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https://www.readbyqxmd.com/read/28815540/long-noncoding-rnas-in-mammalian-development-and-diseases
#1
Parna Saha, Shreekant Verma, Rashmi U Pathak, Rakesh K Mishra
Following analysis of sequenced genomes and transcriptome of many eukaryotes, it is evident that virtually all protein-coding genes have already been discovered. These advances have highlighted an intriguing paradox whereby the relative amount of protein-coding sequences remain constant but nonprotein-coding sequences increase consistently in parallel to increasing evolutionary complexity. It is established that differences between species map to nonprotein-coding regions of the genome that surprisingly is transcribed extensively...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28815535/history-discovery-and-classification-of-lncrnas
#2
Julien Jarroux, Antonin Morillon, Marina Pinskaya
The RNA World Hypothesis suggests that prebiotic life revolved around RNA instead of DNA and proteins. Although modern cells have changed significantly in 4 billion years, RNA has maintained its central role in cell biology. Since the discovery of DNA at the end of the nineteenth century, RNA has been extensively studied. Many discoveries such as housekeeping RNAs (rRNA, tRNA, etc.) supported the messenger RNA model that is the pillar of the central dogma of molecular biology, which was first devised in the late 1950s...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28813177/how-single-cell-genomics-is-changing-evolutionary-and-developmental-biology
#3
John C Marioni, Detlev Arendt
The recent flood of single-cell data not only boosts our knowledge of cells and cell types, but also provides new insight into development and evolution from a cellular perspective. For example, assaying the genomes of multiple cells during development reveals developmental lineage trees-the kinship lineage-whereas cellular transcriptomes inform us about the regulatory state of cells and their gradual restriction in potency-the Waddington lineage. Beyond that, the comparison of single-cell data across species allows evolutionary changes to be tracked at all stages of development from the zygote, via different kinds of stem cells, to the differentiating cells...
August 16, 2017: Annual Review of Cell and Developmental Biology
https://www.readbyqxmd.com/read/28812732/genome-of-the-pitcher-plant-cephalotus-reveals-genetic-changes-associated-with-carnivory
#4
Kenji Fukushima, Xiaodong Fang, David Alvarez-Ponce, Huimin Cai, Lorenzo Carretero-Paulet, Cui Chen, Tien-Hao Chang, Kimberly M Farr, Tomomichi Fujita, Yuji Hiwatashi, Yoshikazu Hoshi, Takamasa Imai, Masahiro Kasahara, Pablo Librado, Likai Mao, Hitoshi Mori, Tomoaki Nishiyama, Masafumi Nozawa, Gergő Pálfalvi, Stephen T Pollard, Julio Rozas, Alejandro Sánchez-Gracia, David Sankoff, Tomoko F Shibata, Shuji Shigenobu, Naomi Sumikawa, Taketoshi Uzawa, Meiying Xie, Chunfang Zheng, David D Pollock, Victor A Albert, Shuaicheng Li, Mitsuyasu Hasebe
Carnivorous plants exploit animals as a nutritional source and have inspired long-standing questions about the origin and evolution of carnivory-related traits. To investigate the molecular bases of carnivory, we sequenced the genome of the heterophyllous pitcher plant Cephalotus follicularis, in which we succeeded in regulating the developmental switch between carnivorous and non-carnivorous leaves. Transcriptome comparison of the two leaf types and gene repertoire analysis identified genetic changes associated with prey attraction, capture, digestion and nutrient absorption...
