Size Does Matter: Staging of Silene latifolia Floral Buds for Transcriptome Studies

Characterization of floral morphoanatomy and identification of marker genes preferentially expressed during specific stages of cotton flower development

Characterization of anther and ovule developmental programs and expression analyses of stage-specific floral marker genes in Gossypium hirsutum allowed to build a comprehensive portrait of cotton flower development before fiber initiation. Gossypium hirsutum is the most important cotton species that is cultivated worldwide. Although cotton reproductive development is important for fiber production, since fiber is formed on the epidermis of mature ovules, cotton floral development remains poorly understood. Therefore, this work aims to characterize the cotton floral morphoanatomy by performing a detailed description of anther and ovule developmental programs and identifying stage-specific floral marker genes in G. hirsutum. Using light microscopy and scanning electron microscopy, we analyzed anther and ovule development during 11 stages of flower development. To better characterize the ovule development in cotton, we performed histochemical analyses to evaluate the accumulation of phenolic compounds, pectin, and sugar in ovule tissues. After identification of major hallmarks of floral development, three key stages were established in G. hirsutum floral development: in stage 1 (early-EF), sepal, petal, and stamen primordia were observed; in stage 2 (intermediate-IF), primordial ovules and anthers are present, and the differentiating archesporial cells were observed, marking the beginning of microsporogenesis; and in stage 6 (late-LF), flower buds presented initial anther tapetum degeneration and microspore were released from the tetrad, and nucellus and both inner and outer integuments are developing. We used transcriptome data of cotton EF, IF and LF stages to identify floral marker genes and evaluated their expression by real-time quantitative PCR (qPCR). Twelve marker genes were preferentially expressed in a stage-specific manner, including the putative homologs for AtLEAFY, AtAPETALA 3, AtAGAMOUS-LIKE 19 and AtMALE STERILITY 1, which are crucial for several aspects of reproductive development, such as flower organogenesis and anther and petal development. We also evaluated the expression profile of B-class MADS-box genes in G. hirsutum floral transcriptome (EF, IF, and LF). In addition, we performed a comparative analysis of developmental programs between Arabidopsis thaliana and G. hirsutum that considered major morphoanatomical and molecular processes of flower, anther, and ovule development. Our findings provide the first detailed analysis of cotton flower development.

Pas de deux: An Intricate Dance of Anther Smut and Its Host

The successful interaction between pathogen/parasite and host requires a delicate balance between fitness of the former and survival of the latter. To optimize fitness a parasite/pathogen must effectively create an environment conducive to reproductive success, while simultaneously avoiding or minimizing detrimental host defense response. The association between Microbotryum lychnidis-dioicae and its host Silene latifolia serves as an excellent model to examine such interactions. This fungus is part of a species complex that infects species of the Caryophyllaceae, replacing pollen with the fungal spores. In the current study, transcriptome analyses of the fungus and its host were conducted during discrete stages of bud development so as to identify changes in fungal gene expression that lead to spore development and to identify changes associated with infection in the host plant. In contrast to early biotrophic phase stages of infection for the fungus, the latter stages involve tissue necrosis and in the case of infected female flowers, further changes in the developmental program in which the ovary aborts and a pseudoanther is produced. Transcriptome analysis via Illumina RNA sequencing revealed enrichment of fungal genes encoding small secreted proteins, with hallmarks of effectors and genes found to be relatively unique to the Microbotryum species complex. Host gene expression analyses also identified interesting sets of genes up-regulated, including those involving stress response, host defense response, and several agamous-like MADS-box genes (AGL61 and AGL80), predicted to interact and be involved in male gametophyte development.

Transcriptional analysis of mating and pre-infection stages of the anther smut, Microbotryum lychnidis-dioicae

Microbotryum lychnidis-dioicae is an obligate biotrophic parasite of the wildflower species Silene latifolia. This dikaryotic fungus, commonly known as an anther smut, requires that haploid, yeast-like sporidia of opposite mating types fuse and differentiate into dikaryotic hyphae that penetrate host tissue as part of the fungal life cycle. Mating occurs under conditions of cool temperatures and limited nutrients. Further development requires host cues or chemical mimics, including a variety of lipids, e.g. phytols. To identify global changes in transcription associated with developmental shifts, RNA-Seq was conducted at several in vitro stages of fungal propagation, i.e. haploid cells grown independently on rich and nutrient-limited media, mated cells on nutrient-limited media as well as a time course of such mated cells exposed to phytol. Comparison of haploid cells grown under rich and nutrient-limited conditions identified classes of genes probably associated with general nutrient availability, including components of the RNAi machinery. Some gene enrichment patterns comparing the nutrient-limited and mated transcriptomes suggested gene expression changes associated with the mating programme (e.g. homeodomain binding proteins, secreted proteins, proteins unique to M. lychnidis-dioicae¸ multicopper oxidases and RhoGEFs). Analysis for phytol treatment compared with mated cells alone allowed identification of genes likely to be involved in the dikaryotic switch (e.g. oligopeptide transporters). Gene categories of particular note in all three conditions included those in the major facilitator superfamily, proteins containing PFAM domains of the secretory lipase family as well as proteins predicted to be secreted, many of which have the hallmarks of fungal effectors with potential roles in pathogenicity.

Defense peptide repertoire of Stellaria media predicted by high throughput next generation sequencing

Being perfectly adapted to diverse environments, chickweed (Stellaria media (L.) Vill), a ubiquitous garden weed, grows widely in Europe and North America. As opposed to the model plants, many weeds, and S. media in particular, have been poorly studied, although they are likely to contain promising components of immunity and novel resistance genes. In this study, for the first time RNA-seq analysis of healthy and infected with Fusarium oxysporum chickweed seedlings, as well as de novo transcriptome assembly and annotation, are presented. Note, this research is focused on antimicrobial peptides (AMPs), the major components of plant immune system. Using custom software developed earlier, 145 unique putative AMPs (pAMPs) including defensins, thionins, hevein-like peptides, snakins, alpha-hairpinins, LTPs, and cysteine-rich peptides with novel cysteine motifs were predicted. Furthermore, changes in AMP expression profile in response to fungal infection were traced. In addition, the comparison of chickweed AMP repertoire with those of other Caryophyllaceae plants whose transcriptomes are presently available is made. As a result, alpha-hairpinins and hevein-like peptides which display characteristic modular structure appear to be specific AMPs distinguishing S. media from Dianthus caryophyllus, Silene vulgaris, and Silene latifolia. Finally, revealing several AMPs with proven antimicrobial activity gives opportunity to conclude that the presented method of AMP repertoire analysis reveals highly active AMPs playing vital role in plant immunity.

Resurgence of Less-Studied Smut Fungi as Models of Phytopathogenesis in the Omics Age

The smut fungi form a large, diverse, and nonmonophyletic group of plant pathogens that have long served as both important pests of human agriculture and, also, as fertile organisms of scientific investigation. As modern techniques of molecular genetic analysis became available, many previously studied species that proved refractive to these techniques fell by the wayside and were neglected. Now, as the advent of rapid and affordable next-generation sequencing provides genomic and transcriptomic resources for even these "forgotten" fungi, several species are making a comeback and retaking prominent places in phytopathogenic research. In this review, we highlight several of these smut fungi, with special emphasis on Microbotryum lychnidis-dioicae, an anther smut whose molecular genetic tools have finally begun to catch up with its historical importance in classical genetics and now provide mechanistic insights for ecological studies, evolution of host-pathogen interaction, and investigations of emerging infectious disease.