MACROALGAL CANDIDATES FOR GENOMICS1

Genomes from over 130 organisms have been either sequenced completely or are currently under investigation. These studies include a wide array of Bacteria, a smaller number of Archaea, model‐system eukaryotes, parasitic protists, and even several microalgae. However, no major effort is underway to acquire a complete nuclear genome sequence from a single macroalga or seaweed despite their crucial contribution to the biodiversity and energy economy of oceans and estuaries. Here we examine various macroalgae as potential candidates for a genome project. A set of criteria is presented, followed by a brief discussion of how well different candidates from the principal macroalgae groups, green, brown, and red algae, meet these criteria. Based on our analyses, we conclude that the red seaweed, Porphyra yezoensis Ueda, should be the leading candidate for a macroalgal genomics initiative. We realize, of course, that others in the phycological community might have a different opinion and that a broad consensus among algal researchers is required to make seaweed genomics a reality; thus the primary intention of this review is to initiate and encourage further discussion as to where the phycological community should focus its genomic efforts.     

GENOMICS IN THE LIGHT OF EVOLUTIONARY TRANSITIONS

Molecular biology has entrenched the gene as the basic hereditary unit and genomes are often considered little more than collections of genes. However, new concepts and genomic data have emerged, which suggest that the genome has a unique place in the hierarchy of life. Despite this, a framework for the genome as a major evolutionary transition has not been fully developed. Instead, genome origin and evolution are frequently considered as a series of neutral or nonadaptive events. In this article, we argue for a Darwinian multilevel selection interpretation for the origin of the genome. We base our arguments on the multilevel selection theory of hypercycles of cooperative interacting genes and predictions that gene‐level trade‐offs in viability and reproduction can help drive evolutionary transitions. We consider genomic data involving mobile genetic elements as a test case of our view. A new concept of the genome as a discrete evolutionary unit emerges and the gene–genome juncture is positioned as a major evolutionary transition in individuality. This framework offers a fresh perspective on the origin of macromolecular life and sets the scene for a new, emerging line of inquiry—the evolutionary ecology of the genome.     

FOUNDING A NEW SCIENCE: MIND GENOMICS

We present in this article our vision for a new science, modeled on the emerging science of genomics and the technology of informatics. Our goal in this new science is to better understand how people react to ideas in a formal and structured way, using the principles of stimulus–response (from experimental psychology), conjoint analysis (from consumer research and statistics), Internet‐based testing (from marketing research) and multiple tests to identify patterns of mind‐sets (patterned after genomics). We show how this formal approach can then be used to construct new, innovative ideas in business. We demonstrate the approach using the development of new ideas for an electronic color palette for cosmetic products to be used by consumers.     

结核分枝杆菌功能基因组研究的方法学

DNA芯片、基因中断、基因互补法、差示荧光诱导法、生物信息学、蛋白质组、DNA库免疫、细菌人工染色体库是结核分枝杆菌研究的主要方法。综合利用上述技术可能是我们开展结核分枝杆菌功能基因组学研究的最佳切入点。     

MARINE MACROALGAL DIVERSITY IN THE REPUBLIC OF PANAMA

The marine flora of Panama remains poorly described to date, having been described from a few sporadic and species poor (<50 species) collections in the early half of the century and a couple of dedicated surveys in the latter half. With the exception of a few studies that have focused on particular genera or species, only a single marine floral survey has been published in the past three decades. In 1999 we collected marine algae from nearly 100 different collection sites along both coasts of Panama over a 10 month period of time. Over 1500 specimens have been curated, representing 250 Caribbean species and 117 Pacific species. This is an increase in algal diversity of approximately 100 and 50% for the Caribbean and Pacific flora, respectively, relative to Earle's compilation of 1972. We estimate that algal diversity in Panama may approach 450 species as the remaining 30% of the collection is identified and previous records are incorporated. Aspects of biogeography will be discussed in light of such extraordinary diversity over a relatively confined region.     

WATER MOTION, MARINE MACROALGAL PHYSIOLOGY, AND PRODUCTION

Water motion is a key determinant of marine macroalgal production, influencing directly or indirectly physiological rates and community structure. Our understanding of how marine macroalgae interact with their hydrodynamic environment has increased substantially over the past 20 years, due to the application of tools such as flow visualization to aquatic vegetation, and in situ measurements of seawater velocity and turbulence. This review considers how the hydrodynamic environment in which macroalgae grow influences their ability to acquire essential resources and how macroalgae might respond physiologically to fluctuations in their hydrodynamic regime with a focus on: (1) the biochemical processes occurring within the diffusion boundary layer (DBL) that might reduce rates of macroalgal production; (2) time scales over which measurements of velocity and DBL processes should be made, discussing the likelihood of in situ mass transfer limitation; (3) if and how macroalgal morphology influences resource acquisition in slow flows; and (4) ecobiomechanics and how hydrodynamic drag might influence resource acquisition and allocation. Finally, the concept that macroalgal production is enhanced in wave-exposed versus sheltered habitats is discussed.     

