New NAM gene expression tracks available on the Maize PanGenome Browser

Submitted by marcela.karey on Wed, 03/30/2022 - 16:29

Gene expression (RNA-Seq) data generated for 26 maize NAM founder genomes recently assembled by the NAM Consortium (see Hufford et al, 2021) is now available in the Maize PanGenome browser.

Plants were either field- or greenhouse-grown, and tissue was collected as follows:

  • Embryo, 16 days after pollination (16DAP_embryo)
  • Endosperm, 16 days after pollination (16DAP_endosperm)
  • Meiotic tassel (V18_tassel)
  • Meiotic ear (V18_ear)
  • Pre-pollination anther at reproductive stage 1 (R1_anther)
  • Root, 8 days after sowing (8DAS_root)
  • Shoot, 8 days after sowing (8DAS_shoot)
  • Vegetative leaf 11 (V11_leaf)
  • Vegetative base 11 (V11_base)
  • Vegetative middle 11 (V11_middle)
  • Vegetative tip 11 (V11_tip)

RNA extractions were done using the QIAGEN RNeasy plant mini-kit following the manufacturers' suggested protocol. RNA-seq reads were mapped using STAR. The reads were used to generate the transcriptomes that went toward the evidence-based gene model prediction annotations. Bigwig files were generated using bedtools genomecov -split -scale 1.0 followed by kentUtils bedGraphToBigWig.

For more information on methods see Hufford et al (2021) or the gitHub repository for the project's gene prediction pipeline: https://github.com/HuffordLab/NAM-genomes.

Instructions to visualize this expression data for the lipoxygenease 9 (lox9, Zm00001eb005920, Zm00001d027893, GRMZM2G017616) exemplary gene in the B73 reference genome are provided in the Maize PanGenome User Guide.

 

Links:

 

Reference:

Hufford, Matthew B., Arun S. Seetharam, Margaret R. Woodhouse, Kapeel M. Chougule, Shujun Ou, Jianing Liu, William A. Ricci, et al. 2021. “De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes.” Science 373(6555): 655-662. doi: 10.1126/science.abg5289

RNA-Seq data generated by the NAM Consortium for the 26 maize NAM genomes. See Hufford et al (2021)

Graphic configuration options (click on the spider gear) and track descriptions (click on the letter "i" to the right of a track name.