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conservation genetics

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https://www.readbyqxmd.com/read/29352511/draft-genome-and-reference-transcriptomic-resources-for-the-urticating-pine-defoliator-thaumetopoea-pityocampa-lepidoptera-notodontidae
#1
B Gschloessl, F Dorkeld, H Berges, G Beydon, O Bouchez, M Branco, A Bretaudeau, C Burban, E Dubois, P Gauthier, E Lhuillier, J Nichols, S Nidelet, S Rocha, L Sauné, R Streiff, M Gautier, C Kerdelhué
The pine processionary moth Thaumetopoea pityocampa (Lepidoptera: Notodontidae) is the main pine defoliator in the Mediterranean region. Its urticating larvae cause severe human and animal health concerns in the invaded areas. This species shows a high phenotypic variability for various traits, such as phenology, fecundity, and tolerance to extreme temperatures. This study presents the construction and analysis of extensive genomic and transcriptomic resources, which are an obligate prerequisite to understand their underlying genetic architecture...
January 20, 2018: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29352088/an-archaeal-fluoride-responsive-riboswitch-provides-an-inducible-expression-system-for-hyperthermophiles
#2
Michael Clayton Speed, Brett W Burkhart, Jonathan W Picking, Thomas J Santangelo
Robust genetic systems for the hyperthermophilic Thermococcales have facilitated overexpression of native genes, allowed for the addition of sequences encoding secretion signals, epitope, and affinity tags to coding regions, and permitted the introduction of sequences encoding new proteins in these fast growing fermentative heterotrophs. Tightly controlled and easily manipulated systems permitting regulated gene expression are however limited for these hosts. Here we describe an alternative method for regulatory control reliant on a cis-encoded functional riboswitch in the model archaeon Thermococcus kodakarensis Despite the hyperthermophilic growth temperatures, the proposed structure of the riboswitch conforms to a fluoride-responsive riboswitch encoded in many bacteria, and similarly functions to regulate a component conserved fluoride export pathway...
January 19, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29352063/arabidopsis-thaliana-fancd2-promotes-meiotic-crossover-formation
#3
Marie-Therese Kurzbauer, Monica Pradillo, Claudia Kerzendorfer, Jason Sims, Rene Ladurner, Cecilia Oliver, Michael Peter Janisiw, Magdalena Mosiolek, Dieter Schweizer, Gregory P Copenhaver, Peter Schlogelhofer
Fanconi anemia (FA) is a human autosomal recessive disorder characterized by chromosomal instability, developmental pathologies, predisposition to cancer and reduced fertility. So far, nineteen genes have been implicated in FA, most of them involved in DNA repair. Some are conserved across higher eukaryotes, including plants. The Arabidopsis thaliana genome encodes a homologue of the Fanconi anemia D2 gene (FANCD2) whose function in DNA repair is not yet fully understood. Here we provide evidence that AtFANCD2 is required for meiotic homologous recombination...
January 19, 2018: Plant Cell
https://www.readbyqxmd.com/read/29351913/the-rig-i-like-receptor-lgp2-inhibits-dicer-dependent-processing-of-long-double-stranded-rna-and-blocks-rna-interference-in-mammalian-cells
#4
Annemarthe G van der Veen, Pierre V Maillard, Jan Marten Schmidt, Sonia A Lee, Safia Deddouche-Grass, Annabel Borg, Svend Kjær, Ambrosius P Snijders, Caetano Reis E Sousa
In vertebrates, the presence of viral RNA in the cytosol is sensed by members of the RIG-I-like receptor (RLR) family, which signal to induce production of type I interferons (IFN). These key antiviral cytokines act in a paracrine and autocrine manner to induce hundreds of interferon-stimulated genes (ISGs), whose protein products restrict viral entry, replication and budding. ISGs include the RLRs themselves: RIG-I, MDA5 and, the least-studied family member, LGP2. In contrast, the IFN system is absent in plants and invertebrates, which defend themselves from viral intruders using RNA interference (RNAi)...
January 19, 2018: EMBO Journal
https://www.readbyqxmd.com/read/29351740/population-size-may-shape-the-accumulation-of-functional-mutations-following-domestication
#5
Jianhai Chen, Pan Ni, Xinyun Li, Jianlin Han, Ivan Jakovlić, Chengjun Zhang, Shuhong Zhao
BACKGROUND: Population genetics theory predicts an important role of differences in the effective population size (N e ) among species on shaping the accumulation of functional mutations by regulating the selection efficiency. However, this correlation has never been tested in domesticated animals. RESULTS: Here, we synthesized 62 whole genome data in eight domesticated species (cat, dog, pig, goat, sheep, chicken, cattle and horse) and compared domesticates with their wild (or ancient) relatives...
