Back to the sea twice: identifying candidate plant genes for molecular evolution to marine life

Background  

Seagrasses are a polyphyletic group of monocotyledonous angiosperms that have adapted to a completely submerged lifestyle in marine waters. Here, we exploit two collections of expressed sequence tags (ESTs) of two wide-spread and ecologically important seagrass species, the Mediterranean seagrass Posidonia oceanica (L.) Delile and the eelgrass Zostera marina L., which have independently evolved from aquatic ancestors. This replicated, yet independent evolutionary history facilitates the identification of traits that may have evolved in parallel and are possible instrumental candidates for adaptation to a marine habitat.     

Dynamics and evolution of the inverted repeat-large single copy junctions in the chloroplast genomes of monocots

Background  

Various expansions or contractions of inverted repeats (IRs) in chloroplast genomes led to fluxes in the IR-LSC (large single copy) junctions. Previous studies revealed that some monocot IRs contain a trnH-rps19 gene cluster, and it has been speculated that this may be an evidence of a duplication event prior to the divergence of monocot lineages. Therefore, we compared the organizations of genes flanking two IR-LSC junctions in 123 angiosperm representatives to uncover the evolutionary dynamics of IR-LSC junctions in basal angiosperms and monocots.     

<Emphasis Type="Italic">SQUA</Emphasis>-like genes in the orchid <Emphasis Type="Italic">Phalaenopsis</Emphasis> are expressed in both vegetative and reproductive tissues

The SQUA family (AP1/FUL family) of MADS-box genes plays an important role in the transition from the vegetative to the reproductive development of angiosperms, and its origin might be concurrent with fixation of floral structure in angiosperms. Here, we isolated two Phalaenopsis MADS-box genes designated ORAP11 and ORAP13, both of which belong to the monocot FUL-like clade of the SQUA family. RT-PCR showed that both genes are strongly expressed in the floral bud, and also detected in the vegetative organs. During later stages, ORAP11 was only detected in the column, but ORAP13 signal was absent from all of the floral organs. In-situ hybridization experiments detected both genes in the tips and margins of developing petals and lips, the developing column, and ovule. Over-expression of both genes in tobacco induced early flowering and changed plant architecture. Our results suggest that in Phalaenopsis, both genes might share partly redundant activities and play important roles in the process of floral transition and morphological architecture. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

VESSEL STRUCTURE OF GNETUM AND THE ORIGIN OF ANGIOSPERMS

Vessel structure of Gnetum gnemon L. and G. montanum Mgf. was investigated by means of light microscopy (brightfield, phase contrast and Nomarski interference optics), and scanning and transmission electron microscopy. The gyres of the first order framework are compound, consisting of three elementary strands (subunits). Pits ranging from slit-shaped to circular are formed either between the elementary strands of one gyre or between adjacent gyres. (Compound gyres are also figured for Alnus and lens-shaped pits in annular-helical elements are demonstrated for Juglans and Salix). In the two species of Gnetum studied, scalariform pits occur in addition to the well known circular pits. Scalariform perforation plates are present besides scalaroid, foraminate, and simple perforation plates as well as intermediates between the above types. These findings invalidate a common argument against the gnetalean origin of angiosperms, namely that pits and perforations of Gnetum are totally unlike those of primitive angiosperms and that therefore Gnetum must be ruled out as a potential ancestor of angiosperms. Variation in vessel structure of Gnetum is so great that it encompasses the typically circular pits of the coniferopsids as well as patterns of pits and perforation plates found in angiosperms. Some photographs of angiospermous taxa are interspersed with those of Gnetum to indicate the striking similarities. The determination of the patterns and shapes of pits and perforations is discussed in terms of four parameters: 1) the ratio of the width of the cell face to the distance between the gyres; 2) the types and distribution of the second order framework; 3) the stretching and distortion of gyres and/or second order framework; and in the case of perforations, 4) the pattern of wall and bar breakdown. Since the first parameter may change continuously, a continuum between circular pits or perforations and scalariform ones may occur. Such a continuum actually exists in Gnetum as well as in angiosperms. Patterns due to the other three of the above parameters are also formed in similar ways in both Gnetum and angiosperms. These similarities may, of course, be interpreted as the result of parallel evolution. However, when one considers the large number of angiospermous features of Gnetum, one is led to ask whether Gnetum may not have been close to the ancestral stock of all or at least some taxa of angiosperms.     

