Morphological and molecular analysis of the Nematostella vectensis cnidom

The starlet sea anemone Nematostella vectensis is an emerging model organism for developmental and evolutionary biology. Due to the availability of genome data and its amenability to genetic manipulation Nematostella serves as a source for comparative molecular and phylogenetic studies. Despite this fact, the characterization of the nematocyst inventory and of nematocyst-specific genes is still fragmentary and sometimes misleading in this cnidarian species. Here, we present a thorough qualitative and quantitative analysis of nematocysts in Nematostella vectensis. In addition, we have cloned major nematocyst components, Nematostella minicollagens 1, 3 and 4, and show their expression patterns by in situ hybridization and immunocytochemistry using specific antibodies. Our data provides tools and insights for further studies on nematocyst morphogenesis in Nematostella and comparative evolution in cnidarians.     

Comparison of developmental trajectories in the starlet sea anemone Nematostella vectensis: embryogenesis, regeneration, and two forms of asexual fission

Abstract. The starlet sea anemone, Nematostella vectensis , is a small burrowing estuarine animal, native to the Atlantic coast of North America. In recent years, this anemone has emerged as a model system in cnidarian developmental biology. Molecular studies of embryology and larval development in N. vectensis have provided important insights into the evolution of key metazoan traits. However, the adult body plan of N. vectensis may arise via four distinct developmental trajectories: (1) embryogenesis following sexual reproduction, (2) asexual reproduction via physal pinching, (3) asexual reproduction via polarity reversal, and (4) regeneration following bisection through the body column. Here, we compare the ontogenetic sequences underlying alternate developmental trajectories. Additionally, we describe the predictable generation of anomalous phenotypes that can occur following localized injuries to the body column. These studies suggest testable hypotheses on the molecular mechanisms underlying alternate developmental trajectories, and they provoke new questions about the evolution of novel developmental trajectories and their initiation via environmental cues.     

A surprising abundance of human disease genes in a simple "basal" animal, the starlet sea anemone (Nematostella vectensis).

Invertebrate animals have provided important insights into the mechanisms of, and treatment for, numerous human diseases. A surprisingly high proportion of genes underlying human disease are present in the genome of a simple, evolutionarily basal invertebrate animal, Nematostella vectensis, including some genes that are absent in established invertebrate model organisms. This, together with the laboratory tractability and regenerative capability of N. vectensis, recommends the species as an important new experimental model for the study of genes underlying human disease.     

Ultrastructural features of the trophonema and oogenesis in the starlet sea anemone, Nematostella vectensis (Edwardsiidae)

Abstract. The starlet sea anemone, Nematostella vectensis Stephenson 1935, is a burrowing, estuarine species that has become a model organism for fundamental studies of cnidarian and metazoan development. During early oogenesis, oocytes appear in the basal region of the gastrodermis in the reproductive mesenteries and gradually bulge into the adjacent connective tissue space (mesoglea) where the majority of oocyte growth and vitellogenesis occurs. However, oocytes do not physically contact the cellular and amorphous matrix of the mesogleal compartment due to a thin, intervening basal lamina. Oocytes retain limited contact with the basal gastrodermal epithelium via groups of ultrastructurally modified gastrodermal cells called trophocytes. Trophocytes are monociliated accessory cells of somatic origin that collectively form a structure called the trophonema, a unique accessory cell/oocyte association not observed outside the Cnidaria. The trophonema consists of 50–60 trophocytes that maintain contact with <1% of the oocyte surface and forms a circular, bowel‐shaped depression on the luminal surface of the gastrodermis as they sink into the mesoglea with the oocyte. The oocyte remains highly polarized throughout oogenesis with the germinal vesicle positioned near the trophonema and presumably representing the future animal pole of the embryo. Contact between the trophonema and the oocyte is restricted to cell junctions connecting peripheral trophocytes and narrow extensions from the oocyte. Previous studies suggest that the trophonema plays a role in transport of extracellular digestive products from the gastrovascular cavity to the oocyte, and the ultrastructural features described in this study are consistent with that view. Vitellogenesis is described for the first time in a sea anemone. Yolk synthesis involves both autosynthetic and heterosynthetic processes including the biosynthetic activity of the Golgi complex and the uptake of extraoocytic yolk precursors via endocytosis, respectively.     

