Lens ervoides: IG 72815 Genome Assembly 1.0

Overview
Assembly Details
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Citation
Ramsay L, Koh CS, Kagale S, Gao D, Kaur S, Haile T, Gela TS, Chen LA, Cao Z, Konkin DJ, Toegelová H, Doležel J, Rosen BD, Stonehouse R, Humann JL, Main D, Coyne CJ, McGee RJ, Cook DR, Penmetsa RV, Vandenberg A, Chan C, Banniza S, Edwards D, Bayer PE, Batley J, Udupa SM, Bett KE. Genomic rearrangements have consequences for introgression breeding as revealed by genome assemblies of wild and cultivated lentil species.. bioRxiv. 2021 Jul 24.
Overview
Date Released
November 2019
Data Source
Source Name
: IG 72815 ASM
Statistics
Assembly Genome Size
2,866,353,354
Number Of Scaffolds
2,291
Scaffold N50 value
176
Scaffold N50 length
4,706,458
Number Of Genes
60,296
This IG 72815 ASM Lens ervoides genome assembly was constructed with long-read data (52x Oxford nanopore reads). The contiguity of the assembly was further validated and improved using HiC data and a genetic map (LR-66; L1-02-827 x IG 72815 intraspecific RIL). The finished assembly is 2.87 Gb arranged in 7 pseudo-molecules and 1,134 unplaced unitigs.
Assembly Details
Workflow/Pipeline Name
USASK BettLab long-read genome assembly workflow
Algorithm
smartdenovo
Program Version
n/a
Assembly of the contigs was done using smartdenovo with an estimated 52x coverage of Oxford Nanopore reads. Contigs were polished with racon, using two rounds of long-read data and one round of Illumina short read data (10x coverage). The GBS-based genetic map for the LR-66 RIL population was used to assign contigs to chromosome bins. Two lanes of HiC data were generated, and used to order and orient contigs within each bin using ALLHiC, as well as using the software's rescue mode to assign contigs that contained no markers in the genetic map to bins. The HiC data was also passed through SALSA and used to break several chimeric contigs. Pseudomolecule assemblies were individually visualized and manual corrections to fix telomere tethering issues made using Juicebox.
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This genome is available for direct download from KnowPulse below. Specifically, you will receive a compressed archive of the genome assembly and associated files including a README with basic information.

Please remember to use the following attribution when you use this genome assembly in your research.

Ramsay L, Koh CS, Kagale S, Gao D, Kaur S, Haile T, Gela TS, Chen LA, Cao Z, Konkin DJ, Toegelová H, Doležel J, Rosen BD, Stonehouse R, Humann JL, Main D, Coyne CJ, McGee RJ, Cook DR, Penmetsa RV, Vandenberg A, Chan C, Banniza S, Edwards D, Bayer PE, Batley J, Udupa SM, Bett KE. Genomic rearrangements have consequences for introgression breeding as revealed by genome assemblies of wild and cultivated lentil species. bioRxiv. 2021 Jul 24. Genome files retrieved from https://knowpulse.usask.ca/genome-assembly/Ler.1DRT

Genome Assembly: Ler.1DRT.zip

  • File Size: 803MB
  • Md5 Checksum: 8a395acf0ee7c058b5226a86a57456a9