Mosacaulis spinifer gen. et sp. nov.: An enigmatic Maastrichtian plant

Dichotomously branched stem fragments with crowded, spirally arranged, trifurcate leaf base remains from the type area of the Maastrichtian (Late Cretaceous; SE Netherlands, NE Belgium) are described as a new genus and species: Mosacaulis spinifer Van der Ham et Van Konijnenburg-van Cittert. They are interpreted as fossils of (pseudo)herbaceous axes with densely spaced, semi-amplexicaul leaves arranged in low spirals, with reproductive structures (sporangia?, prophylls associated with flowering axes?) attached to the adaxial sides of the leaf bases. M. spinifer is considered to be of unknown affinity (incertae sedis), showing resemblances with such disparate lineages as lycopsids and angiosperms. Its seagrass-like habit, gregarious occurrence, the association with genuine seagrass and a diverse marine fauna (including epibionts on the stems), and the absence of any terrigenous material, remains of land plants and terrestrial palynomorphs suggest that M. spinifer grew in a fully marine environment.     

Vicilin-like seed storage proteins in the gymnosperm interior spruce (Picea glauca/engelmanii)

A seed storage protein cDNA was characterized from a library of interior spruce (Picea glauca/engelmanii complex) cotyledonary stage somatic embryos. The deduced amino acid sequence predicts a 448 amino acid (50 kDa) polypeptide with 28–38% identity with angiosperm vicilin-like 7S globulins. XXC/G codon usage is low (47%) relative to monocot angiosperms while pairwise comparisons show that spruce, monocot, and dicot vicilins are approximately equal in amino acid divergence. Although small by comparison, the spruce vicilin contains an N terminal hydrophilic region characteristic of angiosperm large vicilins. Genomic Southern blotting predicts that the cDNA is encoded by a gene family.     

Differences in meristems between monocots and dicots and susceptibility to attack by gall-inducing insects

We used comparative methods that account for the phylogenetic correlations among species to test hypotheses about the community of gall-inducing insects on dicotyledonous and monocotyledonous plants and woody and herbaceous angiosperms in the UK. We found that the species richness of gall-inducing insects on dicots was greater than on monocots and that the odds of a dicot having an associated gall-inducing insect is 42% higher than for a monocot. Woody angiosperms have higher species richness of associated gall-inducing insects than do herbaceous angiosperms. Furthermore, using a Monte Carlo analysis we found that attacks by gall-inducing insects on monocot families were phylogenetically clustered in the order Poales, particularly within the grass family Poaceae. We suggest that the higher risk of attack on dicots and higher species richness of gall-inducing insects on woody angiosperms, which are exclusively dicots, arises because of differences in the abundance or susceptibility of dicot meristems to attack by gall-inducing insects. Architectural and anatomical differences between monocots and dicots that give rise to differences in meristem abundance and anatomy appear to play an important role in determining the occurrence and richness of associated gall-inducing insects on host plants.     

Starch-accumulating (S-type) sieve-element plastids in Hydatellaceae: implications for plastid evolution in flowering plants

TEM investigation of sieve-element plastids in three species of Trithuria, the sole genus of the small aquatic family Hydatellaceae, show that P-type plastids are absent from this genus and only starch-accumulating (S-type) sieve-element plastids are present. This discovery is consistent with the recent transfer of Hydatellaceae from the highly derived monocot order Poales (grasses and their allies) to the early-divergent angiosperm order Nymphaeales (waterlilies) based on molecular phylogenetic data. Species of Poales consistently possess P2-subtype plastids, in common with other monocots, but only S-type plastids are present in Nymphaeales. The results confirm that Hydatellaceae do not belong in monocots. Optimisation of the two major types of sieve-element plastid onto a recent phylogeny of early-divergent angiosperms confirms that S-type is the primitive form and indicates that P-type sieve-element plastids have evolved more than once in angiosperms.     

