Whole Genome Assembly (v2.0) and Annotation (v2.2) of Setaria italica - cv. Yugu1 (JGI)
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| Name | Whole Genome Assembly (v2.0) and Annotation (v2.2) of Setaria italica - cv. Yugu1 (JGI) |
|---|---|
| Description | Assembly Setaria italica cv. Yugu1 was sequenced and assembled by the Joint Genome Institute (JGI) in collaboration with community researchers. Sanger sequencing was performed on whole-genome shotgun clone libraries having different insert sizes. Reads totalling 8.29x coverage were assembled with Arachne giving scaffolds that were arranged predominantly into nine pseudomolecules. AnnotationProtein-coding genes were predicted using the standard JGI plant gene annotation pipeline. They used ESTs and homologous peptides from Arabidopsis, Brachypodium, rice and sorghum, mapped with BLAT alignments of PASA and EXONERATE, with GenomeScan, FGENESH+ and FGENESH_EST. BACs and fosmids were annotated using AUGUSTUS with maize parameters to predict gene models, which were compared to GenBank, TAIR and IRGSP/RAP proteins and manually inspected. Gene models were validated with RNA-seq data. Source : Phytozome |
| Program, Pipeline, Workflow or Method Name | Assembly & annotation, performed by JGI |
| Program Version | v 2.2 |
| Algorithm | |
| Date Performed | Sunday, January 13, 2019 |
| Data Source |
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