Chaoying He

On the origin of floral morphological novelties

Floral morphological novelties, like homeotic changes of whorl 1 organs, can easily arise by modifying existing regulatory networks. Ectopic expression of B‐function MADS‐box genes in whorl 1 leads to a replacement of sepals by petals, as is found in the Liliaceae. In cases where leaf‐like sepals or even inflated calyces develop, which ultimately envelop the mature fruit as in Physalis, ectopic expression of a vegetative MADS‐box gene seems to be responsible. Current knowledge concerning the origin of such morphological novelties is reviewed.

Isolation and characterization of a full-length resistance gene homolog from soybean

Abstract.Using mixed resistance gene analogs as probes, a putative resistance gene (KR1) was isolated from soybean and characterized further. The KR1 protein consists of a Toll/interleukin receptor (TIR) domain, a nucleotide binding site (NBS) domain, an imperfect leucine-rich repeat (LRR) domain and two C-terminal transmembrane segments. Due to these features, KR1 represents a distinct member in the TIR-NBS-LRR class of resistance genes. Southern-blot analysis indicated that there were several KR1-related sequences within the soybean genome, and two polymorphic loci were mapped onto linkage group L. KR1 was induced by SA treatment and soybean mosaic virus (SMV) infection in the resistant line (Kefeng 1). An orthologue (NR1) and a homologue (NR2) of the KR1 gene were also identified in the SMV susceptible-line Nannong1138-2. Sequencing analysis revealed that NR2 was highly homologous to KR1 and NR1, but had a 21-bp deletion. Moreover, the NR1, NR2 transcription and the ratio of NR1/NR2 was up-regulated by viral infection in Nannong1138-2. These results indicated the complexity of the regulatory mechanism in the plant responses to SMV infection.

MPF2-Like-A MADS-Box Genes Control the Inflated Calyx Syndrome in Withania (Solanaceae): Roles of Darwinian Selection

The Chinese lantern, which is the inflated calyx syndrome (ICS) of Physalis, is formed by MPF2 in the presence of the plant hormones, cytokinin and gibberellin. MPF2 knockdown mutants of Physalis have small leaves, no ICS, and are male sterile, thus, revealing three MPF2-related functions. Of the close relatives of Physalis, Tubocapsicum has only a rudimentary calyx, whereas others, like the Withania species, have ICS. From all Withania samples tested, two classes of MPF2-like orthologs, MPF2-like-A and MPF2-like-B, were isolated, whereas only the latter class was obtained from tetraploid Tubocapsicum. Though distinct differences can be observed between MPF2-like-A and MPF2-like-B proteins, that is MPF2-like-A proteins have an aberrant structure in that they have a three amino acid deletion in their C-domain and an eight amino acid extension at the C-terminal end, MPF2-like-A genes are phylogenetically closer to the Physalis MPF2-like genes. Unlike MPF2-like-B, the overexpression of MPF2-like-A in Arabidopsis revealed extra large sepals thus suggesting that MPF2-like-A genes are very likely responsible for the ICS formation in Withania. This correlated with the expression pattern of MPF2-like-A in vegetative and flower tissues, whereas MPF2-like-B is expressed only in vegetative tissues of Withania. In Tubocapsicum, however, MPF2-like-B RNA is detectable in all tissues tested. Finally, positive Darwinian selection was observed in the branch leading to Physalis MPF2-like and Withania MPF2-like-A proteins, followed by purifying selection once the trait had evolved. By contrast, purifying selection was detected for all other MPF2-like proteins tested. The contribution of the MPF2-like gene duplication to subfunctionalization is discussed.

The MADS-domain protein MPF1 of Physalis floridana controls plant architecture, seed development and flowering time

Floral and vegetative development of plants is dependent on the combinatorial action of MADS-domain transcription factors. Members of the STMADS11 subclade, such as MPF1 of Physalis, are abundantly expressed in leaves as well as in floral organs, but their function is not yet clear. Our studies with transgenic Arabidopsis that over-express MPF1 suggest that MPF1 interacts with SOC1 to determine flowering time. However, MPF1 RNAi-mediated knockdown Physalis plants revealed a complex phenotype with changes in flowering time, plant architecture and seed size. Flowering of these plants was delayed by about 20% as compared to wild type. Expression of PFLFY is upregulated in the MPF1 RNAi lines, while PFFT and MPF3 genes are strongly repressed. MPF1 interacts with a subset of MADS-domain factors, namely with PFSOC1 in planta, and with PFSEP3 and PFFUL in yeast, supporting a regulatory role for this protein in flowering. The average size of seeds produced by the transgenic MPF1 RNAi plants is increased almost twofold. The height of these plants is also increased about twofold, but most axillary buds are stunted when compared to controls. Taken together, this suggests that members of the STMADS11 subclade act as positive regulators of flowering but have diverse functions in plant growth.