A whole-plant monocot from the Lower Cretaceous

The Yixian Formation (the Lower Cretaceous) of China is world famous for its fossils of early angiosperms. Despite their great diversity, few of these fossils are preserved as whole plants, making our understanding of early angiosperms incomplete. Here, we report a fossil angiosperm, Sinoherba ningchengensis n. gen. n. sp. (Sinoherbaceae n. fam.), from the Yixian Formation of China. The fossil is of a whole plant, including physically connected root with fibrous rootlets, a stem with branches and nodes, leaves with parallel-reticulate veins, and a panicle of female flowers with an ovary surrounded by perianth. Morphological and phylogenetic analyses reveal that Sinoherba is an herbaceous monocot. This fossil underscores the great diversity of angiosperms in the Lower Cretaceous Yixian Formation and an earlier, pre-Cretaceous origin of angiosperms.     

The largest eukaryotic genome of them all?

We report the largest eukaryotic genome to date in the monocot Paris japonica (Melanthiaceae, 1C = 152.23 pg), measured using flow cytometry. This value is 15% larger than any previous estimate and extends the range of genome sizes to c. 2400‐fold across angiosperms and c. 66 000‐fold across eukaryotes. © 2010 The Linnean Society of London, Botanical Journal of the Linnean Society, 2010, 164 , 10–15.     

THE REPRODUCTIVE BIOLOGY OF A RELICT–ILLICIUM FLORIDANUM ELLIS

The flowers of Illicium floridanum are pollinated by a wide variety of insects, particularly Diptera that emerge from the litter and stream in early spring. Coleoptera rarely visit the flowers. It is suggested that the mode of pollination is ancient and may also exist in species of primitive angiosperms in the South Pacific. Illicium floridanum is self-incompatible and possesses features of a gametophytically controlled incompatibility system. As a result of asexual reproduction, a lack of long-distance dispersal of pollen and self-incompatibility, fruit production is very low. This pattern of reproduction is found in other species of primitive angiosperms; incompatibility mechanisms which undoubtedly aided the angiosperms to become dominant may now be one of the major factors responsible for their extinction.     

Endosperm development in the Araceae (Alismatales) and evolution of developmental modes in monocots

The Araceae, a basal-most family of Alismatales that basally diverged subsequent to Acorales in monocot phylogeny, are known to have diverse modes of endosperm development: nuclear, helobial, and cellular. However, the occurrence of nuclear and helobial endosperm development has long been debated. Here, we report a (re-)investigation of endosperm development in Lysichiton, Orontium, and Symplocarpus of the Orontioideae (a basal Araceae), in which nuclear endosperm development was recorded more than 100 years ago. The results show that all three genera exhibit a cellular, rather than nuclear, endosperm development and suggest that the helobial endosperm development reported as an “unmistakable record” from Ariopsis is likely cellular. Thus the Araceae are very likely characterized by cellular endosperm development alone. An extensive comparison with other monocots in light of phylogenetic relationships demonstrates that a plesiomorphic cellular endosperm development is restricted to the three basal monocot orders Acorales, Alismatales, and Petrosaviales, in which evolutionary changes from cellular to nuclear endosperm development occurred twice as major events, once within Alismatales and once as a synapomorphy of the eight remaining monocot orders, including Dioscoreales, Liliales, Asparagales, and Poales, and that helobial endosperm development, which is known for many monocot families, evolved as homoplasy throughout the monocots.     

