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

Abstract

BackgroundThe 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.ResultsA 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.ConclusionsOur 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.

Chloroplast Genome Differences between Asian and American Equisetum arvense (Equisetaceae) and the Origin of the Hypervariable trnY-trnE Intergenic Spacer

“…5), suggested that the original source sequence was the trnY - trnE IGS. The 19 bp sequence found in this study is 6 bp longer than the trnY anticodon partial sequence proposed as the repeating unit origin [29]. Additionally, the 19 bp sequence had higher similarities than the 13 bp consensus sequence of the trnY anticodon loop region suggested in previous studies [29].…”

“…The lengths of trnY-trnE IGS usually less than I kb in other monilophytes [28]. This unusual trnY-trnE IGS length was also detected in E. ramosissimum , and this unique characteristic may be attributable to a repetition of the trnY anticodon loop [29].…”

Characterization and Phylogenetic Analysis of Chloroplast and Mitochondria Genomes from the Antarctic Polytrichaceae Species Polytrichum juniperinum and Polytrichum strictum

“…According to Sheveleva et al [56], the presence of rpoA gene is quite variable from species to species. The membrane thylakoid gene ycf66 is absent in A. formosae [30,57,58] but remains more stable in Polytrichaceae than in ferns [59]. Only two species of bryophytes are currently known to lack the petN gene [20,21], part of the photosynthetic cytochrome b6lf complex in the chloroplast, and it is possible, according Oliver et al, that another nuclear-encoded gene product performs the same function as a subunit of the complex [20].…”

Evolution from the Prokaryotic to the Higher Plant Chloroplast Signal Recognition Particle: The Signal Recognition Particle RNA Is Conserved in Plastids of a Wide Range of Photosynthetic Organisms

“…In P. patens, the petN-trnC region is clustered with pet genes due to an inversion of a large part of the plastome (Sugiura et al, 2003). Such inversions leading to structural rearrangements of the gene order have also been described for plastid genomes of monilophytes (Gao et al, 2011).…”