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Kim E.,Sackler Institute for Comparative Genomics | Maruyama S.,Japan National Institute for Basic Biology
Acta Societatis Botanicorum Poloniae | Year: 2014

A single origin of plastids and the monophyly of three "primary" plastid-containing groups - the Chloroplastida (or Viridiplantae; green algae+land plants), Rhodophyta, and Glaucophyta - are widely accepted, mainstream hypotheses that form the basis for many comparative evolutionary studies. This "Archaeplastida" hypothesis, however, thus far has not been unambiguously confirmed by phylogenetic studies based on nucleocytoplasmic markers. In view of this as well as other lines of evidence, we suggest the testing of an alternate hypothesis that plastids of the Chloroplastida are of secondary origin. The new hypothesis is in agreement with, or perhaps better explains, existing data, including both the plastidal and nucleocytoplasmic characteristics of the Chloroplastida in comparison to those of other groups. © The Author(s) 2014.

Macrander J.,Ohio State University | Brugler M.R.,Sackler Institute for Comparative Genomics | Brugler M.R.,Brooklyn College | Daly M.,Ohio State University
BMC Genomics | Year: 2015

Background: The use of venom in intraspecific aggression is uncommon and venom-transmitting structures specifically used for intraspecific competition are found in few lineages of venomous taxa. Next-generation transcriptome sequencing allows robust characterization of venom diversity and exploration of functionally unique tissues. Using a tissue-specific RNA-seq approach, we investigate the venom composition and gene ontology diversity of acrorhagi, specialized structures used in intraspecific competition, in aggressive and non-aggressive polyps of the aggregating sea anemone Anthopleura elegantissima (Cnidaria: Anthozoa: Hexacorallia: Actiniaria: Actiniidae). Results: Collectively, we generated approximately 450,000 transcripts from acrorhagi of aggressive and non-aggressive polyps. For both transcriptomes we identified 65 candidate sea anemone toxin genes, representing phospholipase A2s, cytolysins, neurotoxins, and acrorhagins. When compared to previously characterized sea anemone toxin assemblages, each transcriptome revealed greater within-species sequence divergence across all toxin types. The transcriptome of the aggressive polyp had a higher abundance of type II voltage gated potassium channel toxins/Kunitz-type protease inhibitors and type II acrorhagins. Using toxin-like proteins from other venomous taxa, we also identified 612 candidate toxin-like transcripts with signaling regions, potentially unidentified secretory toxin-like proteins. Among these, metallopeptidases and cysteine rich (CRISP) candidate transcripts were in high abundance. Furthermore, our gene ontology analyses identified a high prevalence of genes associated with "blood coagulation" and "positive regulation of apoptosis", as well as "nucleoside: sodium symporter activity" and "ion channel binding". The resulting assemblage of expressed genes may represent synergistic proteins associated with toxins or proteins related to the morphology and behavior exhibited by the aggressive polyp. Conclusion: We implement a multifaceted approach to investigate the assemblage of expressed genes specifically within acrorhagi, specialized structures used only for intraspecific competition. By combining differential expression, phylogenetic, and gene ontology analyses, we identify several candidate toxins and other potentially important proteins in acrorhagi of A. elegantissima. Although not all of the toxins identified are used in intraspecific competition, our analysis highlights some candidates that may play a vital role in intraspecific competition. Our findings provide a framework for further investigation into components of venom used exclusively for intraspecific competition in acrorhagi-bearing sea anemones and potentially other venomous animals. © 2015 Macrander et al.; licensee BioMed Central.

Maruyama S.,Dalhousie University | Maruyama S.,Japan National Institute for Basic Biology | Kim E.,Sackler Institute for Comparative Genomics
Current Biology | Year: 2013

Green algae, land plants, and other photosynthetic eukaryotes possess plastids, such as chloroplasts, which have evolved from cyanobacterial ancestors via endosymbiosis [1]. An early evolutionary merger between heterotrophic eukaryotes and cyanobacteria called primary endosymbiosis gave rise to the first photosynthetic eukaryotes. A series of plastid acquisitions involving engulfment of eukaryotic phototrophs, known as secondary or tertiary endosymbiosis, followed [2]. Through these repeated symbiotic events, photosynthesis spread across a number of eukaryotic lineages [2, 3]. While the origin of eukaryotic photosynthesis was undoubtedly a fundamentally important evolutionary event in Earth's history, without which much of the modern marine phytoplankton would not exist, the cellular processes that shaped this initial plastid genesis remain largely unknown. Here, we report ultrastructural evidence for bacterial phagocytosis in a primary plastid-bearing alga. This mixotrophic green alga utilizes a mouth-like opening, a tubular channel, and a large permanent vacuole to engulf, transport, and digest bacterial cells. This mode of phagocytosis, likely inherited from its plastid-lacking ancestor, differs from those displayed by many other eukaryotes, including animals, amoebas, and ciliates. These results provide insight into the key phagocytosis step during the origin of the first photosynthetic eukaryotes. © 2013 Elsevier Ltd. All rights reserved.

