Small RNAs are pivotal regulators of gene expression that guide transcriptional and posttranscriptional silencing mechanisms in eukaryotes, including plants. Here we report a comprehensive atlas of sRNA and miRNA from 3 species of algae and 31 representative species across vascular plants, including non-model plants. We sequence and quantify sRNAs from 99 different tissues or treatments across species, resulting in a data set of over 132 million distinct sequences. Using miRBase mature sequences as a reference, we identify the miRNA sequences present in these libraries. We apply diverse profiling methods to examine critical sRNA and miRNA features, such as size distribution, tissue-specific regulation and sequence conservation between species, as well as to predict putative new miRNA sequences. We also develop database resources, computational analysis tools and a dedicated website, http://smallrna.udel.edu/. This study provides new insights on plant sRNAs and miRNAs, and a foundation for future studies.

Plant interactions with arbuscular mycorrhizal fungi have long attracted interest for their potential to promote more efficient use of mineral resources in agriculture. Their use, however, remains limited by a lack of understanding of the processes that determine the outcome of the symbiosis. In this study, the impact of host genotype on growth response to mycorrhizal inoculation was investigated in a panel of diverse maize lines. A panel of 30 maize lines was evaluated with and without inoculation with arbuscular mycorrhizal fungi. The line Oh43 was identified to show superior response and, along with five other reference lines, was characterized in greater detail in a split-compartment system, using P to quantify mycorrhizal phosphorus uptake. Changes in relative growth indicated variation in host capacity to profit from the symbiosis. Shoot phosphate content, abundance of root-internal and -external fungal structures, mycorrhizal phosphorus uptake, and accumulation of transcripts encoding plant PHT1 family phosphate transporters varied among lines. Superior response in Oh43 is correlated with extensive development of root-external hyphae, accumulation of specific Pht1 transcripts and high phosphorus uptake by mycorrhizal plants. The data indicate that host genetic factors influence fungal growth strategy with an impact on plant performance.

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Synchronized communication between gametophytic and sporophytic tissue is crucial for successful reproduction, and hormones seem to have a prominent role in it. Here, we studied the role of the Arabidopsis (Arabidopsis thaliana) cytochrome P450 CYP78A9 enzyme during reproductive development. First, controlled pollination experiments indicate that CYP78A9 responds to fertilization. Second, while CYP78A9 overexpression can uncouple fruit development from fertilization, the cyp78a8 cyp78a9 loss-of-function mutant has reduced seed set due to outer ovule integument development arrest, leading to female sterility. Moreover, CYP78A9 has a specific expression pattern in inner integuments in early steps of ovule development as well as in the funiculus, embryo, and integuments of developing seeds. CYP78A9 overexpression did not change the response to the known hormones involved in flower development and fruit set, and it did not seem to have much effect on the major known hormonal pathways. Furthermore, according to previous predictions, perturbations in the flavonol biosynthesis pathway were detected in cyp78a9, cyp78a8 cyp78a9, and empty siliques (es1-D) mutants. However, it appeared that they do not cause the observed phenotypes. In summary, these results add new insights into the role of CYP78A9 in plant reproduction and present, to our knowledge, the first characterization of metabolite differences between mutants in this gene family.Angiosperms have evolved the processes of double fertilization and fruit development as pivotal steps of their survival and dispersal strategies. Pollination and fertilization are essential for fruit initiation, considering that the angiosperm flower initiates terminal senescence and abscission programs if pollination has not taken place (Vivian-Smith et al., 2001; Fuentes and VivianSmith, 2009). For centuries, humans endeavored to prevent this association in order to develop seedless fruits. Most research has concentrated on the role of endogenous phytohormones as triggers for fruit initiation after fertilization, and different strategies such as exogenous application or artificial overproduction of plant hormones (Fuentes and Vivian-Smith, 2009), mutation, and misexpression of specific genes have been tested. The principal lines of evidence suggest that increased auxin and GA content in ovules and ovary leads to parthenocarpic fruits in Arabidopsis (Arabidopsis thaliana;

