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Background  The  rpoB - psbZ  (BZ) region of some fern plastid genomes (plastomes) has been noted to go through considerable genomic changes. Unraveling its evolutionary dynamics across all fern lineages will lead to clarify the fundamental process shaping fern plastome structure and organization.    Results  A total of 24 fern BZ sequences were investigated with taxon sampling covering all the extant fern orders. We found that: (i) a tree fern  Plagiogyria japonica  contained a novel gene order that can be generated from either the ancestral  Angiopteris  type or the derived  Adiantum  type via a single inversion; (ii) the  trnY - trnE  intergenic spacer (IGS) of the filmy fern  Vandenboschia radicans  was expanded 3-fold due to the tandem 27-bp repeats which showed strong sequence similarity with the anticodon domain of  trnY ; (iii) the  trnY - trnE  IGSs of two horsetail ferns  Equisetum ramosissimum  and  E. arvense  underwent an unprecedented 5-kb long expansion, more than a quarter of which was consisted of a single type of direct repeats also relevant to the  trnY  anticodon domain; and (iv)  ycf66  has independently lost at least four times in ferns.    Conclusions  Our results provided fresh insights into the evolutionary process of fern BZ regions. The intermediate BZ gene order was not detected, supporting that the  Adiantum  type was generated by two inversions occurring in pairs. The occurrence of  Vandenboschia  27-bp repeats represents the first evidence of partial tRNA gene duplication in fern plastomes. Repeats potentially forming a stem-loop structure play major roles in the expansion of the  trnY - trnE  IGS.

Evolution of the rpoB-psbZ region in fern plastid genomes: notable structural rearrangements and highly variable intergenic spacers