January 19, 2018: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29351737/identifying-genome-wide-immune-gene-variation-underlying-infectious-disease-in-wildlife-populations-a-next-generation-sequencing-approach-in-the-gopher-tortoise
#6
Jean P Elbers, Mary B Brown, Sabrina S Taylor
BACKGROUND: Infectious disease is the single greatest threat to taxa such as amphibians (chytrid fungus), bats (white nose syndrome), Tasmanian devils (devil facial tumor disease), and black-footed ferrets (canine distemper virus, plague). Although understanding the genetic basis to disease susceptibility is important for the long-term persistence of these groups, most research has been limited to major-histocompatibility and Toll-like receptor genes. To better understand the genetic basis of infectious disease susceptibility in a species of conservation concern, we sequenced all known/predicted immune response genes (i...
January 19, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29351633/evolutionary-genetics-of-cytoplasmic-incompatibility-genes-cifa-and-cifb-in-prophage-wo-of-wolbachia
#7
Amelia R I Lindsey, Danny W Rice, Sarah R Bordenstein, Andrew W Brooks, Seth R Bordenstein, Irene L G Newton
The bacterial endosymbiont Wolbachia manipulates arthropod reproduction to facilitate its maternal spread through host populations. The most common manipulation is cytoplasmic incompatibility (CI): Wolbachia-infected males produce modified sperm that cause embryonic mortality, unless rescued by embryos harboring the same Wolbachia. The genes underlying CI, cifA and cifB, were recently identified in the eukaryotic association module of Wolbachia's prophage WO. Here, we use transcriptomic and genomic approaches to address three important evolutionary facets of the cif genes...
January 17, 2018: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29351555/omega-3-fatty-acid-desaturase-gene-family-from-two-%C3%AF-3-sources-salvia-hispanica-and-perilla-frutescens-cloning-characterization-and-expression
#8
Yufei Xue, Baojun Chen, Aung Naing Win, Chun Fu, Jianping Lian, Xue Liu, Rui Wang, Xingcui Zhang, Yourong Chai
Omega-3 fatty acid desaturase (ω-3 FAD, D15D) is a key enzyme for α-linolenic acid (ALA) biosynthesis. Both chia (Salvia hispanica) and perilla (Perilla frutescens) contain high levels of ALA in seeds. In this study, the ω-3 FAD gene family was systematically and comparatively cloned from chia and perilla. Perilla FAD3, FAD7, FAD8 and chia FAD7 are encoded by single-copy (but heterozygous) genes, while chia FAD3 is encoded by 2 distinct genes. Only 1 chia FAD8 sequence was isolated. In these genes, there are 1 to 6 transcription start sites, 1 to 8 poly(A) tailing sites, and 7 introns...
2018: PloS One
https://www.readbyqxmd.com/read/29351326/increased-natural-reproduction-and-genetic-diversity-one-generation-after-cessation-of-a-steelhead-trout-oncorhynchus-mykiss-conservation-hatchery-program
#9
Barry A Berejikian, Donald M Van Doornik
Spatial and temporal fluctuations in productivity and abundance confound assessments of captive propagation programs aimed at recovery of Threatened and Endangered populations. We conducted a 17 year before-after-control-impact experiment to determine the effects of a captive rearing program for anadromous steelhead trout (Oncorhynchus mykiss) on a key indicator of natural spawner abundance (naturally produced nests or 'redds'). The supplemented population exhibited a significant (2.6-fold) increase in redd abundance in the generation following supplementation...
2018: PloS One
https://www.readbyqxmd.com/read/29351213/cyclin-b3-deficiency-impairs-germline-stem-cell-maintenance-and-its-overexpression-delays-cystoblast-differentiation-in-drosophila-ovary
#10
Dongsheng Chen, Lijuan Zhou, Fuling Sun, Mingzhong Sun, Xiaoqian Tao
It is well known that cyclinB3 (cycB3) plays a key role in the control of cell cycle progression. However, whether cycB3 is involved in stem cell fate determination remains unknown. The Drosophila ovary provides an exclusive model for studying the intrinsic and extrinsic factors that modulate the fate of germline stem cells (GSCs). Here, using this model, we show that DrosophilacycB3 plays a new role in controlling the fate of germline stem cells (GSC). Results from cycB3 genetic analyses demonstrate that cycB3 is intrinsically required for GSC maintenance...
