B104 (beta) genome assembly and annotation

In the interest of the maize research community, the Iowa State Transformation Facility and Lawrence-Dill Plant Informatics and Computation Lab in collaboration with MaizeGDB has released a beta-version of the B104 maize genome and structural annotations prior to scientific publication in accordance with guidelines set forth by the Toronto agreement (http://www.nature.com/nature/journal/v461/n7261/full/461168a.html) for prepublication data sharing (Nature. 2009 461:168). The above groups reserve the first right to publish on the available B104 data including but not limited to whole-genome comparisons, genes, structural annotations, functional annotations, and genome-wide association studies. The group also reserves the right to the first opportunity to improve this sequence and its annotations for a full official genome release (version 1; anticipated release December 2017). Under the Toronto agreement, researchers can use the B104 sequence and annotation to study individual or small sets of genes and localized regions of the genome. Any redistribution of these data should include the full text of the data use policy. Assembly Note: The B104 genome was sequenced using Illumina paired end sequencing on HiSeq2000 at raw read coverage of 50X with read length of 101 bp and insert size 250 bp. Trimmed reads were assembled using a reference- guided assembly approach with B73 reference sequence (AGPv2 5b pseudo molecules). The reads were mapped to the B73 reference, consensus sequences were generated and gaps were filled. All paired end reads were mapped back to the gap-filled scaffolds to identify the regions with abnormal links and corresponding scaffolds were broken from those regions. Unmapped reads were assembled using a de novo approach and scaffolds were added to the final assembly. B104 Gene Models: B104 (beta) gene models were developed by the Lawrence-Dill Plant Informatics Lab in collaboration with MaizeGDB and Dow AgroSciences, and made available through www.maizegdb.org. Genes were annotated using MAKER-P Pipeline, using both evidence-based approach (cDNA and EST data) and an ab initio approach. For evidence based prediction, transcriptome assemblies of diverse tissue types from B104 and other maize lines (B73, Miami white, Mo17, OH43, B97, W22, A188), full length cDNA sequences and annotated B73 proteins from NCBI, Arabidopsis thaliana, Oryza sativa japonica and other plant proteins from Uniprot were used. For ab initio predictions, AUGUSTUS and SNAP gene predictors were used. Gene models are named as recommended by the Maize Nomenclature Committee.

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