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transcriptome evolution

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https://www.readbyqxmd.com/read/28429720/noumeavirus-replication-relies-on-a-transient-remote-control-of-the-host-nucleus
#1
Elisabeth Fabre, Sandra Jeudy, Sébastien Santini, Matthieu Legendre, Mathieu Trauchessec, Yohann Couté, Jean-Michel Claverie, Chantal Abergel
Acanthamoeba are infected by a remarkable diversity of large dsDNA viruses, the infectious cycles of which have been characterized using genomics, transcriptomics and electron microscopy. Given their gene content and the persistence of the host nucleus throughout their infectious cycle, the Marseilleviridae were initially assumed to fully replicate in the cytoplasm. Unexpectedly, we find that their virions do not incorporate the virus-encoded transcription machinery, making their replication nucleus-dependent...
April 21, 2017: Nature Communications
https://www.readbyqxmd.com/read/28429538/finding-a-partner-in-the-ocean-molecular-and-evolutionary-bases-of-the-response-to-sexual-cues-in-a-planktonic-diatom
#2
Swaraj Basu, Shrikant Patil, Daniel Mapleson, Monia Teresa Russo, Laura Vitale, Cristina Fevola, Florian Maumus, Raffaella Casotti, Thomas Mock, Mario Caccamo, Marina Montresor, Remo Sanges, Maria Immacolata Ferrante
Microalgae play a major role as primary producers in aquatic ecosystems. Cell signalling regulates their interactions with the environment and other organisms, yet this process in phytoplankton is poorly defined. Using the marine planktonic diatom Pseudo-nitzschia multistriata, we investigated the cell response to cues released during sexual reproduction, an event that demands strong regulatory mechanisms and impacts on population dynamics. We sequenced the genome of P. multistriata and performed phylogenomic and transcriptomic analyses, which allowed the definition of gene gains and losses, horizontal gene transfers, conservation and evolutionary rate of sex-related genes...
April 21, 2017: New Phytologist
https://www.readbyqxmd.com/read/28429323/protein-targeting-to-the-plastid-of-euglena
#3
Dion G Durnford, Steven D Schwartzbach
The lateral transfer of photosynthesis between kingdoms through endosymbiosis is among the most spectacular examples of evolutionary innovation. Euglena, which acquired a chloroplast indirectly through an endosymbiosis with a green alga, represents such an example. As with other endosymbiont-derived plastids from eukaryotes, there are additional membranes that surround the organelle, of which Euglena has three. Thus, photosynthetic genes that were transferred from the endosymbiont to the host nucleus and whose proteins are required in the new plastid, are now faced with targeting and plastid import challenges...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28429320/euglena-gracilis-genome-and-transcriptome-organelles-nuclear-genome-assembly-strategies-and-initial-features
#4
ThankGod Echezona Ebenezer, Mark Carrington, Michael Lebert, Steven Kelly, Mark C Field
Euglena gracilis is a major component of the aquatic ecosystem and together with closely related species, is ubiquitous worldwide. Euglenoids are an important group of protists, possessing a secondarily acquired plastid and are relatives to the Kinetoplastidae, which themselves have global impact as disease agents. To understand the biology of E. gracilis, as well as to provide further insight into the evolution and origins of the Kinetoplastidae, we embarked on sequencing the nuclear genome; the plastid and mitochondrial genomes are already in the public domain...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28427537/metabolomics-nutrition-and-potential-biomarkers-of-food-quality-intake-and-health-status
#5
Jean-Louis Sébédio
Diet, dietary patterns, and other environmental factors such as exposure to toxins are playing an important role in the prevention/development of many diseases, like obesity, type 2 diabetes, and consequently on the health status of individuals. A major challenge nowadays is to identify novel biomarkers to detect as early as possible metabolic dysfunction and to predict evolution of health status in order to refine nutritional advices to specific population groups. Omics technologies such as genomics, transcriptomics, proteomics, and metabolomics coupled with statistical and bioinformatics tools have already shown great potential in this research field even if so far only few biomarkers have been validated...