Fruits and seeds are the major food source on earth. Both derive from the gynoecium and, therefore, it is crucial to understand the mechanisms that guide the development of this organ of angiosperm species. In Arabidopsis, the gynoecium is composed of two congenitally fused carpels, where two domains: medial and lateral, can be distinguished. The medial domain includes the carpel margin meristem (CMM) that is key for the production of the internal tissues involved in fertilization, such as septum, ovules, and transmitting tract. Interestingly, the medial domain shows a high cytokinin signaling output, in contrast to the lateral domain, where it is hardly detected. While it is known that cytokinin provides meristematic properties, understanding on the mechanisms that underlie the cytokinin signaling pattern in the young gynoecium is lacking. Moreover, in other tissues, the cytokinin pathway is often connected to the auxin pathway, but we also lack knowledge about these connections in the young gynoecium. Our results reveal that cytokinin signaling, that can provide meristematic properties required for CMM activity and growth, is enabled by the transcription factor SPATULA (SPT) in the medial domain. Meanwhile, cytokinin signaling is confined to the medial domain by the cytokinin response repressor ARABIDOPSIS HISTIDINE PHOSPHOTRANSFERASE 6 (AHP6), and perhaps by ARR16 (a type-A ARR) as well, both present in the lateral domains (presumptive valves) of the developing gynoecia. Moreover, SPT and cytokinin, probably together, promote the expression of the auxin biosynthetic gene TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS 1 (TAA1) and the gene encoding the auxin efflux transporter PIN-FORMED 3 (PIN3), likely creating auxin drainage important for gynoecium growth. This study provides novel insights in the spatiotemporal determination of the cytokinin signaling pattern and its connection to the auxin pathway in the young gynoecium.

Desiccation tolerance (DT) is a remarkable process that allows seeds in the dry state to remain viable for long periods of time that in some instances exceed 1,000 y. It has been postulated that seed DT evolved by rewiring the regulatory and signaling networks that controlled vegetative DT, which itself emerged as a crucial adaptive trait of early land plants. Understanding the networks that regulate seed desiccation tolerance in model plant systems would provide the tools to understand an evolutionary process that played a crucial role in the diversification of flowering plants. In this work, we used an integrated approach that included genomics, bioinformatics, metabolomics, and molecular genetics to identify and validate molecular networks that control the acquisition of DT in Arabidopsis seeds. Two DT-specific transcriptional subnetworks were identified related to storage of reserve compounds and cellular protection mechanisms that act downstream of the embryo development master regulators LEAFY COTYLEDON 1 and 2, FUSCA 3, and ABSCICIC ACID INSENSI-TIVE 3. Among the transcription factors identified as major nodes in the DT regulatory subnetworks, PLATZ1, PLATZ2, and AGL67 were confirmed by knockout mutants and overexpression in a desiccationintolerant mutant background to play an important role in seed DT. Additionally, we found that constitutive expression of PLATZ1 in WT plants confers partial DT in vegetative tissues.regulatory network | desiccation tolerance | drought tolerance | seed development | oligosaccharides D esiccation tolerance (DT) can be operationally defined as the ability of an organism to dry to equilibrium with moderately dry air (50 to 70% relative humidity at 20 to 30°C) and then resume normal function when rehydrated (1). DT organisms orchestrate a complex number of responses to protect cellular structures and prevent damage to proteins and nucleic acids. Early land plants evolved mechanisms to survive harsh drying environments to successfully exploit different ecosystems on land. Therefore, it has been postulated that the initial evolution of vegetative DT, in both vegetative and reproductive stages, was a crucial step required for the colonization of land by primitive plants of a fresh water origin (2).Seed DT, a trait that allows terrestrial plants to survive long periods of sparse water until favorable conditions are present for germination, is probably part of the answer to Darwin's "abominable mystery," the sudden appearance of great angiosperm diversity in the fossil record. In angiosperms, DT is acquired at the seed maturation stage, which involves a complex regulatory network (3, 4) that activates a large subset of genes involved in a number of mechanisms that influence seed survival in the dry state. The set of genes required for seed DT includes genes encoding protective proteins such as late embryogenesis abundant (LEA) (5, 6) and heat shock proteins (HSPs) (7), enzymes involved in scavenging reactive oxygen species (8) and the biosynthesis of protective compounds such as o...

