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transcriptome evolution

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https://www.readbyqxmd.com/read/29348510/genome-and-secretome-analysis-of-pochonia-chlamydosporia-provide-new-insight-into-egg-parasitic-mechanisms
#1
Runmao Lin, Feifei Qin, Baoming Shen, Qianqian Shi, Chichuan Liu, Xi Zhang, Yang Jiao, Jun Lu, Yaoyao Gao, Marta Suarez-Fernandez, Federico Lopez-Moya, Luis Vicente Lopez-Llorca, Gang Wang, Zhenchuan Mao, Jian Ling, Yuhong Yang, Xinyue Cheng, Bingyan Xie
Pochonia chlamydosporia infects eggs and females of economically important plant-parasitic nematodes. The fungal isolates parasitizing different nematodes are genetically distinct. To understand their intraspecific genetic differentiation, parasitic mechanisms, and adaptive evolution, we assembled seven putative chromosomes of P. chlamydosporia strain 170 isolated from root-knot nematode eggs (~44 Mb, including 7.19% of transposable elements) and compared them with the genome of the strain 123 (~41 Mb) isolated from cereal cyst nematode...
January 18, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29346618/evidence-of-adaptive-evolution-and-relaxed-constraints-in-sex-biased-genes-of-south-american-and-west-indies-fruit-flies-diptera-tephritidae
#2
Carlos Congrains, Emeline B Campanini, Felipe R Torres, Víctor B Rezende, Aline M Nakamura, Janaína L de Oliveira, André L A Lima, Samira Chahad-Ehlers, Iderval S Sobrinho, Reinaldo A de Brito
Several studies have demonstrated that genes differentially expressed between sexes (sex-biased genes) tend to evolve faster than unbiased genes, particularly in males. The reason for this accelerated evolution is not clear, but several explanations have involved adaptive and non-adaptive mechanisms. Furthermore, the differences of sex-biased expression patterns of closely related species are also little explored out of Drosophila. To address the evolutionary processes involved with sex-biased expression in species with incipient differentiation, we analyzed male and female transcriptomes of Anastrepha fraterculus and A...
January 15, 2018: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29345184/temperature-dependent-small-rna-expression-in-drosophila-melanogaster
#3
Isabel Fast, David Rosenkranz
Temperature has a major impact on gene expression in ectotherms. But until recently, it was not clear in which way, if any, small non-coding RNAs such as miRNAs or piRNAs contribute to thermosensitive gene regulation. We have recently shown that temperature-responsive miRNAs in Drosophila drive adaptation to different ambient temperatures on the transcriptome level. Moreover, we demonstrated that higher temperatures lead to a more efficient piRNA-dependent transposon silencing, possibly due to heat-induced unfolding of RNA secondary structures...
January 18, 2018: RNA Biology
https://www.readbyqxmd.com/read/29339745/genomic-and-transcriptomic-analysis-of-the-asian-honeybee-apis-cerana-provides-novel-insights-into-honeybee-biology
#4
Qingyun Diao, Liangxian Sun, Huajun Zheng, Zhijiang Zeng, Shengyue Wang, Shufa Xu, Huoqing Zheng, Yanping Chen, Yuanyuan Shi, Yuezhu Wang, Fei Meng, Qingliang Sang, Lianfei Cao, Fang Liu, Yongqiang Zhu, Wenfeng Li, Zhiguo Li, Congjie Dai, Minjun Yang, Shenglu Chen, Runsheng Chen, Shaowu Zhang, Jay D Evans, Qiang Huang, Jie Liu, Fuliang Hu, Songkun Su, Jie Wu
The Asian honeybee Apis cerana is one of two bee species that have been commercially kept with immense economic value. Here we present the analysis of genomic sequence and transcriptomic exploration for A. cerana as well as the comparative genomic analysis of the Asian honeybee and the European honeybee A. mellifera. The genome and RNA-seq data yield new insights into the behavioral and physiological resistance to the parasitic mite Varroa the evolution of antimicrobial peptides, and the genetic basis for labor division in A...
January 16, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29337419/evolution-of-resistance-to-chytridiomycosis-is-associated-with-a-robust-early-immune-response
#5
Laura F Grogan, Scott D Cashins, Lee F Skerratt, Lee Berger, Michael S McFadden, Peter Harlow, David A Hunter, Ben C Scheele, Jason Mulvenna
Potentiating the evolution of immunity is a promising strategy for addressing biodiversity diseases. Assisted selection for infection resistance may enable the recovery and persistence of amphibians threatened by chytridiomycosis; a devastating fungal skin disease threatening hundreds of species globally. However, knowledge of the mechanisms involved in the natural evolution of immunity to chytridiomycosis is limited. Understanding the mechanisms of such resistance may help speed assisted-selection. Using a transcriptomics approach we examined gene expression responses of endangered alpine tree frogs (Litoria verreauxii alpina) to subclinical infection, comparing two long-exposed populations with a naïve population...
