Decoding the complexity of coding and non-coding RNAs across maize anther development at the isoform level

Anther is a key male reproductive organ that is essential for the plant life cycle, from the sporophyte to the gametophyte generation. To explore the isoform-level transcriptional landscape of developing anthers in maize (Zea mays L.), we analyzed Iso-Seq data from anthers collected at 10 developmental stages, together with strand-specific RNA-seq, CAGE-seq, and PAS-seq data. Of the 152,026 high-confidence full-length isoforms identified, 68.8% have not been described; these include 22,365 isoforms that originate from previously unannotated loci and 82,167 novel isoforms that originate from annotated protein-coding genes. Using our newly developed strategy to detect dynamic expression patterns of isoforms, we identified 13,899 differentially variable regions (DVRs); surprisingly, 1275 genes contain more than two DVRs, revealing highly efficient utilization of limited genic regions. We identified 7876 long non-coding RNAs (lncRNAs) from 4098 loci, most of which were preferentially expressed during cell differentiation and meiosis. We also detected 371 long-range interactions involving intergenic lncRNAs (lincRNAs); interestingly, 243 were lincRNA–gene ones, and the interacting genes were highly expressed in anthers, suggesting that many potential lncRNA regulators of key genes are required for anther development. This study provides valuable resources and fundamental information for studying the essential transcripts of key genes during anther development.