Purple acid phosphatases (PAPs) play an important role in plant phosphorus nutrition, both by liberating phosphorus from organic sources in the soil and by modulating distribution within the plant throughout growth and development. Furthermore, members of the PAP protein family have been implicated in a broader role in plant mineral homeostasis, stress responses and development. We have identified 33 candidate PAP encoding gene models in the maize (Zea mays ssp. mays var. B73) reference genome. The maize Pap family includes a clear single-copy ortholog of the Arabidopsis gene AtPAP26, shown previously to encode both major intracellular and secreted acid phosphatase activities. Certain groups of PAPs present in Arabidopsis, however, are absent in maize, while the maize family contains a number of expansions, including a distinct radiation not present in Arabidopsis. Analysis of RNA-sequencing based transcriptome data revealed accumulation of maize Pap transcripts in multiple plant tissues at multiple stages of development, and increased accumulation of specific transcripts under low phosphorus availability. These data suggest the maize PAP family as a whole to have broad significance throughout the plant life cycle, while highlighting potential functional specialization of individual family members.

Although cell wall remodeling is an essential feature of plant growth and development, the underlying molecular mechanisms are poorly understood. This work describes the characterization of Arabidopsis (Arabidopsis thaliana) plants with altered expression of ARAF1, a bifunctional a-L-arabinofuranosidase/b-D-xylosidase (At3g10740) belonging to family 51 glycosyl-hydrolases. ARAF1 was localized in several cell types in the vascular system of roots and stems, including xylem vessels and parenchyma cells surrounding the vessels, the cambium, and the phloem. araf1 T-DNA insertional mutants showed no visible phenotype, whereas transgenic plants that overexpressed ARAF1 exhibited a delay in inflorescence emergence and altered stem architecture. Although global monosaccharide analysis indicated only slight differences in cell wall composition in both mutant and overexpressing lines, immunolocalization experiments using anti-arabinan (LM6) and anti-xylan (LM10) antibodies indicated cell type-specific alterations in cell wall structure. In araf1 mutants, an increase in LM6 signal intensity was observed in the phloem, cambium, and xylem parenchyma in stems and roots, largely coinciding with ARAF1 expression sites. The ectopic overexpression of ARAF1 resulted in an increase in LM10 labeling in the secondary walls of interfascicular fibers and xylem vessels. The combined ARAF1 gene expression and immunolocalization studies suggest that arabinan-containing pectins are potential in vivo substrates of ARAF1 in Arabidopsis.Cell walls undergo dynamic changes during plant growth and development. Wall composition and macromolecular assembly vary greatly among taxa, species, organs, and cell types within an individual or domains of a given cell wall. These differences contribute to cell shape and, in some cases, specialized cellular function. Cell wall-related genomic approaches in different physiological contexts have revealed that many cell wall biosynthetic/modifying enzymes and structural proteins are regulated at the transcriptional level. In the case of secondary wall formation, one can correlate morphological and cytological cellular changes with the spatial and temporal regulation of wall-modifying enzymes over a developmental xylem gradient in poplar (Populus spp.;Schrader et al., 2004) and in in vitro tracheary elements (TEs) of zinnia (Zinnia elegans;Milioni et al., 2001;Demura et al., 2002;Pesquet et al., 2005). In a genomic approach of zinnia TEs, Pesquet et al. (2005) identified a family 51 (Carbohydrate Active enZYmes [CAZY] database, http://www.cazy.org; Coutinho and Henrissat, 1999) a-L-arabinofuranosidase (arabinofuranosidase) that was highly expressed in TE induction medium at the onset of secondary wall formation. Interestingly, although relatively little redundancy was observed in sequence data generated from the different genomic studies in zinnia, this family 51 arabinofuranosidase gene was systematically identified. At3g10740 is the closest Arabidopsis (Arabidopsis thaliana) homolog to the arabinofuranosidase...