Quantitative methods in like-for-like comparative analyses of Aphanorrhegma (Physcomitrella) patens phyllid development

Introduction. Aphanorrhegma (Physcomitrella) patens (Hedw.) Lindb. is an attractive model system for comparative analyses of leaf development because it evolved leaves (phyllids) independently to flowering plants, yet its genome contains homologues of many gene families that regulate angiosperm leaf development. In addition, A. patens phyllids are primarily a single cell layer thick, making it simple to identify the cellular basis of defects that perturb shape. Identification of gene functions in shape determination depends on like-forlike comparison of mutant versus wild-type plants. Key results. Here we show that, if heteroblasty is not perturbed, such comparisons should use phyllid L13 or above in the heteroblastic series, and fully expanded phyllids above P7 in the developmental series. Using a quantitative approach, we show that heteroblastic size variation reflects differences in cell proliferation rather than cell size and shape. A comparison of control to pinA pinB mutant phyllid development verifies that PIN proteins promote cell proliferation and suppress expansion to determine phyllid shape. Conclusion. The results and approach that we have generated will be applicable to any study of A. patens phyllid development to reveal the cellular basis of phyllid size and shape variations.We thank The Gatsby Charitable Foundation (GAT2962), The Royal Society (UF130563) and BBSRC (BB/L00224811) for funding our wor

CLAVATA was a genetic novelty for the morphological innovation of 3D growth in land plants

Sexually deceptive orchids of the genus Ophrys may rapidly evolve by adaptation to pollinators. However, understanding of the genetic basis of potential changes and patterns of relationships is hampered by a lack of genomic information. We report the complete plastid genome sequences of Ophrys iricolor and O. sphegodes, representing the two most species-rich lineages of the genus Ophrys. Both plastomes are circular DNA molecules (146754 bp for O. sphegodes and 150177 bp for O. iricolor) with the typical quadripartite structure of plastid genomes and within the average size of photosynthetic orchids. 213 Simple Sequence Repeats (SSRs) (31.5% polymorphic between O. iricolor and O. sphegodes) were identified, with homopolymers and dipolymers as the most common repeat types. SSRs were mainly located in intergenic regions but SSRs located in coding regions were also found, mainly in ycf1 and rpoC2 genes. The Ophrys plastome is predicted to encode 107 distinct genes, 17 of which are completely duplicated in the Inverted Repeat regions. 83 and 87 putative RNA editing sites were detected in 25 plastid genes of the two Ophrys species, all occurring in the first or second codon position. Comparing the rate of nonsynonymous (dN) and synonymous (dS) substitutions, 24 genes (including rbcL and ycf1) display signature consistent with positive selection. When compared with other members of the orchid family, the Ophrys plastome has a complete set of 11 functional ndh plastid genes, with the exception of O. sphegodes that has a truncated ndhF gene. Comparative analysis showed a large co-linearity with other related Orchidinae. However, in contrast to O. iricolor and other Orchidinae, O. sphegodes has a shift of the junction between the Inverted Repeat and Small Single Copy regions associated with the loss of the partial duplicated gene ycf1 and the truncation of the ndhF gene. Data on relative genomic coverage and validation by PCR indicate the presence, with a different ratio, of the two plastome types (i.e. with and without ndhF deletion) in both Ophrys species, with a predominance of the deleted type in O. sphegodes. A search for this deleted plastid region in O. sphegodes nuclear genome shows that the deleted region is inserted in a retrotransposon nuclear sequence. The present study provides useful genomic tools for studying conservation and patterns of relationships of this rapidly radiating orchid genus