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transcriptome evolution

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https://www.readbyqxmd.com/read/28089430/high-variability-of-expression-profiles-of-homeologous-genes-for-wnt-hh-notch-and-hippo-signaling-pathways-in-xenopus-laevis
#1
Tatsuo Michiue, Takayoshi Yamamoto, Yuuri Yasuoka, Toshiyasu Goto, Takafumi Ikeda, Kei Nagura, Takuya Nakayama, Masanori Taira, Tsutomu Kinoshita
Cell signaling pathways, such as Wnt, Hedgehog (Hh), Notch, and Hippo, are essential for embryogenesis, organogenesis, and tissue homeostasis. In this study, we analyzed 415 genes involved in these pathways in the allotetraploid frog, Xenopus laevis. Most genes are retained in two subgenomes called L and S (193 homeologous gene pairs and 29 singletons). This conservation rate of homeologs is much higher than that of all genes in the X. laevis genome (86.9% vs 60.2%). Among singletons, 24 genes are retained in the L subgenome, a rate similar to the average for all genes (82...
January 12, 2017: Developmental Biology
https://www.readbyqxmd.com/read/28087841/single-cell-transcriptome-analysis-of-fish-immune-cells-provides-insight-into-the-evolution-of-vertebrate-immune-cell-types
#2
Santiago J Carmona, Sarah A Teichmann, Lauren Ferreira, Iain C Macaulay, Michael J T Stubbington, Ana Cvejic, David Gfeller
The immune system of vertebrate species consists of many different cell types that have distinct functional roles and are subject to different evolutionary pressures. Here, we first analysed conservation of genes specific for all major immune cell types in human and mouse. Our results revealed higher gene turnover and faster evolution of trans-membrane proteins in NK cells compared to other immune cell types, and especially T cells, but similar conservation of nuclear and cytoplasmic protein coding genes. To validate these findings in a distant vertebrate species, we used single-cell RNA-Sequencing of lck:GFP cells in zebrafish and obtained the first transcriptome of specific immune cell types in a non-mammalian species...
January 13, 2017: Genome Research
https://www.readbyqxmd.com/read/28087775/rapid-expansion-of-immune-related-gene-families-in-the-house-fly-musca-domestica
#3
Timothy B Sackton, Brian P Lazzaro, Clark G Andrew
The house fly, Musca domestica, occupies an unusual diversity of potentially septic niches compared to other sequenced Dipteran insects and is a vector of numerous diseases of humans and livestock. In the present study, we apply whole-transcriptome sequencing to identify genes whose expression is regulated in adult flies upon bacterial infection. We then combine the transcriptomic data with analysis of rates of gene duplication and loss to provide insight into the evolutionary dynamics of immune-related genes...
January 12, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28087686/amoebozoans-are-secretly-but-ancestrally-sexual-evidence-for-sex-genes-and-potential-novel-crossover-pathways-in-diverse-groups-of-amoebae
#4
Yonas I Tekle, Fiona C Wood, Laura A Katz, Mario A Cerón-Romero, Lydia A Gorfu
Sex is beneficial in eukaryotes as it can increase genetic diversity, reshuffle their genomes, and purge deleterious mutations. Yet, its evolution remains a mystery. The eukaryotic clade supergroup Amoebozoa encompasses diverse lineages of polymorphic amoeboid forms, including both free-living and parasitic lineages. The group is generally believed to be asexual, though recent studies show that some of its members are implicated in cryptic forms of sexual cycles. In this study we conduct a comprehensive inventory and analysis of genes involved in meiosis and related processes, in order to investigate the evolutionary history of sex in the clade...
January 13, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28086860/nicotiana-attenuata-data-hub-nadh-an-integrative-platform-for-exploring-genomic-transcriptomic-and-metabolomic-data-in-wild-tobacco
#5
Thomas Brockmöller, Zhihao Ling, Dapeng Li, Emmanuel Gaquerel, Ian T Baldwin, Shuqing Xu
BACKGROUND: Nicotiana attenuata (coyote tobacco) is an ecological model for studying plant-environment interactions and plant gene function under real-world conditions. During the last decade, large amounts of genomic, transcriptomic and metabolomic data have been generated with this plant which has provided new insights into how native plants interact with herbivores, pollinators and microbes. However, an integrative and open access platform that allows for the efficient mining of these -omics data remained unavailable until now...