Ancient complexity of the non-Hox ANTP gene complement in the anthozoan Nematostella vectensis: implications for the evolution of the ANTP superclass

The origin and evolution of ANTP superclass genes has raised controversial discussions. While recent evidence suggests that a true Hox cluster emerged after the cnidarian bilaterian split, the origin of the ANTP superclass as a whole remains unclear. Based on analyses of bilaterian genomes, it seems very likely that clustering has once been a characteristic of all ANTP homeobox genes and that their ancestors have emerged through several series of cis-duplications from the same genomic region. Since the diploblastic Cnidaria possess orthologs of some non-Hox ANTP genes, at least some steps of the expansion of this hypothetical homeobox gene array must have occurred in the last common ancestor of both lineages--but it is unknown to what extent. By screening the unassembled Nematostella genome, we have identified unambiguous orthologs to almost all non-Hox ANTP genes which are present in Bilateria--with the exception of En, Tlx and (possibly) Vax. Furthermore, Nematostella possesses ANTP genes that are missing in some bilaterian lineages, like the rough gene or NK7. In addition, several ANTP homeobox gene families have been independently duplicated in Nematostella. We conclude that the last cnidarian/bilaterian ancestor already harboured the almost full complement of non-Hox ANTP genes before the Hox system evolved.     

Expanded Functional Diversity of Shaker K+ Channels in Cnidarians Is Driven by Gene Expansion

The genome of the cnidarian Nematostella vectensis (starlet sea anemone) provides a molecular genetic view into the first nervous systems, which appeared in a late common ancestor of cnidarians and bilaterians. Nematostella has a surprisingly large and diverse set of neuronal signaling genes including paralogs of most neuronal signaling molecules found in higher metazoans. Several ion channel gene families are highly expanded in the sea anemone, including three subfamilies of the Shaker K⁺ channel gene family: Shaker (Kv1), Shaw (Kv3) and Shal (Kv4). In order to better understand the physiological significance of these voltage-gated K⁺ channel expansions, we analyzed the function of 18 members of the 20 gene Shaker subfamily in Nematostella. Six of the Nematostella Shaker genes express functional homotetrameric K⁺ channels in vitro. These include functional orthologs of bilaterian Shakers and channels with an unusually high threshold for voltage activation. We identified 11 Nematostella Shaker genes with a distinct “silent” or “regulatory” phenotype; these encode subunits that function only in heteromeric channels and serve to further diversify Nematostella Shaker channel gating properties. Subunits with the regulatory phenotype have not previously been found in the Shaker subfamily, but have evolved independently in the Shab (Kv2) family in vertebrates and the Shal family in a cnidarian. Phylogenetic analysis indicates that regulatory subunits were present in ancestral cnidarians, but have continued to diversity at a high rate after the split between anthozoans and hydrozoans. Comparison of Shaker family gene complements from diverse metazoan species reveals frequent, large scale duplication has produced highly unique sets of Shaker channels in the major metazoan lineages.     

Genomic survey of candidate stress-response genes in the estuarine anemone Nematostella vectensis

Salt marshes are challenging habitats due to natural variability in key environmental parameters including temperature, salinity, ultraviolet light, oxygen, sulfides, and reactive oxygen species. Compounding this natural variation, salt marshes are often heavily impacted by anthropogenic insults including eutrophication, toxic contamination, and coastal development that alter tidal and freshwater inputs. Commensurate with this environmental variability, estuarine animals generally exhibit broader physiological tolerances than freshwater, marine, or terrestrial species. One factor that determines an organism's physiological tolerance is its ability to upregulate "stress-response genes" in reaction to particular stressors. Comparative studies on diverse organisms have identified a number of evolutionarily conserved genes involved in responding to abiotic and biotic stressors. We used homology-based scans to survey the sequenced genome of Nematostella vectensis, the starlet sea anemone, an estuarine specialist, to identify genes involved in the response to three kinds of insult-physiochemical insults, pathogens, and injury. Many components of the stress-response networks identified in triploblastic animals have clear orthologs in the sea anemone, meaning that they must predate the cnidarian-triploblast split (e.g., xenobiotic receptors, biotransformative genes, ATP-dependent transporters, and genes involved in responding to reactive oxygen species, toxic metals, osmotic shock, thermal stress, pathogen exposure, and wounding). However, in some instances, stress-response genes known from triploblasts appear to be absent from the Nematostella genome (e.g., many metal-complexing genes). This is the first comprehensive examination of the genomic stress-response repertoire of an estuarine animal and a member of the phylum Cnidaria. The molecular markers of stress response identified in Nematostella may prove useful in monitoring estuary health and evaluating coastal conservation efforts. These data may also inform conservation efforts on other cnidarians, such as the reef-building corals.     