Slow Co-Evolution of the MAGO and Y14 Protein Families Is Required for the Maintenance of Their Obligate Heterodimerization Mode

The exon junction complex (EJC) plays important roles in RNA metabolisms and the development of eukaryotic organisms. MAGO (short form of MAGO NASHI) and Y14 (also Tsunagi or RBM8) are the EJC core components. Their biological roles have been well investigated in various species, but the evolutionary patterns of the two gene families and their protein-protein interactions are poorly known. Genome-wide survey suggested that the MAGO and Y14 two gene families originated in eukaryotic organisms with the maintenance of a low copy. We found that the two protein families evolved slowly; however, the MAGO family under stringent purifying selection evolved more slowly than the Y14 family that was under relative relaxed purifying selection. MAGO and Y14 were obliged to form heterodimer in a eukaryotic organism, and this obligate mode was plesiomorphic. Lack of binding of MAGO to Y14 as functional barrier was observed only among distantly species, suggesting that a slow co-evolution of the two protein families. Inter-protein co-evolutionary signal was further quantified in analyses of the Tol-MirroTree and co-evolution analysis using protein sequences. About 20% of the 41 significantly correlated mutation groups (involving 97 residues) predicted between the two families was clade-specific. Moreover, around half of the predicted co-evolved groups and nearly all clade-specific residues fell into the minimal interaction domains of the two protein families. The mutagenesis effects of the clade-specific residues strengthened that the co-evolution is required for obligate MAGO-Y14 heterodimerization mode. In turn, the obliged heterodimerization in an organism serves as a strong functional constraint for the co-evolution of the MAGO and Y14 families. Such a co-evolution allows maintaining the interaction between the proteins through large evolutionary time scales. Our work shed a light on functional evolution of the EJC genes in eukaryotes, and facilitates to understand the co-evolutionary processes among protein families.

Transcriptome comparison reveals key candidate genes responsible for the unusual reblooming trait in tree peonies.

Tree peonies are important ornamental plants worldwide, but growing them can be frustrating due to their short and concentrated flowering period. Certain cultivars exhibit a reblooming trait that provides a valuable alternative for extending the flowering period. However, the genetic control of reblooming in tree peonies is not well understood. In this study, we compared the molecular properties and morphology of reblooming and non-reblooming tree peonies during the floral initiation and developmental processes. Using transcriptome sequencing technology, we generated 59,275 and 63,962 unigenes with a mean size of 698 bp and 699 bp from the two types of tree peonies, respectively, and identified eight differentially expressed genes that are involved in the floral pathways of Arabidopsis thaliana. These differentially regulated genes were verified through a detailed analysis of their expression pattern during the floral process by real time RT-PCR. From this combined analysis, we identified four genes, PsFT, PsVIN3, PsCO and PsGA20OX, which likely play important roles in the regulation of the reblooming process in tree peonies. These data constitute a valuable resource for the discovery of genes involved in flowering time and insights into the molecular mechanism of flowering to further accelerate the breeding of tree peonies and other perennial woody plants.

The euAP1 Protein MPF3 Represses MPF2 to Specify Floral Calyx Identity and Displays Crucial Roles in Chinese Lantern Development in Physalis

Morphological novelties arise through changes in development. The origin of the Chinese lantern phenotype or inflated calyx syndrome (ICS), a postfloral novelty in Physalis, was previously shown to be associated with the MADS box gene MPF2. This study reveals that molecular interactions between MPF3 (a euAP1 MADS box gene) and MPF2 and their products played crucial roles in the evolution of ICS. The Chinese lantern phenotype or inflated calyx syndrome (ICS) is a postfloral morphological novelty in Physalis. Its origin is associated with the heterotopic expression of the MADS box gene 2 from Physalis floridana (MPF2) in floral organs, yet the process underlying its identity remains elusive. Here, we show that MPF3, which is expressed specifically in floral tissues, encodes a core eudicot APETALA1-like (euAP1) MADS-domain protein. MPF3 was primarily localized to the nucleus, and it interacted with MPF2 and some floral MADS-domain proteins to selectively bind the CC-A-rich-GG (CArG) boxes in the MPF2 promoter. Downregulating MPF3 resulted in a dramatic elevation in MPF2 in the calyces and androecium, leading to enlarged and leaf-like floral calyces; however, the postfloral lantern was smaller and deformed. Starch accumulation in pollen was blocked. MPF3 MPF2 double knockdowns showed normal floral calyces and more mature pollen than those found in plants in which either MPF3 or MPF2 was downregulated. Therefore, MPF3 specifies calyx identity and regulates ICS formation and male fertility through interactions with MPF2/MPF2. Furthermore, both genes were found to activate Physalis floridana invertase gene 4 homolog, which encodes an invertase cleaving Suc, a putative key gene in sugar partitioning. The novel role of the MPF3-MPF2 regulatory circuit in male fertility is integral to the origin of ICS. Our results shed light on the evolution and development of ICS in Physalis and on the functional evolution of euAP1s in angiosperms.

