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transcriptome evolution

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https://www.readbyqxmd.com/read/29163564/non-replicative-integral-membrane-proteins-encoded-by-plant-alpha-like-viruses-emergence-of-diverse-orphan-orfs-and-movement-protein-genes
#1
Andrey G Solovyev, Sergey Y Morozov
Fast accumulation of sequencing data on plant virus genomes and plant transcriptomes demands periodic re-evaluation of current views on the genome evolution of viruses. Here, we substantiate and further detail our previously mostly speculative model on the origin and evolution of triple gene block (TGB) encoding plant virus movement proteins TGB1, TGB2, and TGB3. Recent experimental data on functional competence of transport gene modules consisting of two proteins related to TGB1 and TGB2, as well as sequence analysis data on similarity of TGB2 and TGB3 encoded by a viral genome and virus-like RNAs identified in a plant transcriptomes, suggest that TGB evolution involved events of gene duplication and gene transfer between viruses...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29163058/adaptive-changes-in-the-vestibular-system-of-land-snail-to-a-30-day-spaceflight-and-readaptation-on-return-to-earth
#2
Nikolay Aseyev, Alia Kh Vinarskaya, Matvey Roshchin, Tatiana A Korshunova, Aleksey Yu Malyshev, Alena B Zuzina, Victor N Ierusalimsky, Maria S Lemak, Igor S Zakharov, Ivan A Novikov, Peter Kolosov, Ekaterina Chesnokova, Svetlana Volkova, Artem Kasianov, Leonid Uroshlev, Yekaterina Popova, Richard D Boyle, Pavel M Balaban
The vestibular system receives a permanent influence from gravity and reflexively controls equilibrium. If we assume gravity has remained constant during the species' evolution, will its sensory system adapt to abrupt loss of that force? We address this question in the land snail Helix lucorum exposed to 30 days of near weightlessness aboard the Bion-M1 satellite, and studied geotactic behavior of postflight snails, differential gene expressions in statocyst transcriptome, and electrophysiological responses of mechanoreceptors to applied tilts...
2017: Frontiers in Cellular Neuroscience
https://www.readbyqxmd.com/read/29162694/an-endogenous-retroviral-envelope-syncytin-and-its-cognate-receptor-identified-in-the-viviparous-placental-mabuya-lizard
#3
Guillaume Cornelis, Mathis Funk, Cécile Vernochet, Francisca Leal, Oscar Alejandro Tarazona, Guillaume Meurice, Odile Heidmann, Anne Dupressoir, Aurélien Miralles, Martha Patricia Ramirez-Pinilla, Thierry Heidmann
Syncytins are envelope genes from endogenous retroviruses that have been captured during evolution for a function in placentation. They have been found in all placental mammals in which they have been searched, including marsupials. Placental structures are not restricted to mammals but also emerged in some other vertebrates, most frequently in lizards, such as the viviparous Mabuya Scincidae. Here, we performed high-throughput RNA sequencing of a Mabuya placenta transcriptome and screened for the presence of retroviral env genes with a full-length ORF...
November 21, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29155030/transcriptome-analysis-and-discovery-of-genes-involved-in-immune-pathways-from-coelomocytes-of-onchidium-struma-after-bacterial-challenge
#4
Mingming Zhang, Guo Qiao, Qiang Li, De-Hai Xu, Zhitao Qi, Aiming Wang, Mengyao Xu, Jintian Huang
Onchidium struma widely distributes in subtidal and low-tidal zones, which is considered to be an economical species with rich nutrition, a valuable biomonitor for heavy metal pollution and a representative species for evolution from ocean to land. However, there is limited genetic information available for O. struma development. This study compared transcriptomic profiles of coelomocytes from normal and bacteria infected O. struma by Illumina-based paired-end sequencing to explore the molecular immune mechanism of O...
November 15, 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/29145825/assembling-large-genomes-analysis-of-the-stick-insect-clitarchus-hookeri-genome-reveals-a-high-repeat-content-and-sex-biased-genes-associated-with-reproduction
#5
Chen Wu, Victoria G Twort, Ross N Crowhurst, Richard D Newcomb, Thomas R Buckley
BACKGROUND: Stick insects (Phasmatodea) have a high incidence of parthenogenesis and other alternative reproductive strategies, yet the genetic basis of reproduction is poorly understood. Phasmatodea includes nearly 3000 species, yet only the genome of Timema cristinae has been published to date. Clitarchus hookeri is a geographical parthenogenetic stick insect distributed across New Zealand. Sexual reproduction dominates in northern habitats but is replaced by parthenogenesis in the south...