2017: Advances in Food and Nutrition Research
https://www.readbyqxmd.com/read/28424974/transposable-elements-in-the-anopheles-funestus-transcriptome
#6
Rita D Fernández-Medina, Claudia M A Carareto, Cláudio J Struchiner, José M C Ribeiro
Transposable elements (TEs) are present in most of the eukaryotic genomes and their impact on genome evolution is increasingly recognized. Although there is extensive information on the TEs present in several eukaryotic genomes, less is known about the expression of these elements at the transcriptome level. Here we present a detailed analysis regarding the expression of TEs in Anopheles funestus, the second most important vector of human malaria in Africa. Several transcriptionally active TE families belonging both to Class I and II were identified and characterized...
April 19, 2017: Genetica
https://www.readbyqxmd.com/read/28424354/less-effective-selection-leads-to-larger-genomes
#7
Tristan Lefébure, Claire Morvan, Florian Malard, Clémentine François, Lara Konecny-Dupré, Laurent Guéguen, Michèle Weiss-Gayet, Andaine Seguin-Orlando, Luca Ermini, Clio Der Sarkissian, N Pierre Charrier, David Eme, Florian Mermillod-Blondin, Laurent Duret, Cristina Vieira, Ludovic Orlando, Christophe Douady
The evolutionary origin of the striking genome size variations found in eukaryotes remains enigmatic. The effective size of populations, by controlling selection efficacy, is expected to be a key parameter underlying genome size evolution. However, this hypothesis has proved difficult to investigate using empirical datasets. Here, we tested this hypothesis using twenty-two de novo transcriptomes and low-coverage genomes of asellid isopods, which represent eleven independent habitat shifts from surface water to resource-poor groundwater...
April 19, 2017: Genome Research
https://www.readbyqxmd.com/read/28419974/prediction-and-feature-analysis-of-intron-retention-events-in-plant-genome
#8
Ying Cui, Chao Zhang, Meng Cai
Alternative splicing (AS) is a major contributor to increase the potential informational content of eukaryotic genomes by creating multiple mRNA species and proteins from a single gene. In plants, up to 60% genes are alternatively spliced and the most common type of AS is intron retention (IR). Genomic analyses of IR have illuminated its crucial role in shaping the evolution of genomes, in the control of developmental processes, and in the dynamic regulation of the transcriptome to influence phenotype. To explore the relationship between the sequence feature and the formation mechanism of IR, we statistically analyzed the retained introns and proposed an improved random forest-based hybrid method to predict intron retention events in plant genome...
April 13, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28419380/%C3%AE-carboxysome-bioinformatics-identification-and-evolution-of-new-bacterial-microcompartment-protein-gene-classes-and-core-locus-constraints
#9
Manuel Sommer, Fei Cai, Matthew Melnicki, Cheryl A Kerfeld
Carboxysomes are bacterial microcompartments (BMCs) that enhance CO2 fixation in all cyanobacteria. Structurally, carboxysome shell proteins are classified according to the type of oligomer formed: hexameric (BMC-H), trimeric (BMC-T) and pentameric (BMC-P) proteins. To understand the forces driving the evolution of the carboxysome shell, we conducted a bioinformatic study of genes encoding β-carboxysome shell proteins, taking advantage of the recent large increase in sequenced cyanobacterial genomes. In addition to the four well-established BMC-H (CcmK1-4) classes, our analysis reveals two new CcmK classes, which we name CcmK5 and CcmK6...
April 17, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28413781/sequencing-and-de-novo-transcriptome-assembly-of-the-chinese-giant-salamander-andrias-davidianus
#10
Yong Huang, Xiao Chan Gao, Jian Li Xiong, Hong Tao Ren, Xi Hong Sun
Next-generation technologies for determination of genomics and transcriptomics composition have a wide range of applications. Andrias davidianus, has become an endangered amphibian species of salamander endemic in China. However, there is a lack of the molecular information. In this study, we obtained the RNA-Seq data from a pool of A. davidianus tissue including spleen, liver, muscle, kidney, skin, testis, gut and heart using Illumina HiSeq 2500 platform. A total of 15,398,997,600 bp were obtained, corresponding to 102,659,984 raw reads...