Mendez M.,Columbia University | Mendez M.,Sackler Institute for Comparative Genomics | Mendez M.,Wildlife Conservation Society | Rosenbaum H.C.,Columbia University | And 6 more authors.
Molecular Ecology | Year: 2010

The assessment of population structure is a valuable tool for studying the ecology of endangered species and drafting conservation strategies. As we enhance our understanding about the structuring of natural populations, it becomes important that we also understand the processes behind these patterns. However, there are few rigorous assessments of the influence of environmental factors on genetic patterns in mobile marine species. Given their dispersal capabilities and localized habitat preferences, coastal cetaceans are adequate study species for evaluating environmental effects on marine population structure. The franciscana dolphin, a rare coastal cetacean endemic to the Western South Atlantic, was studied to examine these issues. We analysed genetic data from the mitochondrial DNA and 12 microsatellite markers for 275 franciscana samples utilizing frequency-based, maximum-likelihood and Bayesian algorithms to assess population structure and migration patterns. This information was combined with 10 years of remote sensing environmental data (chlorophyll concentration, water turbidity and surface temperature). Our analyses show the occurrence of genetically isolated populations within Argentina, in areas that are environmentally distinct. Combined evidence of genetic and environmental structure suggests that isolation by distance and a process here termed isolation by environmental distance can explain the observed correlations. Our approach elucidated important ecological and conservation aspects of franciscana dolphins, and has the potential to increase our understanding of ecological processes influencing genetic patterns in other marine species. © 2010 Blackwell Publishing Ltd.

News Article | February 2, 2016
Site: motherboard.vice.com

Researchers have analyzed the whole gross genome for the bedbug Cimex lectularius. Image: Benoit Guenard From New York to London to Istanbul, the bedbug—resistant to most insecticides and able to thrive in damp and dark conditions—continues to terrorise many. But researchers have finally sequenced the common bedbug’s complete genome, and they hope this may help in the future war against the pest. In a study published Tuesday in the journal Nature Communications, researchers from the American Museum of Natural History and Weill Cornell Medicine describe sequencing the genome of Cimex lectularius, the common bed bug species. Their findings could assist other scientists in understanding the pest’s biology and relationship with its environment, which could ultimately lead to the creation of a better pesticide. “This research has provided an enormous amount of information. In the past, it was like you were feeling your way through the dark, but now we have the whole genome and transcriptome,” said George Amato, the director of the Sackler Institute for Comparative Genomics and study lead author, over the phone. The transcriptome is a set of all messenger RNA molecules in one or more cells. The bed bug’s physical appearance, said Amato, doesn’t differ to how it looked 60 million years ago—though it didn’t feed on human blood back then. Its genome, however, has continued to evolve. “We wanted to look at what the differences were in the expressed genes at the different life stages of the bed bug,” he said. The researchers explored whether the bed bug’s genes were similar to the genes of other insect species associated with pesticide resistance. They found that, similar to other pesticide-resistant insects, the bed bug’s genome encodes enzymes and proteins that allow it to fight insecticides by preventing them from penetrating its hard little shell. The researchers also studied which of the bed bug’s genes were expressed when the creature had consumed blood. “Anti-coagulates have turned out to be important bioactive compounds in medicine and biomedical research, so we thought that by elucidating something about the presence of genes in those pathways that they would be of interest to researchers working in those areas,” said Amato. Bed bugs have increased in numbers over recent years, infesting urban areas, causing mass sleeplessness and itching. So the researchers also looked into how bedbugs were spread across a cityscape such as New York to see what sort of effects the distribution of these animals have. “We used the information gathered from the bed bug genome as a way to examine environmental DNA from bedbugs that we could collect from subway systems around the city of New York,” explained Amato. “Is their population structure influenced, for example, by how people use the landscape?” Ultimately, the researchers hope their preliminary investigations will help others come up with stronger solutions against bed bugs. “It’s like having the light turned on. Now scientists are in a much better position to examine all the various areas of interest related to the species,” said Amato.

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