Vigna unguiculata: IT97K-499-3 Genome Assembly v1.2

Overview
Assembly Details
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Citation
Lonardi S, Muñoz-Amatriaín M, Liang Q, Shu S, Wanamaker SI, Lo S, Tanskanen J, Schulman AH, Zhu T, Luo MC, Alhakami H, Ounit R, Hasan AM, Verdier J, Roberts PA, Santos JRP, Ndeve A, Doležel J, Vrána J, Hokin SA, Farmer AD, Cannon SB, Close TJ. The genome of cowpea (Vigna unguiculata [L.] Walp.).. The Plant journal : for cell and molecular biology. 2019 06; 98(5):767-782.
Overview
Date Released
February 2020
Data Source
Source Name
: IT97K-499-3
Source URI
: https://www.ncbi.nlm.nih.gov/biosample/SRS3721827
Statistics
Assembly Genome Size
519.4 Mb
Number Of Scaffolds
675
Scaffold N50 value
6
Scaffold N50 length
41.7 Mb
Number Of Genes
31,948
The IT97K-499-3 Genome Assembly v1.2 genome assembly was constructed through assembly reconciliation between 8 assemblies focusing on the strengths of multiple assembly software. The finished assembly is 519.4 Mb arranged in 11 pseudo-molecules and 675 unplaced scaffolds. Nearly half of the assembled sequence is composed of repetitive elements, which are enriched within recombination‐poor pericentromeric regions.
Assembly Details
Workflow/Pipeline Name
Lonardi S et al., The Plant Journal 2019 06; 98(5):767-782
Algorithm
CANU, Falcon and ABruijn
Program Version
multiple
Using Single Molecule Real-Time Sequencing (Pacific Biosciences) about six million long reads were generated for a total of 56.8Gbp (91x genome equivalent, assuming a genome size of 620Mb), with a read N50 of about 14.5Kbp. Eight draft assemblies were generated, six of which were produced with CANU v1.3 (using multiple parameter settings), one with Falcon v0.7.3 and one Abruijn v0.4. A custom assembly reconciliation algorithm merged the eight assemblies into one final stitched assembly, which was then polished via the PacBio Quiver pipeline in SMRT Portal. Two Bionano Genomics optical maps were used to assemble contigs into scaffolds. Finally, eleven pseudomolecules were produced using ALLMAPS by anchoring and orienting scaffolds to ten genetic maps containing a total of over forty-four thousand SNPs.
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Sources
LegFed DataStore
Access at CyVerse Data Commons
NCBI Bioproject
PRJNA381312
Original Source
Phytozome 13

This data is publicly available at the above locations. If you use this data in your research, please cite:

Lonardi S, Muñoz-Amatriaín M, Liang Q, Shu S, Wanamaker SI, Lo S, Tanskanen J, Schulman AH, Zhu T, Luo MC, Alhakami H, Ounit R, Hasan AM, Verdier J, Roberts PA, Santos JRP, Ndeve A, Doležel J, Vrána J, Hokin SA, Farmer AD, Cannon SB, Close TJ. The genome of cowpea (Vigna unguiculata [L.] Walp.).. The Plant journal : for cell and molecular biology. 2019 06; 98(5):767-782.