November 16, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29143964/signatures-of-selection-in-embryonic-transcriptomes-of-lizards-adapting-in-parallel-to-cool-climate
#6
Nathalie Feiner, Alfredo Rago, Geoffrey M While, Tobias Uller
Populations adapting independently to the same environment provide important insights into the repeatability of evolution at different levels of biological organization. In the 20(th) century, common wall lizards (Podarcis muralis) from southern and western Europe were introduced to England, north of their native range. Non-native populations of both lineages have adapted to the shorter season and lower egg incubation temperature by increasing the absolute rate of embryonic development. Here we tested if this adaptation is accompanied by signatures of directional selection in the transcriptomes of early embryos and, if so, if non-native populations show adaptive convergence...
November 16, 2017: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/29136137/copy-number-variation-and-expression-analysis-reveals-a-non-orthologous-pinta-gene-family-member-involved-in-butterfly-vision
#7
Aide Macias-Muñoz, Kyle J McCulloch, Adriana D Briscoe
Vertebrate (CRALBP) and Drosophila (PINTA) proteins with a CRAL-TRIO domain transport retinal-based chromophores that bind to opsin proteins and are necessary for phototransduction. The CRAL-TRIO domain gene family is composed of genes that encode proteins with a common N-terminal structural domain. While there is an expansion of this gene family in Lepidoptera, there is no lepidopteran ortholog of pinta. Further, the function of these genes in lepidopterans has not yet been established. Here we explored the molecular evolution and expression of CRAL-TRIO domain genes in the butterfly Heliconius melpomene in order to identify a member of this gene family as a candidate chromophore transporter...
November 9, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29134713/comparative-ecological-transcriptomics-and-the-contribution-of-gene-expression-to-the-evolutionary-potential-of-a-threatened-fish
#8
Chris J Brauer, Peter J Unmack, Luciano B Beheregaray
Understanding whether small populations with low genetic diversity can respond to rapid environmental change via phenotypic plasticity is an outstanding research question in biology. RNA sequencing (RNA-seq) has recently provided the opportunity to examine variation in gene expression, a surrogate for phenotypic variation, in non-model species. We used a comparative RNA-seq approach to assess expression variation within and among adaptively divergent populations of a threatened freshwater fish, Nannoperca australis, found across a steep hydroclimatic gradient in the Murray-Darling Basin, Australia...
November 13, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29133310/convergent-origination-of-a-drosophila-like-dosage-compensation-mechanism-in-a-reptile-lineage
#9
Ray Marin, Diego Cortez, Francesco Lamanna, Madapura M Pradeepa, Evgeny Leushkin, Philippe Julien, Angélica Liechti, Jean Halbert, Thoomke Brüning, Katharina Mössinger, Timo Trefzer, Christian Conrad, Halie N Kerver, Juli Wade, Patrick Tschopp, Henrik Kaessmann
Sex chromosomes differentiated from different ancestral autosomes in various vertebrate lineages. Here, we trace the functional evolution of the XY Chromosomes of the green anole lizard (Anolis carolinensis), on the basis of extensive high-throughput genome, transcriptome and histone modification sequencing data and revisit dosage compensation evolution in representative mammals and birds with substantial new expression data. Our analyses show that Anolis sex chromosomes represent an ancient XY system that originated at least ≈160 million years ago in the ancestor of Iguania lizards, shortly after the separation from the snake lineage...
November 13, 2017: Genome Research
https://www.readbyqxmd.com/read/29131842/positive-selection-and-comparative-molecular-evolution-of-reproductive-proteins-from-new-zealand-tree-weta-orthoptera-hemideina
#10
Victoria G Twort, Alice B Dennis, Duckchul Park, Kathryn F Lomas, Richard D Newcomb, Thomas R Buckley
Animal reproductive proteins, especially those in the seminal fluid, have been shown to have higher levels of divergence than non-reproductive proteins and are often evolving adaptively. Seminal fluid proteins have been implicated in the formation of reproductive barriers between diverging lineages, and hence represent interesting candidates underlying speciation. RNA-seq was used to generate the first male reproductive transcriptome for the New Zealand tree weta species Hemideina thoracica and H. crassidens...