June 2017: Genomics Data
https://www.readbyqxmd.com/read/28410430/caste-sex-and-age-dependent-expression-of-immune-related-genes-in-a-japanese-subterranean-termite-reticulitermes-speratus
#11
Yuki Mitaka, Kazuya Kobayashi, Kenji Matsuura
Insects protect themselves from microbial infections through innate immune responses, including pathogen recognition, phagocytosis, the activation of proteolytic cascades, and the synthesis of antimicrobial peptides. Termites, eusocial insects inhabiting microbe-rich wood, live in closely-related family groups that are susceptible to shared pathogen infections. To resist pathogenic infection, termite families have evolved diverse immune adaptations at both individual and societal levels, and a strategy of trade-offs between reproduction and immunity has been suggested...
2017: PloS One
https://www.readbyqxmd.com/read/28406439/protein-coding-genes-retrocopies-and-their-functions
#12
REVIEW
Magdalena Regina Kubiak, Izabela Makałowska
Transposable elements, often considered to be not important for survival, significantly contribute to the evolution of transcriptomes, promoters, and proteomes. Reverse transcriptase, encoded by some transposable elements, can be used in trans to produce a DNA copy of any RNA molecule in the cell. The retrotransposition of protein-coding genes requires the presence of reverse transcriptase, which could be delivered by either non-long terminal repeat (non-LTR) or LTR transposons. The majority of these copies are in a state of "relaxed" selection and remain "dormant" because they are lacking regulatory regions; however, many become functional...
April 13, 2017: Viruses
https://www.readbyqxmd.com/read/28405930/single-cell-sequencing-and-tumorigenesis-improved-understanding-of-tumor-evolution-and-metastasis
#13
REVIEW
Darrell L Ellsworth, Heather L Blackburn, Craig D Shriver, Shahrooz Rabizadeh, Patrick Soon-Shiong, Rachel E Ellsworth
Extensive genomic and transcriptomic heterogeneity in human cancer often negatively impacts treatment efficacy and survival, thus posing a significant ongoing challenge for modern treatment regimens. State-of-the-art DNA- and RNA-sequencing methods now provide high-resolution genomic and gene expression portraits of individual cells, facilitating the study of complex molecular heterogeneity in cancer. Important developments in single-cell sequencing (SCS) technologies over the past 5 years provide numerous advantages over traditional sequencing methods for understanding the complexity of carcinogenesis, but significant hurdles must be overcome before SCS can be clinically useful...
December 2017: Clinical and Translational Medicine
https://www.readbyqxmd.com/read/28404901/long-non-coding-rna-tug1-promotes-endometrial-cancer-development-via-inhibiting-mir-299-and-mir-34a-5p-liu
#14
Lifen Liu, Xin Chen, Ying Zhang, Yanrong Hu, Xiaoqing Shen, Weipei Zhu
It is generally known that the human genome makes a large amount of noncoding RNAs compared with coding genes. Long non-coding RNAs (lncRNAs) which composed of more than 200 nucleotides have been described as the largest subclass of the non-coding transcriptome in human noncoding RNAs. Existing research shows that lncRNAs exerted biological functions in various tumors via participating in both oncogenic and tumor suppressing pathways. The previous studies indicated that lncRNA taurine upregulated 1 (TUG1) play important roles in the initiation and progression of malignancies...
February 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28400779/making-plants-break-a-sweat-the-structure-function-and-evolution-of-plant-salt-glands
#15
REVIEW
Maheshi Dassanayake, John C Larkin
Salt stress is a complex trait that poses a grand challenge in developing new crops better adapted to saline environments. Some plants, called recretohalophytes, that have naturally evolved to secrete excess salts through salt glands, offer an underexplored genetic resource for examining how plant development, anatomy, and physiology integrate to prevent excess salt from building up to toxic levels in plant tissue. In this review we examine the structure and evolution of salt glands, salt gland-specific gene expression, and the possibility that all salt glands have originated via evolutionary modifications of trichomes...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28400476/gad1-upregulation-programs-aggressive-features-of-cancer-cell-metabolism-in-the-brain-metastatic-microenvironment
#16
Patricia M Schnepp, Dennis D Lee, Ian H Guldner, Treasa K O'Tighearnaigh, Erin N Howe, Bhavana Palakurthi, Kaitlyn E Eckert, Tiffany A Toni, Brandon L Ashfeld, Siyuan Zhang
The impact of altered amino acid metabolism on cancer progression is not fully understood. We hypothesized that a metabolic transcriptome shift during metastatic evolution is crucial for brain metastasis. Here we report a powerful impact in this setting caused by epigenetic upregulation of glutamate decarboxylase 1 (GAD1), a regulator of the GABA neurotransmitter metabolic pathway. In cell-based culture and brain metastasis models, we found that downegulation of the DNA methyltransferase DNMT1 induced by the brain microenvironment-derived clusterin resulted in decreased GAD1 promoter methylation and subsequent upregulation of GAD1 expression in brain metastatic tumor cells...
