Maize Genomics Resource
At the University of Georgia
JBrowse Track Descriptions
Gene Annotation
- Loci and gene models are from the AGPv4 annotation (Jiao et al., 2017).
- MSU representative gene models - Isoform with the longest CDS for each locus.
Legacy Gene Annotation
- 5b+ gene models aligned to the AGPv4 assembly
Maize Developmental RNA-Seq Atlas
- RNA-seq reads from Stelpflug et al. (2016) were aligned to the v4 genome assembly with TopHat2 (v2.0.14) (Kim et al., 2013) and Bowtie2 (v2.2.3) (Langmead and Salzberg, 2012).
Maize HapMap
- HapMap 3 variants from Bukowski et al. - Construction of the third-generation Zea mays haplotype map - 2018
Maize Stress RNA-seq Atlas
- RNA-seq reads from five abiotic and biotic stress experiments (see here for complete list) were aligned to the v4 genome assembly with TopHat2 (v2.0.14) (Kim et al., 2013) and Bowtie2 (v2.2.3) (Langmead and Salzberg, 2012).
Maize Variants
- Variants were called according to Hirsch et al. (2014) and according to Diepenbrock et al. (2017).
Protein Searches
- The best match from the Arabidopsis proteome (TAIR10), Brachypodium distachyon proteome (v3), Rice proteome (RAGPv7), Sorghum bicolor proteome (v3), and switchgrass (v4) proteome using BLASTP.
Reference Sequence
- Sequence of version 4 of the B73 genome assembly (Jiao et al., 2017).
TE Annotation
- B73 AGPv4 TE annotation downloaded from Gramene