January 16, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29329439/conserved-proteins-of-the-rna-interference-system-in-the-arbuscular-mycorrhizal-fungus-rhizoglomus-irregulare-provide-new-insight-into-the-evolutionary-history-of-glomeromycota
#6
Soon-Jae Lee, Mengxuan Kong, Paul Harrison, Mohamed Hijri
Horizontal gene transfer (HGT) is an important mechanism in the evolution of many living organisms particularly in Prokaryotes where genes are frequently dispersed between taxa. Although, HGT has been reported in Eukaryotes, its accumulative effect and its frequency has been questioned. Arbuscular mycorrhizal fungi (AMF) are an early diverged fungal lineage belonging to phylum Glomeromycota, whose phylogenetic position is still under debate. The history of AMF and land plant symbiosis dates back to at least 460 million years ago...
January 10, 2018: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29329292/transcriptome-profiling-with-focus-on-potential-key-genes-for-wing-development-and-evolution-in-megaloprepus-caerulatus-the-damselfly-species-with-the-world-s-largest-wings
#7
Wiebke Feindt, Sara J Oppenheim, Robert DeSalle, Paul Z Goldstein, Heike Hadrys
The evolution, development and coloration of insect wings remains a puzzling subject in evolutionary research. In basal flying insects such as Odonata, genomic research regarding bauplan evolution is still rare. Here we focus on the world's largest odonate species-the "forest giant" Megaloprepus caerulatus, to explore its potential for looking deeper into the development and evolution of wings. A recently discovered cryptic species complex in this genus previously considered monotypic is characterized by morphological differences in wing shape and color patterns...
2018: PloS One
https://www.readbyqxmd.com/read/29325559/pangenome-analyses-of-the-wheat-pathogen-zymoseptoria-tritici-reveal-the-structural-basis-of-a-highly-plastic-eukaryotic-genome
#8
Clémence Plissonneau, Fanny E Hartmann, Daniel Croll
BACKGROUND: Structural variation contributes substantially to polymorphism within species. Chromosomal rearrangements that impact genes can lead to functional variation among individuals and influence the expression of phenotypic traits. Genomes of fungal pathogens show substantial chromosomal polymorphism that can drive virulence evolution on host plants. Assessing the adaptive significance of structural variation is challenging, because most studies rely on inferences based on a single reference genome sequence...
January 11, 2018: BMC Biology
https://www.readbyqxmd.com/read/29324689/characterization-of-translationally-controlled-tumour-protein-from-the-sea-anemone-anemonia-viridis-and-transcriptome-wide-identification-of-cnidarian-homologues
#9
Aldo Nicosia, Carmelo Bennici, Girolama Biondo, Salvatore Costa, Marilena Di Natale, Tiziana Masullo, Calogera Monastero, Maria Antonietta Ragusa, Marcello Tagliavia, Angela Cuttitta
Gene family encoding translationally controlled tumour protein (TCTP) is defined as highly conserved among organisms; however, there is limited knowledge of non-bilateria. In this study, the first TCTP homologue from anthozoan was characterised in the Mediterranean Sea anemone, Anemonia viridis. The release of the genome sequence of Acropora digitifera, Exaiptasia pallida, Nematostella vectensis and Hydra vulgaris enabled a comprehensive study of the molecular evolution of TCTP family among cnidarians. A comparison among TCTP members from Cnidaria and Bilateria showed conserved intron exon organization, evolutionary conserved TCTP signatures and 3D protein structure...
January 11, 2018: Genes
https://www.readbyqxmd.com/read/29324038/the-evolution-and-metamorphosis-of-arthropod-proteomics-and-genomics
#10
Judith H Willis
This article presents an overview of the development of techniques for analyzing cuticular proteins (CPs), their transcripts, and their genes over the past 50 years based primarily on experience in the laboratory of J.H. Willis. It emphasizes changes in the kind of data that can be gathered and how such data provided insights into the molecular underpinnings of insect metamorphosis and cuticle structure. It describes the techniques that allowed visualization of the location of CPs at both the anatomical and intracuticular levels and measurement of the appearance and deployment of transcripts from CP genes as well as what was learned from genomic and transcriptomic data...