February 6, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28812685/scallop-genome-provides-insights-into-evolution-of-bilaterian-karyotype-and-development
#5
Shi Wang, Jinbo Zhang, Wenqian Jiao, Ji Li, Xiaogang Xun, Yan Sun, Ximing Guo, Pin Huan, Bo Dong, Lingling Zhang, Xiaoli Hu, Xiaoqing Sun, Jing Wang, Chengtian Zhao, Yangfan Wang, Dawei Wang, Xiaoting Huang, Ruijia Wang, Jia Lv, Yuli Li, Zhifeng Zhang, Baozhong Liu, Wei Lu, Yuanyuan Hui, Jun Liang, Zunchun Zhou, Rui Hou, Xue Li, Yunchao Liu, Hengde Li, Xianhui Ning, Yu Lin, Liang Zhao, Qiang Xing, Jinzhuang Dou, Yangping Li, Junxia Mao, Haobing Guo, Huaiqian Dou, Tianqi Li, Chuang Mu, Wenkai Jiang, Qiang Fu, Xiaoteng Fu, Yan Miao, Jian Liu, Qian Yu, Ruojiao Li, Huan Liao, Xuan Li, Yifan Kong, Zhi Jiang, Daniel Chourrout, Ruiqiang Li, Zhenmin Bao
Reconstructing the genomes of bilaterian ancestors is central to our understanding of animal evolution, where knowledge from ancient and/or slow-evolving bilaterian lineages is critical. Here we report a high-quality, chromosome-anchored reference genome for the scallop Patinopecten yessoensis, a bivalve mollusc that has a slow-evolving genome with many ancestral features. Chromosome-based macrosynteny analysis reveals a striking correspondence between the 19 scallop chromosomes and the 17 presumed ancestral bilaterian linkage groups at a level of conservation previously unseen, suggesting that the scallop may have a karyotype close to that of the bilaterian ancestor...
April 3, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28810711/whole-rna-sequencing-and-transcriptome-assembly-of-candida-albicans-and-candida-africana-under-chlamydospore-inducing-conditions
#6
Domenico Giosa, Maria Rosa Felice, Travis J Lawrence, Megha Gulati, Fabio Scordino, Letterio Giuffrè, Carla Lo Passo, Enrico D'Alessandro, Giuseppe Criseo, David H Ardell, Aaron D Hernday, Clarissa J Nobile, Orazio Romeo
Candida albicans is the most common cause of life-threatening fungal infections in humans, especially in immunocompromised individuals. Crucial to its success as an opportunistic pathogen is the considerable dynamism of its genome, which readily undergoes genetic changes generating new phenotypes and shaping the evolution of new strains. Candida africana is an intriguing C. albicans biovariant strain that exhibits remarkable genetic and phenotypic differences when compared with standard C. albicans isolates...
July 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28809429/dissection-of-the-module-network-implementation-lemontree-enhancements-towards-applications-in-metagenomics-and-translation-in-autoimmune-maladies
#7
Youtao Lu, Xiaoyuan Zhou, Christine Nardini
Under the current deluge of omics, module networks distinctively emerge as methods capable of not only identifying inherently coherent groups (modules), thus reducing dimensionality, but also hypothesizing cause-effect relationships between modules and their regulators. Module networks were first designed in the transcriptomic era and further exploited in the multi-omic context to assess (for example) miRNA regulation of gene expression. Despite a number of available implementations, expansion of module networks to other omics is constrained by a limited characterization of the solutions' (modules plus regulators) accuracy and stability - an immediate need for the better characterization of molecular biology complexity in silico...
August 15, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28806931/draft-de-novo-transcriptome-assembly-and-proteome-characterization-of-the-electric-lobe-of-tetronarce-californica-a-molecular-tool-for-the-study-of-cholinergic-neurotransmission-in-the-electric-organ
#8
Maria Stavrianakou, Ricardo Perez, Cheng Wu, Matthew S Sachs, Rodolfo Aramayo, Mark Harlow
BACKGROUND: The electric organ of Tetronarce californica (an electric ray formerly known as Torpedo californica) is a classic preparation for biochemical studies of cholinergic neurotransmission. To broaden the usefulness of this preparation, we have performed a transcriptome assembly of the presynaptic component of the electric organ (the electric lobe). We combined our assembled transcriptome with a previous transcriptome of the postsynaptic electric organ, to define a MetaProteome containing pre- and post-synaptic components of the electric organ...