PRESENCE OF VESSELS IN WOOD OF SARCANDRA (CHLORANTHACEAE); COMMENTS ON VESSEL ORIGINS IN ANGIOSPERMS

Sarcandra is the only genus of Chloranthaceae hitherto thought to be vesselless. Study of liquid-preserved material of S. glabra revealed that in root secondary xylem some tracheary elements are wider in diameter and have markedly scalariform end walls combined with circular pits on lateral walls. Examination of these wider tracheary elements with scanning electron microscope (SEM) demonstrated various degrees of pit membrane absence in the end walls. Commonly a few threadlike fibrils traverse the pits (perforations); these as well as intact nature of pit membranes in pits at ends of some perforation plates are evidence that lack of pit membranes does not result from damage during processing. Some perforations lack any remnants of pit membranes. Although perforation plates and therefore vessels are present in Sarcandra roots, no perforations were observed in tracheary elements of stems or lignotubers. Further, stem tracheids do not have the prominently scalariform end walls that the vessel elements in roots do. Presence of vessels in Sarcandra removes at least one (probably several) hypothetical events of vessel origin that must be postulated to account for known patterns of vessel distribution in angiosperms, assuming that they are primitively vesselless. Seven (perhaps fewer) vessel origin events in angiosperms could account for these patterns; two of those events (Nelumbo and monocotyledons) are different from the others in nature. Widely accepted data on trends of vessel specialization in woody dicotyledons yield an unappreciated implication: vessel specialization has happened in a highly polyphyletic manner in dicotyledons, and therefore multiple vessel origins represent a logical extension backward in time. If a group of vesselless dictyoledons ancestral to other angiosperms existed, they can be hypothesized to have had a relatively homogeneous floral plan now that Sarcandra-like plants no longer need be imagined within that group. Sarcandra and other Chloranthaceae show that the borderline between vessel absence and presence is less sharp than generally appreciated.     

Phylogenetic variation in the silicon composition of plants

BACKGROUND AND AIMS: Silicon (Si) in plants provides structural support and improves tolerance to diseases, drought and metal toxicity. Shoot Si concentrations are generally considered to be greater in monocotyledonous than in non-monocot plant species. The phylogenetic variation in the shoot Si concentration of plants reported in the primary literature has been quantified. METHODS: Studies were identified which reported Si concentrations in leaf or non-woody shoot tissues from at least two plant species growing in the same environment. Each study contained at least one species in common with another study. KEY RESULTS: Meta-analysis of the data revealed that, in general, ferns, gymnosperms and angiosperms accumulated less Si in their shoots than non-vascular plant species and horsetails. Within angiosperms and ferns, differences in shoot Si concentration between species grouped by their higher-level phylogenetic position were identified. Within the angiosperms, species from the commelinoid monocot orders Poales and Arecales accumulated substantially more Si in their shoots than species from other monocot clades. CONCLUSIONS: A high shoot Si concentration is not a general feature of monocot species. Information on the phylogenetic variation in shoot Si concentration may provide useful palaeoecological and archaeological information, and inform studies of the biogeochemical cycling of Si and those of the molecular genetics of Si uptake and transport in plants.     

Evolutionary timescale of monocots determined by the fossilized birth‐death model using a large number of fossil records

Although the phylogenetic relationships between monocot orders are sufficiently understood, a timescale of their evolution is needed. Several studies on molecular clock dating are available, but their results have been biased by their calibration schemes. Recently, the fossilized birth‐death model, a type of Bayesian dating method, was proposed, and it does not require prior calibration and allows the use all available fossils. Using this model, we conducted divergence‐time estimations of monocots to explore their evolutionary timeline without calibration bias. This is the first application of this model to seed plants. The dataset contained the matK and rbcL chloroplast genes of 118 monocot genera covering all extant orders. We employed information from 247 monocot fossils, which exceeded previous dating analyses that used a maximum of 12 monocot fossils. The crown group of monocots was dated to approximately the Late Jurassic–Early Cretaceous periods, and most extant monocot orders were estimated to diverge throughout the Early Cretaceous. Our results overlapped with the divergence time of insect lineages, such as beetles and flies, suggesting an association with pollinators in early monocot evolution. In addition, we proposed three new orders based on divergence time: Orchidales separated from Asparagales and Tofieldiales and Arales separated from Aslimatales.     

