identifier: CCJH

provenance: he files in this directory are the initial assembly versions, provided here prior to deposition into GenBank. The GenBank version (GCF_003086295.1) is the primary, authoritative instance. The files here are held as part of the PeanutBase, LegumeInfo, and LegumeFederation projects.

source: https://peanutbase.org/data/ and mirrored at LegumeInfo, LegumeFederation, and CyVerse

subject: Arachis hypogaea accession Tifrunner annotation files from genome assembly 1.0

related_to: Genome assembly arahy.Tifrunner.gnm1.KYV3

scientific_name: Arachis hypogaea

taxid: 3818

bioproject: PRJNA291488

scientific_name_abbrev: arahy

genotype: Tifrunner

description: Genome annotation for Arachis hypogaea cultivar Tifrunner, generated with the MAKER pipeline, version 2.31.9. Evidence included gene models from Arachis ipaensis and Arachis duranensis and two transcriptome assemblies: one generated as a genome-guided assembly of 22 tissues from Clevenger et al., 2016 (https://doi.org/10.3389/fpls.2016.01446) and one generated as a genome-guided assembly of 12 libraries from additional tissues and stress conditions (Ozias-Akins et al., unpublished).

dataset_doi: none

genbank_accession: none

original_file_creation_date: 2018-02-15

local_file_creation_date: 2018-02-15

publication_doi: 10.1038/s41588-019-0405-z

dataset_release_date: 2018-02-15

publication_title: none

contributors: The International Peanut Genome Initiative; lead assembly group Jeremy Schmutz, Jerry Jenkins, Jane Grimwood; project leads David Bertioli; Soraya Bertioli; Brian Schleffler; Scott Jackson; Peggy Ozias-Akins; annotation group Andrew Farmer, Jacqueline Campbell, Nathan Weeks

data_curators: Steven Cannon, Andrew Farmer

public_access_level: public

license: open

keywords: peanut, Arachis hypogaea, Tifrunner

citations: Bertioli et al., 2019; https://doi.org/10.1038/s41588-019-0405-z

file_transformation: 
  - Added prefixes to GFF references and IDs

changes: 
  - 2018-03-01 moved file lists into MANIFESTs
  - 2018-06-25 added descriptions file: arahy.Tifrunner.gnm1.ann1.CCJH.info_descriptors.txt - derived from gff3 file as follows: cat arahy.Tifrunner.gnm1.ann1.CCJH.gene_models_main.gff3 | awk '$3=="gene"' | grep "Name=" | grep Z7AAAI | perl -pe 's/%2C/,/g; s/%3B/;/g; s/%3D/=/g'
  - 2019-05-20 Updated README to note publication
  - 2019-07-25 Updated GFF file to fix problem with parent names in exon records (second and subsequent names within an exon with multiple parents had incorect forms).
  - 2020-04-03 adf updated GFF file to fix lingering issues with shared exons and suppressed transcripts reported by user
  - 2020-04-27 use bgzip+samtools faidx for derived fastas
