, Winzer T, Yang X, et al. The opium poppy genome and morphinan production[J]. Science, 2018, 362(6412): 343-347.