Overview
GenusJuglans
Speciesnigra
Common NameBlack Walnut
AbbreviationJ. nigra
Order: Fagales
Family: Juglandaceae
Chromosome Number: 2n=32 1

Biomaterial Browser
The following browser provides a list of biomaterials associated with this organism.
Biomaterial NameTissueTreatment
BW-M-19dormant twigsnone
BW-CH10-28Dleafozone exposure 80ppb for 28 days
BW-OW-9leafcontrol chamber ozone 10ppb+ mecanical wounding on day 28
BW-OW-12leafozone exposure 225ppb for 29 day + mecanical wounding on day 28
BW-M-29female flowersnone
BW-M-28catkins (male flowers-immature/not shed polen yetnone
BW-M-22undamaged twigsnone
BW-M-23damaged twigsmechanical wounding
BW-M-24green twigs/buds-this year growthnone
BW-M-21damaged leavesmechanical wounding

Pages

Transcriptome
Below is a list of transcriptomes available for Juglans nigra. Click the transcriptome name for further details.
Transcriptome NameAnalysis NameProgramDate ConstructedStats
Juglans nigra 120313 (CURRENT)de novo Black Walnut (Juglans nigra)Trinity; CD-HIT-EST2013-12-03Contigs: 78834
Black Walnut Ozone (ARCHIVED)de novo Black Walnut Ozone Treatment ExperimentTrinity2012-12-19Contigs: 61,770
Libraries
The following libraries are associated with this organism.
Library NameType
BAC Library JNC_BaBAC
BAC Library JNC_BbBAC
Mapping Population

Location: University of Missouri, Horticulture and Agroforestry Research Center (HARC) in New Franklin, MO

Principal Investigators: Mark Coggeshall, Jeanne Romero-Severson

A full sibling population was created, representing two nut cultivars in the University of Missouri (MU) germplasm repository, 'Sparrow' and "Schlessler'. The population consists of 323 seedling full sibs (all derived from the 2008 seed years), plus both parents. Full sibling status was confirmed via paternity exclusion genetic testing on all individuals. This paternity exclusion (PE) work was initiated in 2009 and primarily funded through the University of Missouri Center for Agroforestry (UMCA), in cooperation with the Romero-Severson (JRS) lab at the University of Notre Dame (ND).

Phenotyping of this of this population will be initiated in the spring 2015 and will include:
  • leafing date
  • bud burst
  • pistillate & staminate bloom
  • season length
  • anthracnose susceptibility
As circumstances permit, standardized nut characteristics will be assessed using standardized descriptor values developed by IPGRI (1990), including:
  • % kernel
  • veination
  • kernel color
  • harvest date
  • shell thickness
Genotyping of this population is ongoing. A set of SSR markers are being used for the entire population, and a subset of trees are also undergoing ddRADTag genotyping. Please contact us for more information or if you are interested in utilizing this population for research. Genotype and phenotype information will be posted here when publicly available.
A second full-sib population totaling 135 to date, sharing the female parent “Sparrow” with the first population, was started at UM in 2015. The seed parent Sparrow was selected for whole genome resequencing at UC-Davis for a USDA Specialty Crops Research Initiative (SCRI) project headed by David Neale. Data is expected sometime in 2016.
Predicted SSRs (genomic)
Publication: Staton M, Best T, Khodwekar S, Owusu S, Xu T, Xu Y, Jennings T, Cronn R, Arumuganathan AK, Coggeshall M, Gailing O. Preliminary Genomic Characterization of Ten Hardwood Tree Species from Multiplexed Low Coverage Whole Genome Sequencing. PloS one. 2015 Dec 23;10(12):e0145031.

In order to develop SSR resources for ten important North American hardwood tree species, we individually barcoded and multiplex sequenced DNA from ten hardwood forest tree species using short reads produced from an Illumina HiSeq. Raw reads can be downloaded from the NCBI short read archive, project SRP021923. Bioinformatic processing included trimming, assembly, SSR identification and primer design, processing details including scripts are available.

Statistics:
Untrimmed Pairs 17,205,517
Untrimmed Bases 3,475,514,434
Reconstructed Fragments 7,033,939
Reconstructed Fragments - Bases 1,191,496,671
Dinucleotide repeats with primers 11,859
Trinucleotide repeats with primers 753
Tetranucleotide repeats with primers 139

Download Files:
Alignment To English Walnut

Mapping black walnut transcriptome to English walnut genome.

English walnut (Juglans regia) genome fasta at /lustre/projects/staton/projects/hwg_tmp_anlaysis_files/Jregia/raw_data Get Black walnut (Juglans nigra) transcriptome from HWG site.

wget http://160.36.205.61:8095/sites/default/files/sequences/blackWalnut120313/Juglans_nigra_120313_transcripts.fasta

1. Build genome database index.

/lustre/projects/staton/software/gmap-2016-09-14/bin/gmap_build \
--dir=/lustre/projects/staton/projects/hwg_tmp_anlaysis_files/Jregia/jbrowse_tracks/ \
--db=EngWalnut \
walnut.wgs.5d.scafSeq.fa

2. Transcriptome mapping

For Jbrowse tracks, GFF file needs to be the output file with -f 2 Here we keep one best match for each mRNA with -n 0

/lustre/projects/staton/software/gmap-2016-09-14/bin/gmap \
-D /lustre/projects/staton/projects/hwg_tmp_anlaysis_files/Jregia/jbrowse_tracks/ \
-d EngWalnut \
-A \
-n 0 \
-f 2 \
Juglans_nigra_120313_transcripts.fasta \
> 7_Juglans_nigra_120313_transcripts_mapping.gff

3. Mapping analysis:

Black walnut transcripts mapped to English walnut genome by GMAP: 78834 Black walnut (Juglans. nigra) mRNA contigs mapped to English walnut (Juglans. regia) genome. 74984 mRNA are mapped, 91.0% of matches have >90% identity and 83.2% matches are >90% coverage.

Green ash transcripts mapped to European ash genome by GMAP: 107611 Green ash (F. pennsylvanica) mRNA contigs mapped to European ash (F. excelsior) genome. 102977 mRNA are mapped, 78.6% of matches have >90% identity and 73.2% matches are >90% coverage.

Reference: Thomas D. Wu and Colin K. Watanabe. GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics 2005 21:1859-1875

Go to JBrowse