January 7, 2018: Annual Review of Entomology
https://www.readbyqxmd.com/read/29319911/genomic-islands-of-differentiation-in-two-songbird-species-reveal-candidate-genes-for-hybrid-female-sterility
#11
Libor Mořkovský, Václav Janoušek, Jiří Reif, Jakub Rídl, Jan Pačes, Lukáš Choleva, Karel Janko, Michael W Nachman, Radka Reifová
Hybrid sterility is a common first step in the evolution of postzygotic reproductive isolation. According to Haldane's Rule it affects predominantly the heterogametic sex. While the genetic basis of hybrid male sterility in organisms with heterogametic males has been studied for decades, the genetic basis of hybrid female sterility in organisms with heterogametic females has received much less attention. We investigated the genetic basis of reproductive isolation in two closely related avian species, the Common Nightingale (Luscinia megarhynchos) and the Thrush Nightingale (L...
January 10, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29317769/phylogenomic-perspective-on-the-relationships-and-evolutionary-history-of-the-major-otocephalan-lineages
#12
Wei Dai, Ming Zou, Liandong Yang, Kang Du, Weitao Chen, Yanjun Shen, Richard L Mayden, Shunping He
The phylogeny of otocephalan fishes is the subject of broad controversy based on morphological and molecular evidence. The primary unresolved issue pertaining to this lineage relates to the origin of Characiphysi, especially the paraphyly of Characiformes. The considerable uncertainty associated with this lineage has precluded a greater understanding of the origin and evolution of the clade. Herein, a phylogenomic approach was applied to resolve this debate. By analyzing 10 sets of transcriptomic data generated in this study and 12 sets of high-throughput data available in public databases, we obtained 1,110 single-copy orthologous genes (935,265 sites for analysis) from 22 actinopterygians, including 14 otocephalan fishes from six orders: Clupeiformes, Gonorynchiformes, Cypriniformes, Siluriformes, Characiformes, and Gymnotiformes...
January 9, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29317511/exploration-of-the-germline-genome-of-the-ciliate-chilodonella-uncinata-through-single-cell-omics-transcriptomics-and-genomics
#13
Xyrus X Maurer-Alcalá, Rob Knight, Laura A Katz
Separate germline and somatic genomes are found in numerous lineages across the eukaryotic tree of life, often separated into distinct tissues (e.g., in plants, animals, and fungi) or distinct nuclei sharing a common cytoplasm (e.g., in ciliates and some foraminifera). In ciliates, germline-limited (i.e., micronuclear-specific) DNA is eliminated during the development of a new somatic (i.e., macronuclear) genome in a process that is tightly linked to large-scale genome rearrangements, such as deletions and reordering of protein-coding sequences...
January 9, 2018: MBio
https://www.readbyqxmd.com/read/29317285/wide-spread-whole-genome-duplications-contribute-to-genome-complexity-and-species-diversity-in-angiosperms
#14
Ren Ren, Haifeng Wang, Chunce Guo, Ning Zhang, Liping Zeng, Yamao Chen, Hong Ma, Ji Qi
Gene duplications (GDs) provide evolutionary potentials for generating novel functions, while polyploidization or whole genome duplication (WGD) doubles the chromosomes initially and results in hundreds to thousands of retained duplicates. WGDs are strongly supported by evidence commonly found in many species-rich lineages of eukaryotes, thus are considered as a major driving force in species diversification. We performed comparative genomic and phylogenomic analyses on 59 public genomes/transcriptomes and 46 newly sequenced transcriptomes covering major lineages of angiosperms, to detect large-scale gene duplication events by survey of tens of thousands of gene family trees...
January 6, 2018: Molecular Plant
https://www.readbyqxmd.com/read/29315638/comparative-genomics-and-transcriptomics-depict-ericoid-mycorrhizal-fungi-as-versatile-saprotrophs-and-plant-mutualists
#15
Elena Martino, Emmanuelle Morin, Gwen-Aëlle Grelet, Alan Kuo, Annegret Kohler, Stefania Daghino, Kerrie W Barry, Nicolas Cichocki, Alicia Clum, Rhyan B Dockter, Matthieu Hainaut, Rita C Kuo, Kurt LaButti, Björn D Lindahl, Erika A Lindquist, Anna Lipzen, Hassine-Radhouane Khouja, Jon Magnuson, Claude Murat, Robin A Ohm, Steven W Singer, Joseph W Spatafora, Mei Wang, Claire Veneault-Fourrey, Bernard Henrissat, Igor V Grigoriev, Francis M Martin, Silvia Perotto
Some soil fungi in the Leotiomycetes form ericoid mycorrhizal (ERM) symbioses with Ericaceae. In the harsh habitats in which they occur, ERM plant survival relies on nutrient mobilization from soil organic matter (SOM) by their fungal partners. The characterization of the fungal genetic machinery underpinning both the symbiotic lifestyle and SOM degradation is needed to understand ERM symbiosis functioning and evolution, and its impact on soil carbon (C) turnover. We sequenced the genomes of the ERM fungi Meliniomyces bicolor, M...
