Dynamic coding and noncoding RNA interactions coordinate gene expression during meiosis in wheat

We present a high-resolution network of gene expression during meiosis and its regulatory control elements in polyploid wheat. MeioCapture method (Shunmugam et al. 2018 BMC Plant Biology 18: 293) was used for isolating high-purity sporogenous archesporial columns of synchronized male meiocytes from wheat anthers in different meiotic stages. Total RNA extracted from three independent biological replicates per developmental stage of the meiocytes, as well as vegetative flag leaf, young leaves, and reproductive anthers and pollen, was sequenced using Illumina platform, generating 548 million paired-end short mRNA reads. Filtered reads were aligned to the wheat reference genome (IWGSC v1.0) using STAR. Transcript abundance was estimated using the RSEM (v1.3.3) and the IWGSC v1.1 annotation, and read counts and transcripts per million (TPM) values that normalize counts to a consistent number per library (1 million) to facilitate the comparison of relative expression across various samples were generated. Overall design: Gene expression analysis of meiotic stages, including pre-meiotic G2 (Pm), the sub-stages of prophase I [termed leptotene, zygotene, pachytene, and diplotene/diakinesis], metaphase I and metaphase II, as well as vegetative flag leaf and young leaves, and reproductive anthers and pollen