Lens culinaris: CDC Redberry Genome Assembly v2.0

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
February 2020
Data Source
Source Name
: CDC Redberry ASM
Statistics
Assembly Genome Size
3,690,413,039
Number Of Scaffolds
5,969
Scaffold N50 value
1,352,216
Scaffold N50 length
823
Number Of Genes
58,243
This CDC Redberry Lens culinaris genome assembly was constructed with long-read data (34x PacBio SMRT, 20x Oxford nanopore reads). The contiguity of the assembly was further validated and improved using HiC data, as well as both an optical and genetic map (LR-01; ILL 1704 x CDC Robin intraspecific RIL). The finished assembly is 3.69 Gb arranged in 7 pseudo-molecules and 2,068 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 34x coverage of PacBio SMRT and 20x coverage of Oxford nanopore reads. Contigs were polished with racon, using three rounds of long-read data mapped against the and one round of Illumina short read data (10x coverage). Five lanes of HiC data were generated, and a first pass of scaffolding and breaking of chimeric sequence was carried out using SALSA, followed by scaffolding using an optical map using Irys-scaffolding. Scaffolds were assigned to chomosome bins using a genetic map from the LR-01 RIL population exome capture data, and ordered and oriented within each bin using ALLHiC. Pseudomolecule assemblies were individually visualized and manual corrections to correct telomere tethering 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/Lcu.2RBY

Genome Assembly: Lcu.2RBY.zip

  • File Size: 1.3 GB
  • Md5 Checksum: 7ee6956b1a183cf39a48cc75626de281
  • Last updated: Nov 16, 2022