August 14, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28802080/segmental-allotetraploidy-generates-extensive-homeologous-expression-rewiring-and-phenotypic-diversity-at-the-population-level-in-rice
#9
Yue Sun, Ying Wu, Chunwu Yang, Shuai Sun, Xiuyun Lin, Lixia Liu, Chunming Xu, Jonathan F Wendel, Lei Gong, Bao Liu
Allopolyploidization, i.e., concomitant merging and doubling of two or more divergent genomes in a common nucleus/cytoplasm, is known to instantly alter genome-wide transcriptome dynamics, a phenomenon referred to as "transcriptomic shock". However, the immediate effects of transcriptomic alteration in generating phenotypic diversity at the population level remain under-investigated. Here, we employed the MassARRAY-based Sequenom platform to assess and compare orthologous, allelic, and homeologous gene expression status in two tissues (leaf and root) of a set of randomly chosen individuals from populations of parental rice subspecies (indica and japonica), in vitro "hybrids" (parental mixes), reciprocal F1 hybrids and reciprocal tetraploids at the 5(th) -selfed generation (S5)...
August 12, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28801915/manganese-and-1-methyl-4-phenylpyridinium-mpp-induced-neurotoxicity-indicate-differences-in-morphological-electrophysiological-and-genome-wide-alterations-implications-for-idiopathic-parkinson-s-disease
#10
Rajeswara Babu Mythri, Narayana Reddy Raghunath, Santosh Chandrakant Narwade, Mirazkar DasharathaRao Pandareesh, Kollarkandi Rajesh Sabitha, Mohamad Aiyaz, Bipin Chand, Manas Sule, Krittika Ghosh, Senthil Kumar, Bhagyalakshmi Shankarappa, Soundarya Soundararajan, Phalguni Anand Alladi, Meera Purushottam, Narayanappa Gayathri, Deepti Dileep Deobagkar, Thenkanidiyoor Rao Laxmi, Srinivas Bharath Muchukunte Mukunda
Idiopathic Parkinson's disease (iPD) and manganese-induced atypical Parkinsonism are characterized by movement disorder and nigrostriatal pathology. Although clinical features, brain region involved and responsiveness to levodopa distinguish both, differences at the neuronal level are largely unknown. We studied the morphological, neurophysiological and molecular differences in dopaminergic neurons exposed to the PD toxin 1-methyl-4-phenylpyridinium ion (MPP(+) ) and manganese (Mn) followed by validation in the 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) and Mn mouse models...
August 12, 2017: Journal of Neurochemistry
https://www.readbyqxmd.com/read/28798064/accurate-rna-consensus-sequencing-for-high-fidelity-detection-of-transcriptional-mutagenesis-induced-epimutations
#11
Kate S Reid-Bayliss, Lawrence A Loeb
Transcriptional mutagenesis (TM) due to misincorporation during RNA transcription can result in mutant RNAs, or epimutations, that generate proteins with altered properties. TM has long been hypothesized to play a role in aging, cancer, and viral and bacterial evolution. However, inadequate methodologies have limited progress in elucidating a causal association. We present a high-throughput, highly accurate RNA sequencing method to measure epimutations with single-molecule sensitivity. Accurate RNA consensus sequencing (ARC-seq) uniquely combines RNA barcoding and generation of multiple cDNA copies per RNA molecule to eliminate errors introduced during cDNA synthesis, PCR, and sequencing...
August 10, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28797654/do-differences-in-the-activities-of-carbohydrate-metabolism-enzymes-between-lake-whitefish-ecotypes-match-predictions-from-transcriptomic-studies
#12
Anne C Dalziel, Martin Laporte, Helga Guderley, Louis Bernatchez
Transcriptomic studies are facilitating the search for the molecular bases of adaptation in natural populations, but the impact of these differences in mRNA content on animal physiology are often unknown. One way to determine if molecular changes have the potential to influence animal physiology and performance is to test for correlated changes at higher levels of biological organization, including enzyme activity. Here, we measure the activities of carbohydrate metabolism enzymes to test if previously documented genetic and transcriptomic variation between 'dwarf' and 'normal' Lake Whitefish ecotypes are associated with corresponding changes in enzyme activity (measured as maximal rate, Vmax) in liver and skeletal muscle...