PATTERNS OF MACROALGAL SPECIES DIVERSITY IN DANISH ESTUARIES

We analyzed species number of macroalgae in relation to environmental variables at two spatial levels comprising 202 individual sites and 26 entire estuaries in Denmark. The species number of macroalgae increased with salinity and declined with nutrient concentrations both at the sites and in the estuaries. Availability of hard substratum was associated with higher species richness at the sites. The number of macroalgal species in the estuaries increased with higher mean depth and longer coastline, suggesting that both the vertical and horizontal extension of the colonization area are important for the maximum representation of macroalgal species. Mean depth explained as a single predictor 60% of the variability in species number in entire estuaries. Estuaries with high mean depth also tend to be large and have high salinity and transparent waters due to efficient exchange with open waters. In conclusion, we find that the regulation of species richness of macroalgae in Danish estuaries, though complex, is influenced predictably by salinity, water transparency, nutrient concentration, and availability of hard substrata.     

拟南芥基因组研究进展

拟南芥基因组全序列在2000年底已完全测定并公开发表,这是第一个经完全测序的开花植物.序列的获得为进行大规模高等植物基因的鉴定、基因结构与功能的分析、基因表达与调控的研究奠定了坚实物质基础,并将改进和发展一系列进行功能基因组研究的方法与技术.     

PHLOROTANNINS AS CHEMICAL DEFENSE AGAINST MACROALGAL EPIPHYTES ON ASCOPHYLLUM NODOSUM

Brock, E., Åberg, P., & Pavia, H. Department of Marine Botany, Göteborg University, Box 461, SE 40530 Göteborg, Sweden. Phlorotannins are a group of polyphenolic acids present in brown algae. They have been shown to act as defense against herbivores and UV-B radiation. They have also been suggested to function as a defense against epiphytes. In this study the effect of the presence of macroalgal epiphytes on the phlorotannin content in Ascophyllum nodosum was analysed. Six adult plants of A. nodosum were collected from each of four sites in the archipelago on the west coast of Sweden. Four apical parts from each of the 24 plants were analysed for their phlorotannin content. For each plant, two samples were without any visible macroalgal epiphyte growth and two samples were 50-100% covered by epiphytes, mainly of the orders Ceramiales and Ectocarpales. We were not able to detect any general effect of epiphytes on the phlorotannin content. There was, however, a significant interaction between the two factors algal individual and epiphytes, where apical parts with epiphytes present had either higher or lower levels of phlorotannin than samples without epiphytes. Furthermore, there was a general, significant difference in the phlorotannin content among sites. The results suggest that the relationship between macroalgal epiphytes and phlorotannin production in A. nodosum is complex and influenced by several interacting factors.     

FOURIER TRANSFORM INFRARED MICROSPECTROSCOPY AS A TOOL TO IDENTIFY MACROALGAL PROPAGULES1

Understanding of macroalgal dispersal has been hindered by the difficulty in identifying propagules. Different carrageenans typically occur in gametophytes and tetrasporophytes of the red algal family Gigartinaceae, and we may expect that carpospores and tetraspores also differ in composition of carrageenans. Using Fourier transform infrared (FT‐IR) microspectroscopy, we tested the model that differences in carrageenans and other cellular constituents between nuclear phases should allow us to discriminate carpospores and tetraspores of Chondrus verrucosus Mikami. Spectral data suggest that carposporophytes isolated from the pericarp and female gametophytes contained κ‐carrageenan, whereas tetrasporophytes contained λ‐carrageenan. However, both carpospores and tetraspores exhibited absorbances in wave bands characteristic of κ‐, ι‐, and λ‐carrageenans. Carpospores contained more proteins and may be more photosynthetically active than tetraspores, which contained more lipid reserves. We draw analogies to planktotrophic and lecithotrophic larvae. These differences in cellular chemistry allowed reliable discrimination of spores, but pretreatment of spectral data affected the accuracy of classification. The best classification of spores was achieved with extended multiplicative signal correction (EMSC) pretreatment using partial least squares discrimination analysis, with correct classification of 86% of carpospores and 83% of tetraspores. Classification may be further improved by using synchrotron FT‐IR microspectroscopy because of its inherently higher signal‐to‐noise ratio compared with microspectroscopy using conventional sources of IR. This study demonstrates that FT‐IR microspectroscopy and bioinformatics are useful tools to advance our understanding of algal dispersal ecology through discrimination of morphologically similar propagules both within and potentially between species.     