January 7, 2018: New Phytologist
https://www.readbyqxmd.com/read/29312538/genome-wide-gene-expression-analysis-in-the-amphioxus-branchiostoma-belcheri-after-poly-i-c-challenge-using-strand-specific-rna-seq
#16
Qi-Lin Zhang, Zheng-Qing Xie, Ming-Zhong Liang, Bang Luo, Xiu-Qiang Wang, Jun-Yuan Chen
The gene expression associated with immune response to bacteria/bacterial mimic has been extensively analyzed in amphioxus, but remains largely unknown about how gene are involved in the immune response to viral invasion at expression level. Here, we analyze the rRNA-depleted transcriptomes of Branchiostoma belcheri using strand-specific RNA-seq in response to the viral mimic, poly (I:C) (pIC). A total of 5,317 differentially expressed genes were detected at treatment group by comparing with control. The gene with the most significant expression changes (top 15) after pIC challenge and 7 immune-related categories involving 58 differently expressed genes were scrutinized...
December 12, 2017: Oncotarget
https://www.readbyqxmd.com/read/29310597/de-novo-transcriptome-assembly-annotation-and-comparison-of-four-ecological-and-evolutionary-model-salmonid-fish-species
#17
Madeleine Carruthers, Andrey A Yurchenko, Julian J Augley, Colin E Adams, Pawel Herzyk, Kathryn R Elmer
BACKGROUND: Salmonid fishes exhibit high levels of phenotypic and ecological variation and are thus ideal model systems for studying evolutionary processes of adaptive divergence and speciation. Furthermore, salmonids are of major interest in fisheries, aquaculture, and conservation research. Improving understanding of the genetic mechanisms underlying traits in these species would significantly progress research in these fields. Here we generate high quality de novo transcriptomes for four salmonid species: Atlantic salmon (Salmo salar), brown trout (Salmo trutta), Arctic charr (Salvelinus alpinus), and European whitefish (Coregonus lavaretus)...
January 8, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29304730/genomic-abundance-and-transcriptional-activity-of-diverse-gypsy-and-copia-long-terminal-repeat-retrotransposons-in-three-wild-sunflower-species
#18
Fan Qiu, Mark C Ungerer
BACKGROUND: Long terminal repeat (LTR) retrotransposons are highly abundant in plant genomes and require transcriptional activity for their proliferative mode of replication. These sequences exist in plant genomes as diverse sublineages within the main element superfamilies (i.e., gypsy and copia). While transcriptional activity of these elements is increasingly recognized as a regular attribute of plant transcriptomes, it is currently unknown the extent to which different sublineages of these elements are transcriptionally active both within and across species...
January 5, 2018: BMC Plant Biology
https://www.readbyqxmd.com/read/29303983/a-dipteran-s-novel-sucker-punch-evolution-of-arthropod-atypical-venom-with-a-neurotoxic-component-in-robber-flies-asilidae-diptera
#19
Stephan Holger Drukewitz, Nico Fuhrmann, Eivind A B Undheim, Alexander Blanke, Julien Giribaldi, Rosanna Mary, Guillaume Laconde, Sébastien Dutertre, Björn Marcus von Reumont
Predatory robber flies (Diptera, Asilidae) have been suspected to be venomous due to their ability to overpower well-defended prey. However, details of their venom composition and toxin arsenal remained unknown. Here, we provide a detailed characterization of the venom system of robber flies through the application of comparative transcriptomics, proteomics and functional morphology. Our results reveal asilid venoms to be dominated by peptides and non-enzymatic proteins, and that the majority of components in the crude venom is represented by just ten toxin families, which we have named Asilidin1-10...
January 5, 2018: Toxins
https://www.readbyqxmd.com/read/29301490/molecular-characterization-of-larval-development-from-fertilization-to-metamorphosis-in-a-reef-building-coral
#20
Marie E Strader, Galina V Aglyamova, Mikhail V Matz
BACKGROUND: Molecular mechanisms underlying coral larval competence, the ability of larvae to respond to settlement cues, determine their dispersal potential and are potential targets of natural selection. Here, we profiled competence, fluorescence and genome-wide gene expression in embryos and larvae of the reef-building coral Acropora millepora daily throughout 12 days post-fertilization. RESULTS: Gene expression associated with competence was positively correlated with transcriptomic response to the natural settlement cue, confirming that mature coral larvae are "primed" for settlement...
January 4, 2018: BMC Genomics
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