Lens culinaris: CDC Redberry Genome Assembly v2.0

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
Authors

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

Assembly Genome Size
3,690,413,039
Number Of Scaffolds
5,969
Scaffold N50 value
823
Scaffold N50 length
1,352,216
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.
Methodology
Genus
Lens
Scientific Name
Lens culinaris
Data Source Version
Sequences 2019
Data Source Name
CDC Redberry ASM
Abbreviation
Lcu.2RBY
Program, Pipeline, Workflow or Method Name
USASK BettLab long-read genome assembly workflow
Program Version
2020

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.

Download

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: 7a38d550c39a2399b27ae285d1146f1f
  • Last updated: March 6, 2025 (README only). Data files last updated on Nov 16, 2022.