January 13, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28077029/the-behavior-of-mobile-genetic-elements-mges-in-different-environments
#6
Masaki Shintani
Mobile genetic elements (MGEs) including plasmids have an important role in the rapid evolution and adaptation of bacteria. Here, the behavior of MGEs in different environments is reviewed, in particular, behavior of the plasmid pCAR1, a carbazole-degradative plasmid isolated from Pseudomonas resinovorans CA10. pCAR1 belongs to incompatibility P-7 group and is self-transmissible among different bacteria. Comparisons of changes in the transcriptome of different host strains caused by carrying pCAR1 revealed common responses in the hosts and host-specific responses...
January 12, 2017: Bioscience, Biotechnology, and Biochemistry
https://www.readbyqxmd.com/read/28075479/different-contributions-of-local-and-distant-regulatory-changes-to-transcriptome-divergence-between-stickleback-ecotypes
#7
Asano Ishikawa, Makoto Kusakabe, Kohta Yoshida, Mark Ravinet, Takashi Makino, Atsushi Toyoda, Asao Fujiyama, Jun Kitano
Differential gene expression can play an important role in phenotypic evolution and divergent adaptation. Although differential gene expression can be caused by both local- and distant-regulatory changes, we know little about their relative contribution to transcriptome evolution in natural populations. Here, we conducted expression quantitative trait loci (eQTL) analysis to investigate the genetic architecture underlying transcriptome divergence between marine and stream ecotypes of threespine sticklebacks (Gasterosteus aculeatus)...
January 11, 2017: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/28068920/comparative-transcriptomics-provide-insight-into-the-morphogenesis-and-evolution-of-fistular-leaves-in-allium
#8
Siyuan Zhu, Shouwei Tang, Zhijian Tan, Yongting Yu, Qiuzhong Dai, Touming Liu
BACKGROUND: Fistular leaves frequently appear in Allium species, and previous developmental studies have proposed that the process of fistular leaf formation involves programmed cell death. However, molecular evidence for the role of programmed cell death in the formation of fistular leaf cavities has yet to be reported. RESULTS: In this study, we characterized the leaf transcriptomes of nine Allium species, including six fistular- and three solid-leaved species...
January 10, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28066713/sequencing-and-de-novo-transcriptome-assembly-of-anthopleura-dowii-verrill-1869-from-mexico
#9
Jorge-Tonatiuh Ayala-Sumuano, Alexei Licea-Navarro, Enrique Rudiño-Piñera, Estefanía Rodríguez, Claudia Rodríguez-Almazán
Next-generation technologies for determination of genomics and transcriptomics composition have a wide range of applications. Moreover, the development of tools for big data set analysis has allowed the identification of molecules and networks involved in metabolism, evolution or behavior. By natural habitats aquatic organisms have implemented molecular strategies for survival, including the production and secretion of toxic compounds for their predators; therefore these organisms are possible sources of proteins or peptides with potential biotechnological application...
March 2017: Genomics Data
https://www.readbyqxmd.com/read/28063346/integrating-genomic-resources-of-flatfish-pleuronectiformes-to-boost-aquaculture-production
#10
Diego Robledo, Miguel Hermida, Juan A Rubiolo, Carlos Fernández, Andrés Blanco, Carmen Bouza, Paulino Martínez
Flatfish have a high market acceptance thus representing a profitable aquaculture production. The main farmed species is the turbot (Scophthalmus maximus) followed by Japanese flounder (Paralichthys olivaceous) and tongue sole (Cynoglossus semilaevis), but other species like Atlantic halibut (Hippoglossus hippoglossus), Senegalese sole (Solea senegalensis) and common sole (Solea solea) also register an important production and are very promising for farming. Important genomic resources are available for most of these species including whole genome sequencing projects, genetic maps and transcriptomes...
