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Background  Asexual seed formation (apomixis) has been observed in diverse plant families but is rare in crop plants. The generation of apomictic crops would revolutionize agriculture, as clonal seed production provides a low cost and efficient way to produce hybrid seed.  Hieracium  (Asteraceae) is a model system for studying the molecular components of gametophytic apomixis (asexual seed reproduction).    Results  In this study, a reference transcriptome was produced from apomictic  Hieracium  undergoing the key apomictic events of apomeiosis, parthenogenesis and autonomous endosperm development. In addition, transcriptome sequences from pre-pollination and post-pollination stages were generated from a  loss of parthenogenesis  ( lop ) mutant accession that exhibits loss of parthenogenesis and autonomous endosperm development. The transcriptome is composed of 147,632 contigs, 50% of which were annotated with orthologous genes and their probable function. The transcriptome was used to identify transcripts differentially expressed during apomictic and pollination dependent  (lop)  seed development. Gene Ontology enrichment analysis of differentially expressed transcripts showed that an important difference between apomictic and pollination dependent seed development was the expression of genes relating to epigenetic gene regulation. Genes that mark key developmental stages, i.e. aposporous embryo sac development and seed development, were also identified through their enhanced expression at those stages.    Conclusion  The production of a comprehensive floral reference transcriptome for  Hieracium  provides a valuable resource for research into the molecular basis of apomixis and the identification of the genes underlying the  LOP  locus.    Electronic supplementary material  The online version of this article (10.1186/s12870-018-1423-1) contains supplementary material, which is available to authorized users.

Comparative transcriptome analysis of the wild-type model apomict Hieracium praealtum and its loss of parthenogenesis (lop) mutant