2017: PloS One
https://www.readbyqxmd.com/read/29127881/grapevine-immune-signaling-network-in-response-to-drought-stress-as-revealed-by-transcriptomic-analysis
#11
Muhammad S Haider, Mahantesh M Kurjogi, M Khalil-Ur-Rehman, Muhammad Fiaz, Tariq Pervaiz, Songtao Jiu, Jia Haifeng, Wang Chen, Jinggui Fang
Drought is a ubiquitous abiotic factor that severely impedes growth and development of horticulture crops. The challenge postured by global climate change is the evolution of drought-tolerant cultivars that could cope with concurrent stress. Hence, in this study, biochemical, physiological and transcriptome analysis were investigated in drought-treated grapevine leaves. The results revealed that photosynthetic activity and reducing sugars were significantly diminished which were positively correlated with low stomatal conductance and CO2 exchange in drought-stressed leaves...
October 31, 2017: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/29122854/the-substrates-of-nonsense-mediated-mrna-decay-in-caenorhabditis-elegans
#12
Virginia S Muir, Audrey P Gasch, Philip Anderson
Nonsense-mediated mRNA decay (NMD) is a conserved pathway that strongly influences eukaryotic gene expression.  Inactivating or inhibiting NMD affects the abundance of a substantial fraction of the transcriptome in numerous species.  Transcripts whose abundance is altered in NMD-deficient cells may represent either direct substrates of NMD or indirect effects of inhibiting NMD.  We present a genome-wide investigation of the direct substrates of NMD in Caenorhabditis elegans  Our goals were (i) to identify mRNA substrates of NMD and (ii) to distinguish those mRNAs from others whose abundance is indirectly influenced by the absence of NMD...
November 9, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29118334/temporal-and-spatial-expression-of-genes-involved-in-dna-methylation-during-reproductive-development-of-sexual-and-apomictic-eragrostis-curvula
#13
J P Selva, L Siena, J M Rodrigo, I Garbus, D Zappacosta, J R Romero, J P A Ortiz, S C Pessino, O Leblanc, V Echenique
Recent reports in model plant species have highlighted a role for DNA methylation pathways in the regulation of the somatic-to-reproductive transition in the ovule, suggesting that apomixis (asexual reproduction through seeds) likely relies on RdDM downregulation. Our aim was therefore to explore this hypothesis by characterizing genes involved in DNA methylation in the apomictic grass Eragrostis curvula. We explored floral transcriptomes to identify homologs of three candidate genes, for which mutations in Arabidopsis and maize mimic apomixis (AtAGO9/ZmAGO104, AtCMT3/ZmDMT102/ZmDMT105, and AtDDM1/ZmCHR106), and compared both their spatial and temporal expression patterns during reproduction in sexual and apomictic genotypes...
November 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29116634/evolution-and-strain-variation-in-bcg
#14
Abdallah M Abdallah, Marcel A Behr
BCG vaccines were derived by in vitro passage, during the years 1908-1921, at the Pasteur Institute of Lille. Following the distribution of stocks of BCG to vaccine production laboratories around the world, it was only a few decades before different BCG producers recognized that there were variants of BCG, likely due to different passaging conditions in the different laboratories. This ultimately led to the lyophilization of stable BCG products in the 1950s and 1960s, but not before considerable evolution of the different BCG strains had taken place...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/29111455/meta-transcriptomics-and-the-evolutionary-biology-of-rna-viruses
#15
REVIEW
Mang Shi, Yong-Zhen Zhang, Edward C Holmes
Metagenomics is transforming the study of virus evolution, allowing the full assemblage of virus genomes within a host sample to be determined rapidly and cheaply. The genomic analysis of complete transcriptomes, so-called meta-transcriptomics, is providing a particularly rich source of data on the global diversity of RNA viruses and their evolutionary history. Herein we review some of the insights that meta-transcriptomics has provided on the fundamental patterns and processes of virus evolution, with a focus on the recent discovery of a multitude of novel invertebrate viruses...
