Publications

2021
Edwards MB, Choi GPT, Derieg NJ, Min Y, Diana AC, Hodges SA, Mahadevan L, Kramer EM, Ballerini ES. Genetic architecture of floral traits in bee- and hummingbird-pollinated sister species of Aquilegia (columbine). Evolution. 2021;75 (9) :2197–2216. Publisher's Version evolut2197.pdf
2018
Filiault DL, Ballerini ES, Mandáková T, Aköz G, Derieg NJ, Schmutz J, Jenkins J, Grimwood J, Shu S, Hayes RD, et al. The Aquilegia genome provides insight into adaptive radiation and reveals an extraordinarilypolymorphic chromosome with a unique history. eLife. 2018;10.7554/eLife.36426. Publisher's Version elife-36426-v2.pdf
2017
Min Y, Kramer EM. The Aquilegia JAGGED homolog promotes proliferation of adaxial cell types in both leaves and stems. New Phytologist. 2017;216 :536-548. nph.14282.pdf
Sharma B, Kramer EM. Aquilegia B gene homologs promote petaloidy of the sepals and maintenance of the C domain boundary. EvoDevo. 2017;8 :22. s13227-017-0085-7.pdf
Qin G, Xu C, Ming R, Tang H, Guyot R, Kramer EM, Hu Y, Yi X, Qi Y, Xu X, et al. The pomegranate (Punica granatum L.) genome and the genomics of punicalagin biosynthesis. Plant Journal. 2017;doi:10.1111/tpj.13625.Abstract

Pomegranate (Punica granatum L.) is a perennial fruit crop grown since ancient times that has been planted worldwide and is known for its functional metabolites, particularly punicalagins. We have sequenced and assembled the pomegranate genome with 328 Mb anchored into nine pseudo-chromosomes and annotated 29 229 gene models. A Myrtales lineage-specific whole-genome duplication event was detected that occurred in the common ancestor before the divergence of pomegranate and Eucalyptus. Repetitive sequences accounted for 46.1% of the assembled genome. We found that the integument development gene INNER NO OUTER (INO) was under positive selection and potentially contributed to the development of the fleshy outer layer of the seed coat, an edible part of pomegranate fruit. The genes encoding the enzymes for synthesis and degradation of lignin, hemicelluloses and cellulose were also differentially expressed between soft- and hard-seeded varieties, reflecting differences in their accumulation in cultivars differing in seed hardness. Candidate genes for punicalagin biosynthesis were identified and their expression patterns indicated that gallic acid synthesis in tissues could follow different biochemical pathways. The genome sequence of pomegranate provides a valuable resource for the dissection of many biological and biochemical traits and also provides important insights for the acceleration of breeding. Elucidation of the biochemical pathway(s) involved in punicalagin biosynthesis could assist breeding efforts to increase production of this bioactive compound.

KEYWORDS:  adaption; genome; pomegranate; punicalagin biosynthesis; system evolution

Holappa LD, Ronald PC, Kramer EM. Evolutionary analysis of Snf1-Related Protein Kinase2 (SnRK2) and Calcium Sensor (SCS) gene lineages, and dimerization of rice homologs, suggest deep biochemical conservation across angiosperms. . Frontiers in Plant Science. 2017;8 :396. fpls-08-00395.pdf
2015
Kramer EM. Stranger in a strange land: The utility and interpretation of heterologous expression. Frontiers Plant Science. 2015;6 :734. Publisher's Version fpls-06-00734.pdf
Yant L, Collani S, Puzey J, Levy C, Kramer EM. Molecular basis for three-dimensional elaboration of the Aquilegia petal spur. Proc Biol Sci. 2015;282 :20142778.Abstract

By enforcing specific pollinator interactions, Aquilegia petal nectar spurs maintain reproductive isolation between species. Spur development is the result of three-dimensional elaboration from a comparatively two-dimensional primordium. Initiated by localized, oriented cell divisions surrounding the incipient nectary, this process creates a pouch that is extended by anisotropic cell elongation. We hypothesized that the development of this evolutionary novelty could be promoted by non-mutually exclusive factors, including (i) prolonged, KNOX-dependent cell fate indeterminacy, (ii) localized organ sculpting and/or (iii) redeployment of hormone-signalling modules. Using cell division markers to guide transcriptome analysis of microdissected spur tissue, we present candidate mechanisms underlying spur outgrowth. We see dynamic expression of factors controlling cell proliferation and hormone signalling, but no evidence of contribution from indeterminacy factors. Transcriptome dynamics point to a novel recruitment event in which auxin-related factors that normally function at the organ margin were co-opted to this central structure. Functional perturbation of the transition between cell division and expansion reveals an unexpected asymmetric component of spur development. These findings indicate that the production of this three-dimensional form is an example of organ sculpting via localized cell division with novel contributions from hormone signalling, rather than a product of prolonged indeterminacy.

yant_et_al_proc_biol_sci._2015.pdf
2014
Nikolov LA, Staedler YM, Manickam S, Schonenberger J, Endress PK, Kramer EM, Davis CC. Floral structure and development in Rafflesiaceae with emphasis on their exceptional gynoecia. Am J Bot. 2014;101 :225-43.Abstract

PREMISE OF THE STUDY: The holoparasitic plant family Rafflesiaceae include the world's largest flowers. Despite their iconic status, relatively little is known about the morphology and development of their flowers. A recent study clarified the organization of the outer (sterile) floral organs, surprisingly revealing that their distinctive floral chambers arose via different developmental pathways in the two major genera of the family. Here, we expand that research to investigate the structure and development of the reproductive organs of Rafflesiaceae. METHODS: Serial sectioning, scanning electron microscopy, and x-ray tomography of floral buds were employed to reconstruct the structure and development of all three Rafflesiaceae genera. KEY RESULTS: Unlike most angiosperms, which form their shoot apex from the primary morphological surface, the shoot apex of Rafflesiaceae instead forms secondarily via internal cell separation (schizogeny) along the distal boundary of the host-parasite interface. Similarly, the radially directed ovarial clefts of the gynoecium forms via schizogeny within solid tissue, and no carpels are initiated from the floral apex. CONCLUSIONS: The development of the shoot apex and gynoecium of Rafflesiaceae are highly unusual. Although secondary formation of the morphological surface from the shoot apex has been documented in other plant groups, secondary derivation of the inner gynoecium surface is otherwise unknown. Both features are likely synapomorphies of Rafflesiaceae. The secondary derivation of the shoot apex may protect the developing floral shoot as it emerges from within dense host tissue. The secondary formation of the ovarial clefts may generate the extensive placental area necessary to produce hundreds of thousands of ovules.

nikolov_et_al_am_j_bot_2014.pdf

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