ena-STUDY-CORNELL UNIVERSITY-11-08-2021-20:46:23:354-1142
The v2 release is based on an improved contig assembly using the same PacBio HiFi dataset, but with the hifiasm assembler. The v2 assembly was manually curated to resolve overlapping contigs that were not addressed during BioNano hybrid scaffolding (this was not done for v1). Scaffolds were placed into pseudomolecules using the v1 chromosomes as a guide and were validated by HiC contact map visualization as before.
PepsiCo releases version 2 of OT3098 reference genomeBy: Dr. Mandy Waters, PepsiCoMethod comparison between OT3098 v1 and v2:Written by Dr. Kevin Fengler, Corteva AgrisciencesThe v1 contig assembly was built from 35x PacBio HiFi (read N50 = 17.3 kb, min predicted accuracy > .992) using the HiCanu assembler which resulted in 1,890 contigs with a contig N50= 30.3 Mb and a total assembly size of 10.97 Gb. The contigs were then scaffolded with BioNano genome maps (450 maps, map N50= 98.5, total length = 11.2 Gb) on the BioNano Access platform to create hybrid scaffolds (n= 100, scaffold N50 = 293.9 Mb, total length = 10.84 Gb). Hybrid scaffolds were tentatively placed into pseudomolecules using oat consensus markers. The final ordering of scaffolds was refined using HiC data and contact map visualization using JuiceBox and the Juicer tools.The v2 release is based on an improved contig assembly using the same PacBio HiFi dataset, but with the hifiasm assembler. The v2 assembly exhibited a significant improvement in contiguity (1,343 contigs, contig N50 = 71 Mb, total size= 10.75 Gb). This assembly was similarly scaffolded with the same BioNano maps as v1, however, the improved contigs significantly improved the contiguity of the scaffolds as well (84 scaffolds, scaffold N50= 374 kb, total size = 10.83 Gb). The v2 assembly was manually curated to resolve overlapping contigs that were not addressed during BioNano hybrid scaffolding (this was not done for v1). Scaffolds were placed into pseudomolecules using the v1 chromosomes as a guide and were validated by HiC contact map visualization as before.Nomenclature, orientation, and stats:Chromosomes in v1 were oriented such that the short arm was on top. The OT3098 v2 pseudomolecules use chromosome names and orientations adopted by PanOat in an effort to maintain consistency with future assemblies. The PanOat consortium is currently constructing chromosome-scale reference for multiple oat (Avena sativa) genotypes and has therefore adopted a chromosome nomenclature (naming and orientation). Chromosome names specify homologous group (1 to 7) and sub genome (A/C/D). Chromosomes were oriented in such a way that proximal regions of homoeologous chromosomes are collinear. PepsiCo would like to thank Dr. Martin Mascher for updating the v2 pseudomolecule orientation and naming in accordance with PanOat.Future release of data:PepsiCo is currently working to annotate a set of PacBio transcripts. After annotation is complete researchers will be able to access these data as a track on the genome browser. Additional files including a GFF, ORF nucleotide fasta, and ORF translated peptide fasta will also be available via the download site on GrainGenes. These data are anticipated to be available mid-May 2021. Additionally, Dr. Nick Tinker has mapped relevant SNP markers to v2, which will be available as a track on the genome browser, GFF for download, and visualized as CMaps physical maps.Use:Researchers are free to use and publish with all OT3098 genomic resources shared on GrainGenes. Given that no direct publication will be submitted for this individual genome assembly we choose to opt out of the Toronto Agreement, so researchers can freely use these resources as they become available:• Genome Browser: https://wheat.pw.usda.gov/jb?data=/ggds/oat-ot3098v2-pepsico• BLAST: https://wheat.pw.usda.gov/blast/ (select “PepsiCo OT3098 Hexaploid Oat v2pseudomolecules (2021)” under the “Oat Selections”)• Data Download: https://wheat.pw.usda.gov/GG3/content/pepsico-oat-oc3098-v2-files-2021Citation:If you use these resources, please cite:"Avena sativa – OT3098 v2, PepsiCo, https://wheat.pw.usda.gov/jb?data=/ggds/oat-ot3098v2-pepsico”
