Dynamic transcription of all genes in Triticum urartu endosperms throughout grain-filling stages

Endosperms (with the embryo, aleurone, seed coat, and pericarp removed) at 5, 10, 15, 20, and 25 DPAs of the T. urartu accession PI 428198 were used for RNA-Seq analysis. Each sample had three independent biological replicates. The total RNA of endosperms was isolated and a library with an insert length of ~350 bp was sequenced using the Illumina HiSeq 2000 (San Diego, CA, USA). An integrated reference sequence of T. urartu PI 428198 was prepared by combining the annotated gene set (ftp://ftp.ensemblgenomes.org/pub/plants/release3 9/fasta/triticum_urartu) with cloned low-molecule-weight glutenin subunit genes and gliadin genes after gene redundancy removal. The relative transcript abundance of seed storage protein genes and the 41,507 predicted genes from genome sequences were calculated using the unique aligned reads as the expected number of fragments per kilobase of the transcript sequence per million base pairs sequenced (FPKM). Overall design: Elucidate the transcription dynamics of each gene in Triticum urartu endosperms throughout grain-filling stages using RNA-Seq analysis