Evolutionary developmental genetics of fruit morphological variation within the Solanaceae

Morphological variations of fruits such as shape and size, and color are a result of adaptive evolution. The evolution of morphological novelties is particularly intriguing. An understanding of these evolutionary processes calls for the elucidation of the developmental and genetic mechanisms that result in particular fruit morphological characteristics, which determine seed dispersal. The genetic and developmental basis for fruit morphological variation was established at a microevolutionary time scale. Here, we summarize the progress on the evolutionary developmental genetics of fruit size, shape and color in the Solanaceae. Studies suggest that the recruitment of a pre-existing gene and subsequent modification of its interaction and regulatory networks are frequently involved in the evolution of morphological diversity. The basic mechanisms underlying changes in plant morphology are alterations in gene expression and/or gene function. We also deliberate on the future direction in evolutionary developmental genetics of fruit morphological variation such as fruit type. These studies will provide insights into plant developmental processes and will help to improve the productivity and fruit quality of crops.

Deciphering the Physalis floridana Double-Layered-Lantern1 Mutant Provides Insights into Functional Divergence of the GLOBOSA Duplicates within the Solanaceae

A single gene mutation yields novel morphologies and uncovers a divergent pattern of paralogous genes within the Solanaceae. Physalis spp. develop the “Chinese lantern” trait, also known as inflated calyx syndrome, that is a morphological novelty. Here, we identified the double-layered-lantern1 (doll1) mutant, a recessive and monofactorial mutation, in Physalis floridana; its corolla and androecium were transformed into the calyx and gynoecium, respectively. Two GLOBOSA-like MADS-box paralogous genes PFGLO1 and PFGLO2 were found in Physalis floridana, while the mutated phenotype was cosegregated with a large deletion harboring PFGLO1 and was complemented by the PFGLO1 genomic locus in transgenic plants, and severe PFGLO1 knockdowns phenocopied doll1. Thus, DOLL1 encodes the PFGLO1 protein and plays a primary role in determining corolla and androecium identity. However, specific PFGLO2 silencing showed no homeotic variation but rather affected pollen maturation. The two genes featured identical floral expression domains, but the encoding proteins shared 67% identity in sequences. PFGLO1 was localized in the nucleus when expressed in combination with a DEFICIENS homolog from Physalis floridana, whereas PFGLO2 was imported to the nucleus on its own. The two proteins were further found to have evolved different interacting partners and regulatory patterns, supporting the hypothesis that PFGLO2 is functionally separated from organ identity. Such a divergent pattern of duplicated GLO genes is unusual within the Solanaceae. Moreover, the phenotypes of the PFGLO1PFGLO2 double silencing mutants suggested that PFGLO2, through genetically interacting with PFGLO1, also exerts a role in the control of organ number and tip development of the second floral whorl. Our results, therefore, shed new light on the functional evolution of the duplicated GLO genes.

Phylogeny, structural evolution and functional diversification of the plant PHOSPHATE1 gene family: a focus on Glycine max.

BackgroundPHOSPHATE1 (PHO1) gene family members have diverse roles in plant growth and development, and they have been studied in Arabidopsis, rice, and Physcomitrella. However, it has yet to be described in other plants. Therefore, we surveyed the evolutionary patterns of genomes within the plant PHO1 gene family, focusing on soybean (Glycine max) due to its economic importance.ResultsOur data show that PHO1 genes could be classified into two major groups (Class I and Class II). Class I genes were only present and expanded in dicotyledonous plants and Selaginella moellendorffii; Class II genes were found in all land plants. Class I sequence losses in other lineages may be attributed to gene loss after duplication events in land plant evolution. Introns varied from 7 to 14, and ancestral state reconstruction analyses revealed that genes with 13 introns were ancestral, thus suggesting that the intron loss was a chief constituent of PHO1 gene evolution. In the soybean genome, only 12 PHO1-like genes (GmaPHO1) were detected at the mRNA level. These genes display tissue-specific or tissue-preferential expression patterns during soybean plant and fruit development. Class I genes were more broadly expressed than Class II. GmaPHO1 genes had altered expression in response to salt, osmotic, and inorganic phosphate stresses.ConclusionsOur study revealed that PHO1 genes originated from a eukaryotic ancestor and that two major classes formed in land plants. Class I genes are only present in dicots and lycophytes. GmaPHO1genes had diverse expression patterns in soybean, indicating their dramatic functional diversification.