PepsiCo releases version 2 of OT3098 reference genomeBy: Dr. Mandy Waters, PepsiCoMethod comparison between OT3098 v1 and v2:Written by Dr. Kevin Fengler, Corteva AgrisciencesThe v1 contig assembly was built from 35x PacBio HiFi (read N50 = 17.3 kb, min predicted accuracy > .992) using the HiCanu assembler which resulted in 1,890 contigs with a contig N50= 30.3 Mb and a total assembly size of 10.97 Gb. The contigs were then scaffolded with BioNano genome maps (450 maps, map N50= 98.5, total length = 11.2 Gb) on the BioNano Access platform to create hybrid scaffolds (n= 100, scaffold N50 = 293.9 Mb, total length = 10.84 Gb). Hybrid scaffolds were tentatively placed into pseudomolecules using oat consensus markers. The final ordering of scaffolds was refined using HiC data and contact map visualization using JuiceBox and the Juicer tools.The v2 release is based on an improved contig assembly using the same PacBio HiFi dataset, but with the hifiasm assembler. The v2 assembly exhibited a significant improvement in contiguity (1,343 contigs, contig N50 = 71 Mb, total size= 10.75 Gb). This assembly was similarly scaffolded with the same BioNano maps as v1, however, the improved contigs significantly improved the contiguity of the scaffolds as well (84 scaffolds, scaffold N50= 374 kb, total size = 10.83 Gb). The v2 assembly was manually curated to resolve overlapping contigs that were not addressed during BioNano hybrid scaffolding (this was not done for v1). Scaffolds were placed into pseudomolecules using the v1 chromosomes as a guide and were validated by HiC contact map visualization as before.Nomenclature, orientation, and stats:Chromosomes in v1 were oriented such that the short arm was on top. The OT3098 v2 pseudomolecules use chromosome names and orientations adopted by PanOat in an effort to maintain consistency with future assemblies. The PanOat consortium is currently constructing chromosome-scale reference for multiple oat (Avena sativa) genotypes and has therefore adopted a chromosome nomenclature (naming and orientation). Chromosome names specify homologous group (1 to 7) and sub genome (A/C/D). Chromosomes were oriented in such a way that proximal regions of homoeologous chromosomes are collinear. PepsiCo would like to thank Dr. Martin Mascher for updating the v2 pseudomolecule orientation and naming in accordance with PanOat.Future release of data:PepsiCo is currently working to annotate a set of PacBio transcripts. After annotation is complete researchers will be able to access these data as a track on the genome browser. Additional files including a GFF, ORF nucleotide fasta, and ORF translated peptide fasta will also be available via the download site on GrainGenes. These data are anticipated to be available mid-May 2021. Additionally, Dr. Nick Tinker has mapped relevant SNP markers to v2, which will be available as a track on the genome browser, GFF for download, and visualized as CMaps physical maps.Use:Researchers are free to use and publish with all OT3098 genomic resources shared on GrainGenes. Given that no direct publication will be submitted for this individual genome assembly we choose to opt out of the Toronto Agreement, so researchers can freely use these resources as they become available:• Genome Browser: https://wheat.pw.usda.gov/jb?data=/ggds/oat-ot3098v2-pepsico• BLAST: https://wheat.pw.usda.gov/blast/ (select “PepsiCo OT3098 Hexaploid Oat v2pseudomolecules (2021)” under the “Oat Selections”)• Data Download: https://wheat.pw.usda.gov/GG3/content/pepsico-oat-oc3098-v2-files-2021Citation:If you use these resources, please cite:"Avena sativa – OT3098 v2, PepsiCo, https://wheat.pw.usda.gov/jb?data=/ggds/oat-ot3098v2-pepsico”