Comparative analysis of whole flower transcriptomes in the Zingiberales

The advancement of next generation sequencing technologies (NGS) has revolutionized our ability to generate large quantities of data at a genomic scale. Despite great challenges, these new sequencing technologies have empowered scientists to explore various relevant biological questions on non-model organisms, even in the absence of a complete sequenced reference genome. Here, we analyzed whole flower transcriptome libraries from exemplar species across the monocot order Zingiberales, using a comparative approach in order to gain insight into the evolution of the molecular mechanisms underlying flower development in the group. We identified 4,153 coding genes shared by all floral transcriptomes analyzed, and 1,748 genes that are only retrieved in the Zingiberales. We also identified 666 genes that are unique to the ginger lineage, and 2,001 that are only found in the banana group, while in the outgroup species Dichorisandra thyrsiflora J.C. Mikan (Commelinaceae) we retrieved 2,686 unique genes. It is possible that some of these genes underlie lineage-specific molecular mechanisms of floral diversification. We further discuss the nature of these lineage-specific datasets, emphasizing conserved and unique molecular processes with special emphasis in the Zingiberales. We also briefly discuss the strengths and shortcomings of de novo assembly for the study of developmental processes across divergent taxa from a particular order. Although this comparison is based exclusively on coding genes, with particular emphasis in transcription factors, we believe that the careful study of other regulatory mechanisms, such as non-coding RNAs, might reveal new levels of complexity, which were not explored in this work

Structural and Functional Loss in Restored Wetland Ecosystems

In restored wetland ecosystems with apparently natural hydrology and biological structure, biogeochemical function may remain degraded, even a century after restoration efforts

The use and limits of ITS data in the analysis of intraspecific variation in Passiflora L. (Passifloraceae)

The discovery and characterization of informative intraspecific genetic markers is fundamental for evolutionary and conservation genetics studies. Here, we used nuclear ribosomal ITS sequences to access intraspecific genetic diversity in 23 species of the genus Passiflora L. Some degree of variation was detected in 21 of these. The Passiflora and Decaloba (DC.) Rchb. subgenera showed significant differences in the sizes of the two ITS regions and in GC content, which can be related to reproductive characteristics of species in these subgenera. Furthermore, clear geographical patterns in the spatial distribution of sequence types were identified in six species. The results indicate that ITS may be a useful tool for the evaluation of intraspecific genetic variation in Passiflora

Taxonomy and evolutionary relationships of Passiflora subg. Decaloba supersect. Decaloba sect. Xerogona (Passifloraceae): contributions of palynological, morphological and molecular studies

Passiflora subg. Decaloba supersect. Decaloba sect. Xerogona (Passifloraceae) is a tropical and subtropical group comprising 14 species that occur in tropical biomes throughout Latin America, including the Atlantic Forest. The section Xerogona comprises herbaceous vines characterized by a lack of petiole glands on their leaves, of bracts and of ocelli on their leaf blades, as well as by their capsular fruits. We analyzed the phylogeny on the basis of morphological characters (including pollen characters) and molecular data. The inferred phylogeny was used in order to characterize, circumscribe and delimit the section and the species. We examined the phylogenetic relationships among the species, evaluating the circumscription of the section on the basis of the trnL-trnF intergenic spacer region of chloroplast DNA and the internal transcribed spacer region of nuclear ribosomal DNA. We constructed phylogenetic trees on the basis of the morphological and molecular data. We found that P. subg. Decaloba supersect. Decaloba sect. Xerogona appears to be monophyletic only in the molecular analyses. The phylogenetic analyses performed here also indicated that P. subg. Decaloba is monophyleti

On the origin of the sweet-smelling Parma violet cultivars (Violaceae) : wide intraspecific hybridization, sterility, and sexual reproduction

A-07-04Parma violets are reputed for their double, fragrant flowers and have been cultivated for centuries in Europe. However, due to a rather atypical morphology their taxonomic affinity has not been clarified. Authors have proposed an origin from three possible species, Viola alba, V. odorata, or V. suavis, or a hybrid origin. Using both ITS sequence variation and allozyme variation in 14 putative loci, we showed that the Parma violet cultivars have their origin within Viola alba and that they are best included in the Mediterranean subsp. dehnhardtii. There is no trace of interspecific hybridization. However, the cultivars appear to have a single origin in a wide hybrid within V. alba, involving parental plants from the eastern and western Mediterranean region; historical literature sources seem to indicate Turkey and Italy, respectively. The Parma violet cultivars possess high levels of allozyme heterozygosity and to some extent also within-individual ITS sequence variation. Losses of heterozygosity and within-individual ITS sequence variation in some of the cultivars indicate subsequent rare events of sexual reproduction, presumably through cleistogamous seed set. We unambiguously identify the closest wild relative of this group of cultivars, allowing growers to develop new selection procedures, and show a peculiar molecular process associated with human selection

Positive selection on the K domain of the AGAMOUS protein in the Zingiberales suggests a mechanism for the evolution of androecial morphology

The ABC model of flower development describes the molecular basis for specification of floral organ identity in model eudicots such as Arabidopsis and Antirrhinum. According to this model, expression of C-class genes is linked to stamen and gynoecium organ identity. The Zingiberales is an order of tropical monocots in which the evolution of floral morphology is characterized by a marked increase in petaloidy in the androecium. Petaloidy is a derived characteristic of the ginger families and seems to have arisen in the common ancestor of the ginger clade. We hypothesize that duplication of the C-class AGAMOUS (AG) gene followed by divergence of the duplicated AG copies during the diversification of the ginger clade lineages explains the evolution of petaloidy in the androecium. In order to address this hypothesis, we carried out phylogenetic analyses of the AG gene family across the Zingiberales and investigated patterns of gene expression within the androecium

Positive selection on the K domain of the AGAMOUS protein in the Zingiberales suggests a mechanism for the evolution of androecial morphology

The ABC model of flower development describes the molecular basis for specification of floral organ identity in model eudicots such as Arabidopsis and Antirrhinum. According to this model, expression of C-class genes is linked to stamen and gynoecium organ identity. The Zingiberales is an order of tropical monocots in which the evolution of floral morphology is characterized by a marked increase in petaloidy in the androecium. Petaloidy is a derived characteristic of the ginger families and seems to have arisen in the common ancestor of the ginger clade. We hypothesize that duplication of the C-class AGAMOUS (AG) gene followed by divergence of the duplicated AG copies during the diversification of the ginger clade lineages explains the evolution of petaloidy in the androecium. In order to address this hypothesis, we carried out phylogenetic analyses of the AG gene family across the Zingiberales and investigated patterns of gene expression within the androecium

A Method for Extracting High-Quality RNA from Diverse Plants for Next-Generation Sequencing and Gene Expression Analyses

Premise of the study: To study gene expression in plants, high-quality RNA must be extracted in quantities sufficient for subsequent cDNA library construction. Field-based collections are often limited in quantity and quality of tissue and are typically preserved in RNAlater. Obtaining sufficient and high-quality yield from variously preserved samples is essential to studies of comparative biology. We present a protocol for the extraction of high-quality RNA from even the most recalcitrant plant tissues. Methods and Results: Tissues from mosses, cycads, and angiosperm floral organs and leaves were preserved in RNAlater or frozen fresh at −80°C. Extractions were performed and quality was measured for yield and purity. Conclusions: This protocol results in the extraction of high-quality RNA from a variety of plant tissues representing vascular and nonvascular plants. RNA was used for cDNA synthesis to generate libraries for next-generation sequencing and for expression studies using quantitative PCR (qPCR) and semiquantitative reverse transcription PCR (RT-PCR)