THE ORGANIZATION OF THE VASCULAR SYSTEM IN THE STEMS OF THE NYMPHAEACEAE. II. NYMPHAEA SUBGENERA ANECPHYA,LOTOS, AND BRACHYCERAS

The anatomy and organization of the stem vascular system was analyzed in representative taxa of Nymphaea (subgenera Anecphya, Lotos, and Brachyceras). The stem vascular system consists of a series of concentric axial stem bundles from which traces to lateral organs depart. At the node each leaf is supplied with a median and two lateral leaf traces. At the same level a root trace supplies vascular tissue to adventitious roots borne on the leaf base. Flowers and vegetative buds occupy leaf sites in the genetic spiral and in the parastichies seen on the stem exterior. Certain leaves have flowers related to them spatially and by vascular association. Flowers (and similarly vegetative buds) are vascularized by a peduncle trace that arises from a peduncle fusion bundle located in the pith. The peduncle fusion bundle is formed by the fusion of vascular tissue derived from axial stem bundles that supply traces to certain leaves. The organization of the vascular system in the investigated taxa of Nymphaea is unique to angiosperms but similar to other subgenera of Nymphaea.     

Comparative analysis of rice MADS-box genes expressed during flower development

MADS-box genes involved in flower development have been isolated and studied in a wide variety of plant species. However, most of these studies are related to dicot species like Antirrhinum majus, Arabidopsis thaliana and Petunia hybrida. Although the floral structures of typical monocot and dicot flowers differ substantially, previous studies indicate that MADS-box genes controlling floral organ identity in dicots can also be identified in monocot plants like rice and maize. To extend this study further to obtain a more global picture of monocot and dicot MADS-box gene evolution, we performed a phylogenetic study using MADS-box genes from A. thaliana and Oryza sativa. Furthermore, we investigated whether the identified orthologues of Arabidopsis and rice have a conserved expression profile that could indicate conservation of function.     

PHLOEM OF PRIMITIVE ANGIOSPERMS. I. SIEVE-ELEMENT ONTOGENY IN THE PETIOLE OF LIRIODENDRON TULIPIFERA L. (MAGNOLIACEAE)

As part of a continuing study of sieve elements in primitive angiosperms, a study of this cell type was undertaken in Liriodendron tulipifera. A typical ontogenetic sequence was observed in which synthetic processes such as wall thickening are followed in time by cellular lysis of nucleus, ribosomes, microtubules, vacuoles, and dictyosomes. This lysis is selective in that certain cellular components (e.g., the plasmalemma) remain unaffected. Concomitant with lysis is the formation of sieve-area pores from plasmodesmata. Comparison of pore size on end and lateral walls indicates that the use of the term “sieve tube” rather than “sieve cell” to describe these elements is appropriate.     

Correlations of Life Form,Pollination Mode and Sexual System in Aquatic Angiosperms

Aquatic plants are phylogenetically well dispersed across the angiosperms. Reproductive and other life-history traits of aquatic angiosperms are closely associated with specific growth forms. Hydrophilous pollination exhibits notable examples of convergent evolution in angiosperm reproductive structures, and hydrophiles exhibit great diversity in sexual system. In this study, we reconstructed ancestral characters of aquatic lineages based on the phylogeny of aquatic angiosperms. Our aim is to find the correlations of life form, pollination mode and sexual system in aquatic angiosperms. Hydrophily is the adaptive evolution of completely submersed angiosperms to aquatic habitats. Hydroautogamy and maleflower-ephydrophily are the transitional stages from anemophily and entomophily to hydrophily. True hydrophily occurs in 18 submersed angiosperm genera, which is associated with an unusually high incidence of unisexual flowers. All marine angiosperms are submersed, hydrophilous species. This study would help us understand the evolution of hydrophilous pollination and its correlations with life form and sexual system.