UPTAKE OF NEUROTRANSMITTER CANDIDATES BY PIGEON OPTIC TECTUM

—The kinetics of the uptake of various compounds into the crude mitochondrial fraction (P₂-fraction) of the pigeon optic tectum were studied. Aspartate, GABA, glutamate, glycine, proline and choline were taken up by high and low affinity systems. Only low affinity uptake was found for leucine and dopamine. The uptake for taurine was not saturable. The uptakes for all of the above compounds were temperature and sodium dependent. The high affinity system was more effected by sodium withdrawal than the low affinity system. Continuous sucrose gradients from 0.4 to 1.5 m were run with incubated P₂ fractions. Particle-bound radioactivity sedimented in a density range of 1.0 to 1.2 m -sucrose. Additional experiments with glutamate showed that its uptake is competitively inhibited by aspartate. The addition of a 1000-fold excess of glutamate to a P₂ fraction incubated at a concentration of 10^–6m -glutamate led to a massive decrease of particle-bound radioactivity, suggesting a coupled action of uptake and efflux.     

PROPOSAL OF ECTOCARPUS SILICULOSUS (ECTOCARPALES,PHAEOPHYCEAE) AS A MODEL ORGANISM FOR BROWN ALGAL GENETICS AND GENOMICS1,2

The emergence of model organisms that permit the application of a powerful combination of genomic and genetic approaches has been a major factor underlying the advances that have been made in the past decade in dissecting the molecular basis of a wide range of biological processes. However, the phylogenetic distance separating marine macroalgae from these model organisms, which are mostly from the animal, fungi, and higher plant lineages, limits the latters' applicability to problems specific to macroalgal biology. There is therefore a pressing need to develop similar models for the macroalgae. Here we describe a survey of potential model brown algae in which particular attention was paid to characteristics associated with a strong potential for genomic and genetic analysis, such as a small nuclear genome size, sexuality, and a short life cycle. Flow cytometry of nuclei isolated from zoids showed that species from the Ectocarpales possess smaller haploid genomes (127–290 Mbp) than current models among the Laminariales (580–720 Mbp) and Fucales (1095–1271 Mbp). Species of the Ectocarpales may complete their life histories in as little as 6 weeks in laboratory culture and are amenable to genetic analyses. Based on this study, we propose Ectocarpus siliculosus (Dillwyn) Lyngbye as an optimal choice for a general model organism for the molecular genetics of the brown algae.     

JOURNAL OF GENETICS AND GENOMICS 2017 Vol. 44 TOTAL CONTENTS

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JOURNAL OF GENETICS AND GENOMICS 2016 Vol.43 TOTAL CONTENTS

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LANDSCAPE GENOMICS IN ATLANTIC SALMON (SALMO SALAR): SEARCHING FOR GENE–ENVIRONMENT INTERACTIONS DRIVING LOCAL ADAPTATION

A growing number of studies are examining the factors driving historical and contemporary evolution in wild populations. By combining surveys of genomic variation with a comprehensive assessment of environmental parameters, such studies can increase our understanding of the genomic and geographical extent of local adaptation in wild populations. We used a large‐scale landscape genomics approach to examine adaptive and neutral differentiation across 54 North American populations of Atlantic salmon representing seven previously defined genetically distinct regional groups. Over 5500 genome‐wide single nucleotide polymorphisms were genotyped in 641 individuals and 28 bulk assays of 25 pooled individuals each. Genome scans, linkage map, and 49 environmental variables were combined to conduct an innovative landscape genomic analysis. Our results provide valuable insight into the links between environmental variation and both neutral and potentially adaptive genetic divergence. In particular, we identified markers potentially under divergent selection, as well as associated selective environmental factors and biological functions with the observed adaptive divergence. Multivariate landscape genetic analysis revealed strong associations of both genetic and environmental structures. We found an enrichment of growth‐related functions among outlier markers. Climate (temperature–precipitation) and geological characteristics were significantly associated with both potentially adaptive and neutral genetic divergence and should be considered as candidate loci involved in adaptation at the regional scale in Atlantic salmon. Hence, this study significantly contributes to the improvement of tools used in modern conservation and management schemes of Atlantic salmon wild populations.