Shaping the Organ: A Biologist Guide to Quantitative Models of Plant Morphogenesis

Organ morphogenesis is the process of shape acquisition initiated with a small reservoir of undifferentiated cells. In plants, morphogenesis is a complex endeavor that comprises a large number of interacting elements, including mechanical stimuli, biochemical signaling, and genetic prerequisites. Because of the large body of data being produced by modern laboratories, solving this complexity requires the application of computational techniques and analyses. In the last two decades, computational models combined with wet-lab experiments have advanced our understanding of plant organ morphogenesis. Here, we provide a comprehensive review of the most important achievements in the field of computational plant morphodynamics. We present a brief history from the earliest attempts to describe plant forms using algorithmic pattern generation to the evolution of quantitative cell-based models fueled by increasing computational power. We then provide an overview of the most common types of “digital plant” paradigms, and demonstrate how models benefit from diverse techniques used to describe cell growth mechanics. Finally, we highlight the development of computational frameworks designed to resolve organ shape complexity through integration of mechanical, biochemical, and genetic cues into a quantitative standardized and user-friendly environment.

Topological morphogenesis of neuroepithelial organoids

Animal organs exhibit complex topologies involving cavities and tubular networks, which underlie their form and function. However, how topology emerges during organ morphogenesis remains elusive. Here, we combine tissue reconstitution and quantitative microscopy to show that trans and cis epithelial fusion govern tissue topology and shape. These two modes of topological transitions can be regulated in neuroepithelial organoids, leading to divergent topologies. The morphological space can be captured by a single control parameter which is analogous to the reduced Gaussian rigidity of an epithelial surface. Finally, we identify a pharmacologically accessible pathway that regulates the frequency of trans and cis fusion, and demonstrate the control of organoid topology and shape. The physical principles uncovered here provide fundamental insights into the self-organization of complex tissues.

Genome-wide identification and expression profiling of the PIN auxin transporter gene family in L. chinense

BackgroundThe genus Liriodendron is ancient and contains only two species, L. chinense and L. tulipifera. These two Liriodendron sister species, with a typical intercontinental discontinuous distribution in east Asia (L. chinense) and eastern North America (L. tulipifera), have great scientific value for paleobotany systematics. L. chinense is now recognized as an endangered species partially due to its low natural settling rate. In order to improve our understanding of how this species develops and grows and contribute to protecting this valuable relict species from extinction, it is necessary to explore the mechanisms underlying organ morphogenesis and embryonic development, in which auxin plays an important role. The auxin efflux carrier PIN-FORMED (PIN) proteins are required for the polar transport of auxin between cells through their asymmetric distribution on the plasma membrane, thus mediating the differential distribution of auxin in plants and, finally, affecting plant growth and developmental processes.ResultsIn this study, 11 PIN genes were identified in the L. chinense genome. The structural characteristics and evolutionary status of LcPIN genes were thoroughly investigated and interpreted combining physicochemical property analysis, evolutionary analysis, gene structure analysis, chromosomal localization, etc. In addition, motif sequences were used to predict possible functional sites. Further qRT-PCR experiments and transcriptome data analysis indicated that LcPIN genes may potentially play an important role during organ development and somatic embryogenesis in Liriodendron. For example, specific expression of LcPIN3 and LcPIN6a at different developmental stages of stamens and petals suggests their involvement in the development of these organs.ConclusionThis study provides a foundation for further genetic and functional analyses of PIN-mediated auxin patterning during organ morphogenesis and embryogenesis in L. chinense.