Molecular evolution of SPARC: absence of the acidic module and expression in the endoderm of the starlet sea anemone, Nematostella vectensis

The matricellular glycoprotein SPARC is composed of three functional domains that are evolutionarily conserved in organisms ranging from nematodes to mammals: a Ca²⁺-binding glutamic acid-rich acidic domain at the N-terminus (domain I), a follistatin-like module (domain II), and an extracellular Ca²⁺-binding (EC) module that contains two EF-hands and two collagen-binding epitopes (domain III). We report that four SPARC orthologs (designated nvSPARC1-4) are expressed by the genome of the starlet anemone Nematostella vectensis, a diploblastic basal cnidarian composed of an ectoderm and endoderm separated by collagen-based mesoglea. We also report that domain I is absent from all N. vectensis SPARC orthologs. In situ hybridization data indicate that N. vectensis SPARC mRNAs are restricted to the endoderm during post-gastrula development. The absence of the Ca²⁺-binding N-terminal domain in cnidarians and conservation of collagen-binding epitopes suggests that SPARC first evolved as a collagen-binding matricellular glycoprotein, an interaction likely to be dependent on the binding of Ca²⁺-ions to the two EF-hands in the EC domain. We propose that further Ca²⁺-dependent activities emerged with the acquisition of an acidic N-terminal module in triplobastic organisms.     

Global population genetic structure of the starlet anemone <Emphasis Type="Italic">Nematostella vectensis</Emphasis>: multiple introductions and implications for conservation policy

Distinguishing natural versus anthropogenic dispersal of organisms is essential for determining the native range of a species and implementing an effective conservation strategy. For cryptogenic species with limited historical records, molecular data can help to identify introductions. Nematostella vectensis is a small, burrowing estuarine sea anemone found in tidally restricted salt marsh pools. This species’ current distribution extends over three coast lines: (i) the Atlantic coast of North America from Nova Scotia to Georgia, (ii) the Pacific coast of North America from Washington to central California, and (iii) the southeast coast of England. The 1996 IUCN Red List designates N. vectensis as “vulnerable” in England. Amplified fragment length polymorphism (AFLP) fingerprinting of 516 individuals from 24 N. vectensis populations throughout its range and mtDNA sequencing of a subsample of these individuals strongly suggest that anthropogenic dispersal has played a significant role in its current distribution. Certain western Atlantic populations of N. vectensis exhibit greater genetic similarity to Pacific populations or English populations than to other western Atlantic populations. At the same time, F-statistics showing high degrees of genetic differentiation between geographically proximate populations support a low likelihood for natural dispersal between salt marshes. Furthermore, the western Atlantic harbors greater genetic diversity than either England or the eastern Pacific. Collectively, these data clearly imply that N. vectensis is native to the Atlantic coast of North America and that populations along the Pacific coast and in England are cases of successful introduction.     

Analysis of rare amino acid replacements supports the Coelomata clade

The recent analysis of a novel class of rare genomic changes, RGC_CAMs (after conserved amino acids-multiple substitutions), supported the Coelomata clade of animals as opposed to the Ecdysozoa clade (Rogozin et al. 2007). A subsequent reanalysis, with the sequences from the sea anemone Nematostella vectensis included in the set of outgroup species, suggested that this result was an artifact caused by reverse amino replacements and claimed support for Ecdysozoa (Irimia et al. 2007). We show that the internal branch connecting the sea anemone to the bilaterian animals is extremely short, resulting in a weak statistical support for the Coelomata clade. Direct estimation of the level of homoplasy, combined with taxon sampling with different sets of outgroup species, reinforces the support for Coelomata, whereas the effect of reversals is shown to be relatively minor.     

种子异型性及其生态意义的研究进展

种子异型性是指同一植株产生不同形状或行为种子的现象。根据异型种子在植株上的生长位置, 种子异型性可划分为地上下结实性和地上种子异型性两类。此现象已在26科129属292种被子植物中报道。异型性种子植物主要分布于干旱半干旱区、荒漠和盐渍土地区等干扰强烈的环境, 在菊科和藜科中最为常见, 主要出现在一年生植物中。种子异型性在避免密集负效应、减弱同胞子代间的竞争、采取两头下注策略以适应时空异质性环境等方面具有重要的进化生态意义。该文系统总结了国内外种子异型性的研究工作, 主要内容包括: 1)种子异型性的概念、类型和种类, 2)具有异型种子植物的生境和生活型, 3)异型种子的生态学特性, 4)种子异型性的理论模型, 5)种子异型性的生态意义。在综述文献的基础上, 对今后的研究进行了展望。针对国内外的研究现状, 提出两点建议: 1)系统调查具有种子异型性现象的植物种类, 摸清其生物学特性; 2)确定研究种子异型性现象的模式植物, 从生态学、生理学和分子生物学等学科角度来研究种子异型性的个体发育机制及分子调控机理。     

