Phaseolus vulgaris: UI111 Genome Assembly v1.1

Overview
Assembly Details
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Citation
Phaseolus vulgaris UI111 v1.1, DOE-JGI and USDA-NIFA, http://phytozome.jgi.doe.gov/
Overview
Date Released
October 2019
Data Source
Source Name
: UI111
Source URI
: https://phytozome-next.jgi.doe.gov/info/PvulgarisUI111_v1_1
Statistics
Assembly Genome Size
554.9 Mb
Number Of Scaffolds
58
Scaffold N50 value
5
Scaffold N50 length
51 Mb
Number Of Genes
27,385
This is a high-quality PacBio-based assembly of the Phaseolus vulgaris UI111 genome. It consists of 141.5x long-read sequence coverage assembled into 11 chromosomes, which contain 98.9% of the sequence. Additionally, homozygous SNPs and INDELs were corrected using ~180x of Illumina reads (2x150, 400bp insert).
Assembly Details
Workflow/Pipeline Name
Phytozome Assembly workflow
Algorithm
MECAT
Program Version
unknown
PacBio sequence was assembled using MECAT and polished using QUIVER. The assembly was corrected by breaking down the v2 release of Phaseolus vulgaris into 23,601 nonredundant, non-overlapping 1,500 bp syntenic markers. Additionally, the F2 and F5 maps were utilized and resulted in 6 breaks to the assembly. Scaffolds were re-orientated, ordered and joined together according to the 3 marker sets for a total of 109 joins. This yielded in 98.9% of the assembled sequence to be contained in the 11 chromosomes.
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Sources
Original Source
Phytozome 13

This data is publicly available at the above location. It can be used with citation for small-scale analysis.

Phaseolus vulgaris UI111 v1.1, DOE-JGI and USDA-NIFA, http://phytozome.jgi.doe.gov/

For large-scale analysis please access the phytozome website for collaborator contact information.