August 7, 2017: Comparative Biochemistry and Physiology. Part B, Biochemistry & Molecular Biology
https://www.readbyqxmd.com/read/28790409/plant-organ-evolution-revealed-by-phylotranscriptomics-in-arabidopsis-thaliana
#13
Li Lei, Joshua G Steffen, Edward J Osborne, Christopher Toomajian
The evolution of phenotypes occurs through changes both in protein sequence and gene expression levels. Though much of plant morphological evolution can be explained by changes in gene expression, examining its evolution has challenges. To gain a new perspective on organ evolution in plants, we applied a phylotranscriptomics approach. We combined a phylostratigraphic approach with gene expression based on the strand-specific RNA-seq data from seedling, floral bud, and root of 19 Arabidopsis thaliana accessions to examine the age and sequence divergence of transcriptomes from these organs and how they adapted over time...
August 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28790203/the-in-feed-antibiotic-carbadox-induces-phage-gene-transcription-in-the-swine-gut-microbiome
#14
Timothy A Johnson, Torey Looft, Andrew J Severin, Darrell O Bayles, Daniel J Nasko, K Eric Wommack, Adina Howe, Heather K Allen
Carbadox is a quinoxaline-di-N-oxide antibiotic fed to over 40% of young pigs in the United States that has been shown to induce phage DNA transduction in vitro; however, the effects of carbadox on swine microbiome functions are poorly understood. We investigated the in vivo longitudinal effects of carbadox on swine gut microbial gene expression (fecal metatranscriptome) and phage population dynamics (fecal dsDNA viromes). Microbial metagenome, transcriptome, and virome sequences were annotated for taxonomic inference and gene function by using FIGfam (isofunctional homolog sequences) and SEED subsystems databases...
August 8, 2017: MBio
https://www.readbyqxmd.com/read/28776934/development-of-genome-and-transcriptome-derived-microsatellites-in-related-species-of-snapping-shrimps-with-highly-duplicated-genomes
#15
Kaitlyn M Gaynor, Joseph W Solomon, Stefanie Siller, Linnet Jessell, J Emmett Duffy, Dustin R Rubenstein
Molecular markers are powerful tools for studying patterns of relatedness and parentage within populations and for making inferences about social evolution. However, the development of molecular markers for simultaneous study of multiple species presents challenges, particularly when species exhibit genome duplication or polyploidy. We developed microsatellite markers for Synalpheus shrimp, a genus in which species exhibit not only great variation in social organization, but also interspecific variation in genome size and partial genome duplication...
August 4, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28774726/girardia-dorotocephala-transcriptome-sequence-assembly-and-validation-through-characterization-of-piwi-homologs-and-stem-cell-progeny-markers
#16
Eugene Matthew P Almazan, Sydney L Lesko, Michael P Markey, Labib Rouhana
Planarian flatworms are popular models for the study of regeneration and stem cell biology in vivo. Technical advances and increased availability of genetic information have fueled the discovery of molecules responsible for stem cell pluripotency and regeneration in flatworms. Unfortunately, most of the planarian research performed worldwide utilizes species that are not natural habitants of North America, which limits their availability to newcomer laboratories and impedes their distribution for educational activities...
August 1, 2017: Developmental Biology
https://www.readbyqxmd.com/read/28759647/connectivity-in-gene-coexpression-networks-negatively-correlates-with-rates-of-molecular-evolution-in-flowering-plants
#17
Rishi R Masalia, Adam J Bewick, John M Burke
Gene coexpression networks are a useful tool for summarizing transcriptomic data and providing insight into patterns of gene regulation in a variety of species. Though there has been considerable interest in studying the evolution of network topology across species, less attention has been paid to the relationship between network position and patterns of molecular evolution. Here, we generated coexpression networks from publicly available expression data for seven flowering plant taxa (Arabidopsis thaliana, Glycine max, Oryza sativa, Populus spp...