Coalescent methods for estimating phylogenetic trees

We review recent models to estimate phylogenetic trees under the multispecies coalescent. Although the distinction between gene trees and species trees has come to the fore of phylogenetics, only recently have methods been developed that explicitly estimate species trees. Of the several factors that can cause gene tree heterogeneity and discordance with the species tree, deep coalescence due to random genetic drift in branches of the species tree has been modeled most thoroughly. Bayesian approaches to estimating species trees utilizes two likelihood functions, one of which has been widely used in traditional phylogenetics and involves the model of nucleotide substitution, and the second of which is less familiar to phylogeneticists and involves the probability distribution of gene trees given a species tree. Other recent parametric and nonparametric methods for estimating species trees involve parsimony criteria, summary statistics, supertree and consensus methods. Species tree approaches are an appropriate goal for systematics, appear to work well in some cases where concatenation can be misleading, and suggest that sampling many independent loci will be paramount. Such methods can also be challenging to implement because of the complexity of the models and computational time. In addition, further elaboration of the simplest of coalescent models will be required to incorporate commonly known issues such as deviation from the molecular clock, gene flow and other genetic forces.     

Molecular Markers and the Management of Tropical Trees: the Case of Indigenous Fruits

Millions of people in the tropics benefit from the harvest, cultivation and consumption of indigenous fruit trees (IFTs). Knowledge concerning the structuring of genetic variation within these species is crucial for sustainable use and conservation, but the availability of such information has been limited. By reference to case study species that are currently the subject of active domestication initiatives, in this essay we provide guidance for the suitable application of molecular marker methods for characterising IFTs. We discuss three particular areas where molecular markers are able to provide unique insights for further promotion activities: (i) in understanding the past domestication of taxa, (ii) in determining effective population sizes; and (iii) in assessing the value of a decentralised approach for future domestication. Despite the potential utility of molecular markers, a disjunction between assessment and practical application is evident, which reflects a lack of integration of laboratory research with other species promotion activities. Greater emphasis is required on team-based research and partnerships, more work should be undertaken in agricultural landscapes, and further research on mating systems and gene flow are crucial. Our essay provides a model for molecular marker studies on other trees that are important to rural communities in the tropics.     

The sesquiterpenoids and their chemotaxonomic implications in Senecio L. (Asteraceae)

Sesquiterpenoids are important characteristic compounds in Asteraceae plants. These compounds have been proposed to be potential chemotaxonomic markers, but this application has not been comprehensively investigated. In this paper, sesquiterpenoids from 149 species of the genus Senecio were investigated to assess their taxonomic utility. The presence and absence were encoded as binary taxonomic characteristics and subsequently utilised in a clustering analysis. The previously biosynthesis pathway of sesquiterpenoids was taken into account to explore the relationship among these species contained different sesquiterpenoid types. In addition, the DNA phylogeny was also considered to explore the distribution and evolution of sesquiterpenoids in genus Senecio further. As a result, seven chemical major sections within the Senecio were recognised based on the chemical character. Although with several exceptions, the biosynthesis pathway, molecular phylogeny and the geographical origin of these sesquiterpenoid were found to be related to the chemical sections, which largely confirmed the validity of our chemo-classification for genus Senecio. In conclusion, we suggest that the sesquiterpenoid character in Senecio has some value for the genus taxonomy but should be analysed carefully and critically.     

The molecular mechanisms and factors affecting the feeding habits of silkworm (Lepidoptera: Bombyxidae)

Food is critical to the survival and development of insects. Bombyx mori (Lepidoptera: Bombycidae), a Lepidoptera model insect with economic significance, is a well-known oligophagous insect that mainly feeds on mulberry leaves. The feeding characteristics of this particular species provide an excellent model for studying the food selection of insect host plants. In recent years, there has been an increasing number of studies on the factors affecting the feeding of silkworms, especially with the development of molecular technology. Many mysteries have been gradually solved. This paper summarizes and discusses the factors that affect the feeding of silkworms, with a focus on the molecular mechanisms of silkworm feeding. It is hoped that this work will be helpful for further research on artificial diets for silkworms and disease control in lepidopteran insects.     

Symbiotic conversations are revealed under genetic interrogation

The recent development and application of molecular genetics to the symbionts of invertebrate animal species have advanced our knowledge of the biochemical communication that occurs between the host and its bacterial symbionts. In particular, the ability to manipulate these associations experimentally by introducing genetic variants of the symbionts into naive hosts has allowed the discovery of novel colonization mechanisms and factors. In addition, the role of the symbionts in inducing normal host development has been revealed, and its molecular basis described. In this Review, I discuss many of these developments, focusing on what has been discovered in five well-understood model systems.