December 24, 2016: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/28062756/phylogenetic-origin-and-diversification-of-rnai-pathway-genes-in-insects
#11
Daniel Dowling, Thomas Pauli, Alexander Donath, Karen Meusemann, Lars Podsiadlowski, Malte Petersen, Ralph S Peters, Christoph Mayer, Shanlin Liu, Xin Zhou, Bernhard Misof, Oliver Niehuis
RNA interference (RNAi) refers to the set of molecular processes found in eukaryotic organisms in which small RNA molecules mediate the silencing or down-regulation of target genes. In insects, RNAi serves a number of functions, including regulation of endogenous genes, anti-viral defense, and defense against transposable elements. Despite being well studied in model organisms, such as Drosophila, the distribution of core RNAi pathway genes and their evolution in insects is not well understood. Here we present the most comprehensive overview of the distribution and diversity of core RNAi pathway genes across 100 insect species, encompassing all currently recognized insect orders...
January 6, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28062755/evolutionary-conservation-and-divergence-of-gene-coexpression-networks-in-gossypium-cotton-seeds
#12
Guanjing Hu, Ran Hovav, Corrinne E Grover, Adi Faigenboim-Doron, Noa Kadmon, Justin T Page, Joshua A Udall, Jonathan F Wendel
The cotton genus (Gossypium) provides a superior system for the study of diversification, genome evolution, polyploidization, and human-mediated selection. To gain insight into phenotypic diversification in cotton seeds, we conducted coexpression network analysis of developing seeds from diploid and allopolyploid cotton species and explored network properties. Key network modules and functional associations were identified related to seed oil content and seed weight. We compared species-specific networks to reveal topological changes, including rewired edges and differentially coexpressed genes, associated with speciation, polyploidy, and cotton domestication...
January 6, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28056785/determination-of-dosage-compensation-and-comparison-of-gene-expression-in-a-triploid-hybrid-fish
#13
Li Ren, Chenchen Tang, Wuhui Li, Jialin Cui, Xingjun Tan, Yafeng Xiong, Jie Chen, Jun Wang, Jun Xiao, Yi Zhou, Jing Wang, Min Tao, Chun Zhang, Shaojun Liu
BACKGROUND: Polyploidy and hybridization are both recognized as major forces in evolution. Most of our current knowledge about differences in gene regulation in polyploid hybrids comes from plant studies. The gene expression of diverged genomes and regulatory interactions are still unclear in lower vertebrates. RESULTS: We generated 229 million cleaned reads (42.23 Gbp) from triploid of maternal grass carp (Ctenopharyngodon idellus, Cyprininae, 2n = 48) × paternal blunt snout bream (Megalobrama amblycephala, Cultrinae, 2n = 48) and their diploid parents using next-generation sequencing...
January 5, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28053006/co-option-and-de-novo-gene-evolution-underlie-molluscan-shell-diversity
#14
Felipe Aguilera, Carmel McDougall, Bernard M Degnan
Molluscs fabricate shells of incredible diversity and complexity by localized secretions from the dorsal epithelium of the mantle. Although distantly-related molluscs express remarkably different secreted gene products, it remains unclear if the evolution of shell structure and pattern is underpinned by the differential co-option of conserved genes or the integration of lineage-specific genes into the mantle regulatory program. To address this, we compare the mantle transcriptomes of 11 bivalves and gastropods of varying relatedness...
January 4, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28052920/evolution-of-transcript-modification-by-n6-methyladenosine-in-primates
#15
Lijia Ma, Boxuan Zhao, Kai Chen, Amber Thomas, Jigyasa H Tuteja, Xin He, Chuan He, Kevin White
Phenotypic differences within populations and between closely related species are often driven by variation and evolution of gene expression (King and Wilson 1975; Romero et al. 2012; Villar et al. 2014). However, most analyses have focused on the effects of genomic variation at cis-regulatory elements such as promoters and enhancers that control transcriptional activity, and little is understood about the influence of post-transcriptional processes on transcript evolution. Post-transcriptional modification of RNA by N6-methyladenosine (m6A) has been shown to be widespread throughout the transcriptome (Desrosiers et al...