2017: PloS One
https://www.readbyqxmd.com/read/28756777/genomic-innovations-transcriptional-plasticity-and-gene-loss-underlying-the-evolution-and-divergence-of-two-highly-polyphagous-and-invasive-helicoverpa-pest-species
#18
S L Pearce, D F Clarke, P D East, S Elfekih, K H J Gordon, L S Jermiin, A McGaughran, J G Oakeshott, A Papanikolaou, O P Perera, R V Rane, S Richards, W T Tay, T K Walsh, A Anderson, C J Anderson, S Asgari, P G Board, A Bretschneider, P M Campbell, T Chertemps, J T Christeller, C W Coppin, S J Downes, G Duan, C A Farnsworth, R T Good, L B Han, Y C Han, K Hatje, I Horne, Y P Huang, D S T Hughes, E Jacquin-Joly, W James, S Jhangiani, M Kollmar, S S Kuwar, S Li, N-Y Liu, M T Maibeche, J R Miller, N Montagne, T Perry, J Qu, S V Song, G G Sutton, H Vogel, B P Walenz, W Xu, H-J Zhang, Z Zou, P Batterham, O R Edwards, R Feyereisen, R A Gibbs, D G Heckel, A McGrath, C Robin, S E Scherer, K C Worley, Y D Wu
BACKGROUND: Helicoverpa armigera and Helicoverpa zea are major caterpillar pests of Old and New World agriculture, respectively. Both, particularly H. armigera, are extremely polyphagous, and H. armigera has developed resistance to many insecticides. Here we use comparative genomics, transcriptomics and resequencing to elucidate the genetic basis for their properties as pests. RESULTS: We find that, prior to their divergence about 1.5 Mya, the H. armigera/H. zea lineage had accumulated up to more than 100 more members of specific detoxification and digestion gene families and more than 100 extra gustatory receptor genes, compared to other lepidopterans with narrower host ranges...
July 31, 2017: BMC Biology
https://www.readbyqxmd.com/read/28753860/metabolic-imaging-of-prostate-cancer-reveals-intrapatient-intermetastasis-response-heterogeneity-to-systemic-therapy
#19
Fannie Morin, Jean-Mathieu Beauregard, Michelle Bergeron, Molière Nguile Makao, Louis Lacombe, Vincent Fradet, Yves Fradet, Frédéric Pouliot
Although intrapatient heterogeneity of prostate cancer (PCa) has recently been characterized via genomic and transcriptomic studies, the heterogeneity of systemic treatment responses has yet to be reported or imaged. Our objective was to evaluate the intrapatient intermetastasis response to systemic treatment among patients with metastatic PCa. We evaluated the metabolic response for each individual metastatic lesion (n=165) in 15 patients with metastatic PCa who underwent (18)F-fluorodeoxyglucose positron emission tomography/computed tomography before and at least 3 mo after initiation of a systemic therapy that did not change in that period...
February 23, 2017: European Urology Focus
https://www.readbyqxmd.com/read/28752948/genomic-insights-into-specialized-metabolism-in-the-marine-actinomycete-salinispora
#20
Anne-Catrin Letzel, Li Jing, Gregory Amos, Natalie Millán-Aguiñaga, Joape Ginigini, Usama Ramadan Abdelmohsen, Susana P Gaudêncio, Nadine Ziemert, Bradley S Moore, Paul R Jensen
Comparative genomics is providing new opportunities to address the diversity and distributions of genes encoding the biosynthesis of specialized metabolites. An analysis of 119 genome sequences representing three closely related species of the marine actinomycete genus Salinispora reveals extraordinary biosynthetic diversity in the form of 176 distinct biosynthetic gene clusters (BGCs) of which only 24 have been linked to their products. Remarkably, more than half of the BGCs were observed in only one or two strains, suggesting they were acquired relatively recently in the evolutionary history of the genus...
July 28, 2017: Environmental Microbiology
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