PeanutBase Datastore Collections

All of the files housed by PeanutBase are available at the LIS Datastore.

The LIS Datastore (used by PeanutBase) is organized by Genus and species, with individual data collections under species directories for: genomes, annotations, expression, genetic data, markers, synteny, diversity, and others. Each collection contains a README file which describes that collection.

Arachis data collections

Arachis hypogaea

Genomes

Tifrunner.gnm1.KYV3: Genome assembly 1 for Arachis hypogaea, cultivar Tifrunner
Tifrunner.gnm2.J5K5: Genome assembly 2 for Arachis hypogaea, cultivar Tifrunner. This version has structural changes relative to assembly 1.
BaileyII.gnm1.1JTF: Arachis hypogaea accession Bailey II, genome assembly 1
Fuhuasheng.gnm1.XX5Y: Genome assembly for tetraploid peanut cultivar Fuhuasheng, from Chen et al., 2019
Shitouqi.gnm1.L4VP: Genome assembly for peanut cultivar Shitouqui, from Zhuang et al., 2019.

Annotations

BaileyII.gnm1.ann1.PQM7: Annotation 1 for Arachis hypogaea accession Bailey II, genome assembly 1
Tifrunner.gnm2.ann1.4K0L: Gene models for genome assembly 2 for Arachis hypogaea, cultivar Tifrunner.
Tifrunner.gnm1.ann1.CCJH: Arachis hypogaea accession Tifrunner annotation files from genome assembly 1.0
Tifrunner.gnm2.ann2.PVFB: Annotation 2, using the BIND pipeline, for Arachis hypogaea, cultivar Tifrunner

Expression

Tifrunner.gnm2.ann2.expr.Tifrunner.Clevenger_2016: A Developmental Transcriptome Map for Allotetraploid Arachis hypogaea

Markers

Tifrunner.gnm1.mrk.Axiom_Arachis2: Axiom_Arachis2 is a SNP marker set developed by Clevenger, et al. DOI:10.1016/j.molp.2016.11.015
Tifrunner.gnm1.mrk.Agarwal_Clevenger_2018: Genetic map of Tifrunner x GT-C20 for the study of early and late leaf spots (ELS and LLS) and tomato spotted wilt virus (TSWV).
Tifrunner.gnm1.mrk.Axiom_Arachis_58K: Axiom_Arachis_58K is a high-density SNP array with 58,233 SNPs reduced from 163,782 SNPs derived from DNA resequencing and RNA-sequencing of 41 groundnut accessions and wild diploid ancestors.

Diversity

aradu1_araip1.gnm1.div.Otyama_Kulkarni_2020: Diversity data for the U.S. peanut core collection, genotyped relative to the diploid A. duranensis and A. ipaensis genome assemblies.
aradu1_araip1.gnm1.div.Otyama_Wilkey_2019: Genotype data for US Peanut Mini Core collection.
aradu1_araip1.gnm1.div.Clevenger_Korani_2018: Genotyping of African germplasm collection

Arachis duranensis

Genomes

V14167.gnm2.J7QH: Genome assembly 2 for Arachis duranensis, accession V14167
V14167.gnm1.SWBf: Genome assembly 1 for Arachis duranensis, accession V14167
K30060.gnm1.W9B1: Genome assembly 1 for Arachis duranensis, accession K30060
K30065.gnm1.M24N: Genome assembly 1 for Arachis duranensis, accession K30065, collected from rio seco Bolivia

Annotations

V14167.gnm1.ann1.cxSM: genome annotations

Markers

V14167.gnm1.mrk.Li_Cui_2022: Markers from the Affymetrix version 2.0 SNP array mapped to the Arachis duranensis V14167 v1.0 assembly.

Synteny

V14167.gnm1.syn.qmkW: Synteny mappings among the genomes. See genome assemblies indicated in the synteny comparisons.

Arachis ipaensis

Genomes

K30076.gnm1.bXJ8: Genome assembly 1 for Arachis ipaensis, accession K30076.
K30076.gnm2.1GWY: Genome Assembly 2 for A. ipaensis K30076. A high-quality chromosome-scale assembly, based on PacBio RSII and Sequel reads, ordered into pseudomolecules by Dovetail using Hi-C Chicago libraries and the HiRise and SNAP.

Annotations

K30076.gnm1.ann1.J37m: genome annotations for Arachis ipaensis K30076.gnm1.ann1

Markers

K30076.gnm1.mrk.Li_Cui_2022: Markers from the Affymetrix version 2.0 SNP array mapped to the Arachis ipaensis K30076 v1.0 assembly.

Synteny

K30076.gnm1.syn.S8s4: Synteny mappings among the genomes. See genome assemblies indicated in the synteny comparisons.

Arachis cardenasii

Genomes

K10017.gnm1.DQ4M: Genome assembly 1 for Arachis cardenasii, accession K10017

Arachis stenosperma

Genomes

V10309.gnm1.PFL2: Genome assembly 1 for Arachis stenosperma, genotype V10309

Annotations

V10309.gnm1.ann1.CZRZ: GenBank RefSeq annotation for Genome assembly 1 for Arachis stenosperma, genotype V10309