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transcriptome evolution

Peng He, Patamarerk Engsontia, Guang-Lei Chen, Qian Yin, Jun Wang, Xu Lu, Ya-Nan Zhang, Zhao-Qun Li, Ming He
BACKGROUND: The white-backed planthopper (WBPH) Sogatella furcifera Horváth, the brown planthopper (BPH) Nilaparvata lugens, and the small brown planthopper (SBPH) Laodelphax striatellus (Hemiptera: Delphacidae) are rice pests that damage rice plants by sap-sucking and by transmitting viruses. Host-seeking behavior involves chemosensory receptor genes, which include odorant receptors (ORs), ionotropic receptors (IRs) and gustatory receptors (GRs). RESULTS: We used genome and transcriptome data to identify 141 ORs, 28 GRs and 25 IRs in BPH, 135 ORs, 18 GRs and 16 IRs in WBPH and 37 ORs, 14 GRs and 6 IRs in SBPH...
March 15, 2018: Pest Management Science
Karissa L Cross, Payal Chirania, Weili Xiong, Clifford J Beall, James G Elkins, Richard J Giannone, Ann L Griffen, Adam M Guss, Robert L Hettich, Snehal S Joshi, Elaine M Mokrzan, Roman K Martin, Igor B Zhulin, Eugene J Leys, Mircea Podar
The human oral microbiota encompasses representatives of many bacterial lineages that have not yet been cultured. Here we describe the isolation and characterization of previously uncultured Desulfobulbus oralis , the first human-associated representative of its genus. As mammalian-associated microbes rarely have free-living close relatives, D. oralis provides opportunities to study how bacteria adapt and evolve within a host. This sulfate-reducing deltaproteobacterium has adapted to the human oral subgingival niche by curtailing its physiological repertoire, losing some biosynthetic abilities and metabolic independence, and by dramatically reducing environmental sensing and signaling capabilities...
March 13, 2018: MBio
Tomas Strucko, Katharina Zirngibl, Filipa Pereira, Eleni Kafkia, Elsayed T Mohamed, Mandy Rettel, Frank Stein, Adam M Feist, Paula Jouhten, Kiran Raosaheb Patil, Jochen Forster
Most microbial species, including model eukaryote Saccharomyces cerevisiae, possess genetic capability to utilize many alternative nutrient sources. Yet, it remains an open question whether these manifest into assimilatory phenotypes. Despite possessing all necessary pathways, S. cerevisiae grows poorly or not at all when glycerol is the sole carbon source. Here we discover, through multiple evolved lineages, genetic determinants underlying glycerol catabolism and the associated fitness trade-offs. Most evolved lineages adapted through mutations in the HOG pathway, but showed hampered osmotolerance...
March 10, 2018: Metabolic Engineering
Tong Tong, Si Chen, Lianrong Wang, You Tang, Jae Yong Ryu, Susu Jiang, Xiaolin Wu, Chao Chen, Jie Luo, Zixin Deng, Zhiqiang Li, Sang Yup Lee, Shi Chen
The chemical diversity of physiological DNA modifications has expanded with the identification of phosphorothioate (PT) modification in which the nonbridging oxygen in the sugar-phosphate backbone of DNA is replaced by sulfur. Together with DndFGH as cognate restriction enzymes, DNA PT modification, which is catalyzed by the DndABCDE proteins, functions as a bacterial restriction-modification (R-M) system that protects cells against invading foreign DNA. However, the occurrence of dnd systems across a large number of bacterial genomes and their functions other than R-M are poorly understood...
March 12, 2018: Proceedings of the National Academy of Sciences of the United States of America
Anusree Mahanta, Piyali Ganguli, Pankaj Barah, Ram Rup Sarkar, Neelanjana Sarmah, Saurav Phukan, Mayuri Bora, Shashi Baruah
Diseases by protozoan pathogens pose a significant public health concern, particularly in tropical and subtropical countries, where these are responsible for significant morbidity and mortality. Protozoan pathogens tend to establish chronic infections underscoring their competence at subversion of host immune processes, an important component of disease pathogenesis and of their virulence. Modulation of cytokine and chemokine levels, their crosstalks and downstream signaling pathways, and thereby influencing recruitment and activation of immune cells is crucial to immune evasion and subversion...
2018: Frontiers in Immunology
Stefan A Rensing
500Ma ago the terrestrial habitat was a barren, unwelcoming place for species other than, for example, bacteria or fungi. Most probably, filamentous freshwater algae adapted to aerial conditions and eventually conquered land. Adaptation to a severely different habitat apparently included sturdy cell walls enabling an erect body plan as well as protection against abiotic stresses such as ultraviolet radiation, drought and varying temperature. To thrive on land, plants probably required more elaborate signaling pathways to react to diverse environmental conditions, and phytohormones to control developmental programs...