January 4, 2017: Genome Research
https://www.readbyqxmd.com/read/28050011/consensus-molecular-subtypes-and-the-evolution-of-precision-medicine-in-colorectal-cancer
#16
Rodrigo Dienstmann, Louis Vermeulen, Justin Guinney, Scott Kopetz, Sabine Tejpar, Josep Tabernero
Critical driver genomic events in colorectal cancer have been shown to affect the response to targeted agents that were initially developed under the 'one gene, one drug' paradigm of precision medicine. Our current knowledge of the complexity of the cancer genome, clonal evolution patterns under treatment pressure and pharmacodynamic effects of target inhibition support the transition from a one gene, one drug approach to a 'multi-gene, multi-drug' model when making therapeutic decisions. Better characterization of the transcriptomic subtypes of colorectal cancer, encompassing tumour, stromal and immune components, has revealed convergent pathway dependencies that mandate a 'multi-molecular' perspective for the development of therapies to treat this disease...
January 4, 2017: Nature Reviews. Cancer
https://www.readbyqxmd.com/read/28049606/an-insight-into-the-sialome-of-hyalomma-excavatum
#17
José M C Ribeiro, Mirko Slovák, Ivo M B Francischetti
Tick saliva contains hundreds or thousands of proteins that help blood feeding by impairing their hosts' hemostasis, inflammation and immunity. Salivary gland transcriptomes allow the disclosure of this pharmacologically active potion that consists of several multi-gene families, many of which are tick-specific. We here report the "de novo" assembly of ∼138 million reads deriving from a cDNA library from salivary glands of adult male and female Hyalomma excavatum leading to the public deposition of 5337 coding sequences to GenBank...
December 21, 2016: Ticks and Tick-borne Diseases
https://www.readbyqxmd.com/read/28049478/the-transcriptome-of-the-mosquito-aedes-fluviatilis-diptera-culicidae-and-transcriptional-changes-associated-with-its-native-wolbachia-infection
#18
E P Caragata, F S Pais, L A Baton, J B L Silva, M H F Sorgine, L A Moreira
BACKGROUND: Wolbachia is a bacterial endosymbiont that naturally infects a wide range of insect species, and causes drastic changes to host biology. Stable infections of Wolbachia in mosquitoes can inhibit infection with medically important pathogens such as dengue virus and malaria-causing Plasmodium parasites. However, some native Wolbachia strains can enhance infection with certain pathogens, as is the case for the mosquito Aedes fluviatilis, where infection with Plasmodium gallinaceum is enhanced by the native wFlu Wolbachia strain...
January 3, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28049427/identification-of-candidate-infection-genes-from-the-model-entomopathogenic-nematode-heterorhabditis-bacteriophora
#19
Jonathan Vadnal, Ramesh Ratnappan, Melissa Keaney, Eric Kenney, Ioannis Eleftherianos, Damien O'Halloran, John M Hawdon
BACKGROUND: Despite important progress in the field of innate immunity, our understanding of host immune responses to parasitic nematode infections lags behind that of responses to microbes. A limiting factor has been the obligate requirement for a vertebrate host which has hindered investigation of the parasitic nematode infective process. The nematode parasite Heterorhabditis bacteriophora offers great potential as a model to genetically dissect the process of infection. With its mutualistic Photorhabdus luminescens bacteria, H...
January 3, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28049147/merkel-cell-polyomavirus-exhibits-dominant-control-of-the-tumor-genome-and-transcriptome-in-virus-associated-merkel-cell-carcinoma
#20
Gabriel J Starrett, Christina Marcelus, Paul G Cantalupo, Joshua P Katz, Jingwei Cheng, Keiko Akagi, Manisha Thakuria, Guilherme Rabinowits, Linda C Wang, David E Symer, James M Pipas, Reuben S Harris, James A DeCaprio
: Merkel cell polyomavirus is the primary etiological agent of the aggressive skin cancer Merkel cell carcinoma (MCC). Recent studies have revealed that UV radiation is the primary mechanism for somatic mutagenesis in nonviral forms of MCC. Here, we analyze the whole transcriptomes and genomes of primary MCC tumors. Our study reveals that virus-associated tumors have minimally altered genomes compared to non-virus-associated tumors, which are dominated by UV-mediated mutations. Although virus-associated tumors contain relatively small mutation burdens, they exhibit a distinct mutation signature with observable transcriptionally biased kataegic events...
January 3, 2017: MBio
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