October 27, 2017: Virus Research
https://www.readbyqxmd.com/read/29110697/exutr-a-novel-pipeline-for-large-scale-prediction-of-3-utr-sequences-from-ngs-data
#16
Zixia Huang, Emma C Teeling
BACKGROUND: The three prime untranslated region (3'-UTR) is known to play a pivotal role in modulating gene expression by determining the fate of mRNA. Many crucial developmental events, such as mammalian spermatogenesis, tissue patterning, sex determination and neurogenesis, rely heavily on post-transcriptional regulation by the 3'-UTR. However, 3'-UTR biology seems to be a relatively untapped field, with only limited tools and 3'-UTR resources available. To elucidate the regulatory mechanisms of the 3'-UTR on gene expression, firstly the 3'-UTR sequences must be identified...
November 6, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29109049/combined-transcriptomic-proteomic-analysis-of-salivary-gland-and-secreted-saliva-in-three-planthopper-species
#17
Hai-Jian Huang, Jia-Bao Lu, Qiao Li, Yan-Yuan Bao, Chuan-Xi Zhang
The planthoppers are piercing-sucking pests that continuously inject saliva into host plants using specialized stylets. However, knowledge on the constituent and function of planthopper saliva proteins was still limited. In this study, the transcriptomic and proteomic approach were adopted to characterize the composition of salivary glands and their secreted saliva in three planthoppers, respectively. Gene repertoires of salivary glands in brown planthopper (Nilaparvata lugens, BPH), white-backed planthopper (Sogatella furcifera, WBPH) and small brown planthopper (Laodelphax striatellus, SBPH) were very similar, which actively involved in protein synthesis and energy metabolism...
November 3, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/29097405/the-evolution-of-gene-specific-transcriptional-noise-is-driven-by-selection-at-the-pathway-level
#18
Gustavo Valadares Barroso, Natasa Puzovic, Julien Y Dutheil
Biochemical reactions within individual cells result from the interactions of molecules, typically in small numbers. Consequently, the inherent stochasticity of binding and diffusion processes generate noise along the cascade that leads to the synthesis of a protein from its encoding gene. As a result, isogenic cell populations display phenotypic variability even in homogeneous environments. The extent and consequences of this stochastic gene expression have only recently been assessed on a genome-wide scale, in particular owing to the advent of single cell transcriptomics...
November 2, 2017: Genetics
https://www.readbyqxmd.com/read/29096695/floral-micromorphology-and-transcriptome-analyses-of-a-fragrant-vandaceous-orchid-vanda-mimi-palmer-for-its-fragrance-production-sites
#19
Conie Toh, Ab Rahim Mohd-Hairul, Nooraini Mohd Ain, Parameswari Namasivayam, Rusea Go, Nur Ashikin Psyquay Abdullah, Meilina Ong Abdullah, Janna Ong Abdullah
BACKGROUND: Vanda Mimi Palmer (VMP) is commercially valuable for its strong fragrance but little is known regarding the fragrance production and emission sites on the flowers. RESULTS: Olfactory perception detected fragrance only from the petals and sepals. Light and Environmental Scanning Electron microscopy analyses on fresh tissues showed distributions of stomata and trichomes concentrated mostly around the edges. These results paralleled the rich starch deposits and intense neutral red stain, indicating strong fragrance and trichomes as potential main fragrance release sites...
November 2, 2017: BMC Research Notes
https://www.readbyqxmd.com/read/29095994/pyomelanin-produced-by-vibriocholerae-confers-resistance-to-predation-by-acanthamoebacastellanii
#20
Parisa Noorian, Hu Jie, Zhiliang Chen, Staffan Kjelleberg, Marc R Wilkins, Shuyang Sun, Diane McDougald
Protozoan predation is one of the main environmental factors constraining bacterial growth in aquatic environments, and thus has led to the evolution of a number of defence mechanisms that protect bacteria from predation. These mechanisms may also function as virulence factors in infection of animal and human hosts. Whole transcriptome shotgun sequencing of Vibrio cholerae biofilms during predation by the amoebae, Acanthamoeba castellanii, revealed that 131 transcripts were significantly differentially regulated when compared to the non-grazed control...
October 31, 2017: FEMS Microbiology Ecology
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