March 8, 2018: Current Opinion in Plant Biology
S W A Himaya, Richard J Lewis
Cone snail venoms are considered a treasure trove of bioactive peptides. Despite over 800 species of cone snails being known, each producing over 1000 venom peptides, only about 150 unique venom peptides are structurally and functionally characterized. To overcome the limitations of the traditional low-throughput bio-discovery approaches, multi-omics systems approaches have been introduced to accelerate venom peptide discovery and characterisation. This "venomic" approach is starting to unravel the full complexity of cone snail venoms and to provide new insights into their biology and evolution...
March 9, 2018: International Journal of Molecular Sciences
Nadine Graupner, Manfred Jensen, Christina Bock, Sabina Marks, Sven Rahmann, Daniela Beisser, Jens Boenigk
Shifts in the nutritional mode between phototrophy, mixotrophy and heterotrophy are a widespread phenomenon in the evolution of eukaryotic diversity. The transition between nutritional modes is particularly pronounced in chrysophytes and occurred independently several times through parallel evolution. Thus, chrysophytes provide a unique opportunity for studying the molecular basis of nutritional diversification and of the accompanying pathway reduction and degradation of plastid structures. In order to analyze the succession in switching the nutritional mode from mixotrophy to heterotrophy, we compared the transcriptome of the mixotrophic Poterioochromonas malhamensis with the transcriptomes of three obligate heterotrophic species of Ochromonadales...
March 6, 2018: FEMS Microbiology Ecology
Mark A Phuong, Gusti N Mahardika
To expand our capacity to discover venom sequences from the genomes of venomous organisms, we applied targeted sequencing techniques to selectively recover venom gene superfamilies and non-toxin loci from the genomes of 32 cone snail species (family, Conidae), a diverse group of marine gastropods that capture their prey using a cocktail of neurotoxic peptides (conotoxins). We were able to successfully recover conotoxin gene superfamilies across all species with high confidence (> 100X coverage) and used these data to provide new insights into conotoxin evolution...
March 5, 2018: Molecular Biology and Evolution
Junjie Luo, Yirong Wang, Jian Yuan, Zhilei Zhao, Jian Lu
The repertoire of miRNAs has considerably expanded during metazoan evolution, and duplication is an important mechanism for generating new functional miRNAs. However, relatively little is known about the functional divergence between paralogous miRNAs and the possible co-evolution between duplicated miRNAs and the genomic contexts. By systematically examining small RNA expression profiles across various human tissues and interrogating the publicly available miRNA:mRNA pairing chimeras, we found that changes in expression patterns and targeting preferences are widespread for duplicated miRNAs in vertebrates...
March 6, 2018: RNA
Kai K Lie, Ole K Tørresen, Monica Hongrø Solbakken, Ivar Rønnestad, Ave Tooming-Klunderud, Alexander J Nederbragt, Sissel Jentoft, Øystein Sæle
BACKGROUND: The ballan wrasse (Labrus bergylta) belongs to a large teleost family containing more than 600 species showing several unique evolutionary traits such as lack of stomach and hermaphroditism. Agastric fish are found throughout the teleost phylogeny, in quite diverse and unrelated lineages, indicating stomach loss has occurred independently multiple times in the course of evolution. By assembling the ballan wrasse genome and transcriptome we aimed to determine the genetic basis for its digestive system function and appetite regulation...
March 6, 2018: BMC Genomics
Qi-Lin Zhang, Qian-Hua Zhu, Ming-Zhong Liang, Feng Wang, Jun Guo, Xian-Yu Deng, Jun-Yuan Chen, Yu-Jun Wang, Lian-Bing Lin
Amphioxus, a basal chordate, is widely considered to be an existing proxy of the invertebrate ancestor of vertebrates, and it exhibits susceptibility to various pathogen infections and pathogenic mimic challenges. Here, in order to understand more clearly its antibacterial mechanisms, we analyzed the ribosomal RNA (rRNA)-depleted transcriptome of Chinese amphioxus (Branchiostoma belcheri) infected with Vibrio parahaemolyticus (V. p.) via next-generation deep sequencing technology (RNA-seq). We identified a total of 3214 differentially expressed genes (DEGs) by comparing V...
March 3, 2018: Fish & Shellfish Immunology
Nathan A M Chrismas, Alexandre M Anesio, Patricia Sánchez-Baracaldo
In recent years, genomic analyses have arisen as an exciting way of investigating the functional capacity and environmental adaptations of numerous micro-organisms of global relevance, including cyanobacteria. In the extreme cold of Arctic, Antarctic and alpine environments, cyanobacteria are of fundamental ecological importance as primary producers and ecosystem engineers. While their role in biogeochemical cycles is well appreciated, little is known about the genomic makeup of polar and alpine cyanobacteria...