April 11, 2017: Cancer Research
https://www.readbyqxmd.com/read/28400424/increased-taxon-sampling-reveals-thousands-of-hidden-orthologs-in-flatworms
#17
Jose M Martin-Duran, Joseph F Ryan, Bruno Vellutini, Kevin Pang, Andreas Hejnol
Gains and losses shape the gene complement of animal lineages and are a fundamental aspect of genomic evolution. Acquiring a comprehensive view of the evolution of gene repertoires is limited by the intrinsic limitations of common sequence similarity searches and available databases. Thus, a subset of the gene complement of an organism consists of hidden orthologs, i.e., those with no apparent homology to sequenced animal lineages - mistakenly considered new genes - but actually representing rapidly evolving orthologs or undetected paralogs...
April 11, 2017: Genome Research
https://www.readbyqxmd.com/read/28400402/molecular-targeted-therapies-in-adrenal-pituitary-and-parathyroid-malignancies
#18
Anna Angelousi, Georgios K Dimitriadis, Gn Zografos, Svenja Nölting, Gregory A Kaltsas, Ashley B Grossman
Tumourigenesis is a relatively common event in endocrine tissues. Currently, specific guidelines have been developed for common malignant endocrine tumours which also incorporate advances in molecular targeted therapies (MTT), as in thyroid cancer and gastrointestinal neuroendocrine malignancies. However, there is little information regarding the role and efficacy of MTT in the relatively rare malignant endocrine tumours mainly involving the adrenal medulla, adrenal cortex, pituitary and parathyroid glands...
April 11, 2017: Endocrine-related Cancer
https://www.readbyqxmd.com/read/28397791/adaptation-and-evolution-of-deep-sea-scale-worms-annelida-polynoidae-insights-from-transcriptome-comparison-with-a-shallow-water-species
#19
Yanjie Zhang, Jin Sun, Chong Chen, Hiromi K Watanabe, Dong Feng, Yu Zhang, Jill M Y Chiu, Pei-Yuan Qian, Jian-Wen Qiu
Polynoid scale worms (Polynoidae, Annelida) invaded deep-sea chemosynthesis-based ecosystems approximately 60 million years ago, but little is known about their genetic adaptation to the extreme deep-sea environment. In this study, we reported the first two transcriptomes of deep-sea polynoids (Branchipolynoe pettiboneae, Lepidonotopodium sp.) and compared them with the transcriptome of a shallow-water polynoid (Harmothoe imbricata). We determined codon and amino acid usage, positive selected genes, highly expressed genes and putative duplicated genes...
April 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28391323/genomic-and-transcriptomic-analysis-reveals-spliced-leader-trans-splicing-in-cryptomonads
#20
Scott William Roy
Spliced leader trans-splicing (SLTS) is a poorly understood mechanism that is found in a diversity of eukaryotic lineages. In SLTS, a short RNA sequence is added near the 5' ends of the transcripts of protein-coding genes by a modified spliceosomal reaction. Available data suggest that SLTS has evolved many times, and might be more likely to evolve in animals. That SLTS might be more likely to evolve in the context of the generally complex transcriptomes characteristic of animals suggests the possibility that SLTS functions in gene regulation or transcriptome diversification, however no general novel function for SLTS is known...
March 1, 2017: Genome Biology and Evolution
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