April 1, 2018: FEMS Microbiology Ecology
Michael Tessler, David Marancik, Donald Champagne, Alistair Dove, Alvin Camus, Mark E Siddall, Sebastian Kvist
Leeches (Annelida: Hirudinea) possess powerful salivary anticoagulants and, accordingly, are frequently employed in modern, authoritative medicine. Members of the almost exclusively marine family Piscicolidae account for 20% of leech species diversity, and feed on host groups (e.g., sharks) not encountered by their freshwater and terrestrial counterparts. Moreover, some species of Ozobranchidae feed on endangered marine turtles and have been implicated as potential vectors for the tumor-associated turtle herpesvirus...
March 5, 2018: Journal of Parasitology
Eugenia Sanchez, Eliane Küpfer, Daniel J Goedbloed, Arne W Nolte, Tim Lüddecke, Stefan Schulz, Miguel Vences, Sebastian Steinfartz
The postembryonic development of amphibians has been characterized as divided into three predominant periods, hereafter named primary developmental stages: premetamorphosis (PreM), prometamorphosis (ProM), metamorphic climax (Meta), and completion of metamorphosis (PostM), largely based on examination of anuran development. Here, we categorized the postembryonic development of larvae of a poisonous fire salamander (Salamandra salamandra) by integrating morphology and gene expression (transcriptomic) data. Morphological analysis revealed three distinct clusters suggestive of PreM, ProM, and Meta, which were confirmed in parallel by microarray-derived gene expression analysis...
March 5, 2018: Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution
Alexander M Gorbushin
The evolution of complement system in invertebrates is poorly investigated. While the repertoire of complement genes in several Ecdysozoa lineages is found substantially different from that of Deuterostomia, the composition and function of the complement in the second protostome lineage, Lophotrochozoa, remains unclear. Here we report the general description of new transcriptomic data on the common periwinkle, Littorina littorea, and trace the evolutionary trajectories of the ancestral proto-complement repertoire...
February 28, 2018: Developmental and Comparative Immunology
Marja Steenman, Olivier Espitia, Blandine Maurel, Beatrice Guyomarch, Marie-Françoise Heymann, Marc-Antoine Pistorius, Benjamin Ory, Dominique Heymann, Rémi Houlgatte, Yann Gouëffic, Thibaut Quillard
Calcification is independently associated with cardiovascular events and morbidity. The calcification burden in atherosclerotic lesions quantitatively and qualitatively differs between arterial beds. Cardiovascular risk factors (CVRF) differentially affect plaque development between arterial beds. The aim of this study was to evaluate the impact of CVRF on atherosclerotic plaque calcification and to further study the molecular arterial heterogeneity that could account for these differences. Histological analysis was performed on atherosclerotic plaques from 153 carotid, 97 femoral and 28 infrapopliteal arteries...
March 2, 2018: Scientific Reports
Hanako Shimura, Chikara Masuta, Yasunori Koda
In nature, mycorrhizal association with soilborne fungi is indispensable for orchid families. Fungal structures from compatible endo-mycorrhizal fungi in orchid cells are digested in cells to be supplied to orchids as nutrition. Because orchid seeds lack the reserves for germination, they keep receiving nutrition through mycorrhizal formation from seed germination until shoots develop (leaves) and become photoautotrophic. Seeds of all orchid species surely geminate with the help of their own fungal partners, and this specific partnership has been acquired for a long evolutional history between orchids and fungi...
2018: Methods in Molecular Biology
David V Dylus, Anna Czarkwiani, Liisa M Blowes, Maurice R Elphick, Paola Oliveri
BACKGROUND: Amongst the echinoderms the class Ophiuroidea is of particular interest for its phylogenetic position, ecological importance and developmental and regenerative biology. However, compared to other echinoderms, notably echinoids (sea urchins), relatively little is known about developmental changes in gene expression in ophiuroids. To address this issue, we have generated and assembled a large RNAseq data set of four key stages of development in the brittle star Amphiura filiformis and a de novo reference transcriptome of comparable quality to that of a model echinoderm-the sea urchin Strongylocentrotus purpuratus...
February 28, 2018: Genome Biology
Gunter Vogt
In the last 15 years, considerable attempts have been undertaken to develop the obligately parthenogenetic marbled crayfish Procambarus virginalis as a new model in biology. Its main advantage is the production of large numbers of offspring that are genetically identical to the mother, making this crustacean particularly suitable for research in epigenetics. Now, a draft genome, transcriptome and genome-wide methylome are available opening new windows for research. In this article, I summarize the biological advantages and genomic and epigenetic features of marbled crayfish and, based on first promising data, discuss what this new model could contribute to answering of ''big'' biological questions...
March 2018: Journal of Biosciences
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