January 19, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29351064/molecular-target-analysis-of-stearoyl-coa-desaturase-genes-of-protozoan-parasites
#11
He Lu, Xin Qin, Jing Zhang, Shuang Zhang, Yu Zhu, Wei Hua Wu
Protozoan parasites can synthesize polyunsaturated fatty acids. They possess stearoyl-CoA desaturase to convert stearate into oleate and linoleate. Stearoyl-CoA desaturase are the key enzymes required for the synthesis of unsaturated fatty acids. It seems attractive to evaluate the possibility of using unsaturated fatty acid biosynthesis pathways as drug targets. In this study, the authors investigate codon usage bias, base composition variations and protein sequence in ten available complete stearoyl-CoA desaturase gene sequences from Toxoplasma gondii, Neospora caninum etc...
March 26, 2018: Acta Parasitologica
https://www.readbyqxmd.com/read/29350309/population-genetics-of-the-endangered-and-wild-edible-plant-ottelia-acuminata-in-southwestern-china-using-novel-ssr-markers
#12
Shu Hua Zhai, Gen Shen Yin, Xiao Hong Yang
Ottelia acuminata is an edible aquatic plant species that is endemic to southwestern China. This plant has experienced habitat degradation resulting from environmental change and extensive human disturbance. Determining the genetic variation and genetic structure of O. acuminata populations could help develop strategies to collect, evaluate, utilize and conserve the species. To this end, we genotyped 183 individuals sampled throughout the species distribution using twelve novel nuclear microsatellite loci (nSSRs)...
January 19, 2018: Biochemical Genetics
https://www.readbyqxmd.com/read/29350244/autophagy-related-atg-11-atg9-and-the-phosphatidylinositol-3-kinase-control-atg2-mediated-formation-of-autophagosomes-in-arabidopsis
#13
Sangwoo Kang, Kwang Deok Shin, Jeong Hun Kim, Taijoon Chung
Using quantitative assays for autophagy, we analyzed 4 classes of atg mutants, discovered new atg2 phenotypes and ATG gene interactions, and proposed a model of autophagosome formation in plants. Plant and other eukaryotic cells use autophagy to target cytoplasmic constituents for degradation in the vacuole. Autophagy is regulated and executed by a conserved set of proteins called autophagy-related (ATG). In Arabidopsis, several groups of ATG proteins have been characterized using genetic approaches. However, the genetic interactions between ATG genes have not been established and the relationship between different ATG groups in plants remains unclear...
January 19, 2018: Plant Cell Reports
https://www.readbyqxmd.com/read/29350155/yersinia-pestis-survival-and-replication-in-potential-ameba-reservoir
#14
David W Markman, Michael F Antolin, Richard A Bowen, William H Wheat, Michael Woods, Mercedes Gonzalez-Juarrero, Mary Jackson
Plague ecology is characterized by sporadic epizootics, then periods of dormancy. Building evidence suggests environmentally ubiquitous amebae act as feral macrophages and hosts to many intracellular pathogens. We conducted environmental genetic surveys and laboratory co-culture infection experiments to assess whether plague bacteria were resistant to digestion by 5 environmental ameba species. First, we demonstrated that Yersinia pestis is resistant or transiently resistant to various ameba species. Second, we showed that Y...
February 2018: Emerging Infectious Diseases
https://www.readbyqxmd.com/read/29349820/an-experimental-test-of-alternative-population-augmentation-scenarios
#15
J A Kronenberger, J C Gerberich, S W Fitzpatrick, E D Broder, L M Angeloni, W C Funk
Human land use is fragmenting habitats worldwide and inhibiting dispersal among previously connected populations of organisms, often leading to inbreeding depression and reduced evolutionary potential in the face of rapid environmental change. One management practice used to combat this is the augmentation of isolated populations with immigrants as a means of demographic and genetic rescue. Augmentation with immigrants that are genetically and adaptively similar to the target population is highly effective at increasing population fitness, but if immigrants are very genetically or adaptively divergent, augmentation can lead to outbreeding depression...
January 19, 2018: Conservation Biology: the Journal of the Society for Conservation Biology
https://www.readbyqxmd.com/read/29349607/molecular-characterization-of-fagaceae-species-using-inter-primer-binding-site-ipbs-markers
#16
João Paulo Coutinho, Ana Carvalho, Antonio Martín, José Lima-Brito
Retrotransposons (RTNs) contribute for genome evolution, influencing its size and structure. We investigated the utility of the RTN-based markers inter-primer binding site (iPBS) for the molecular characterization of 25 Fagaceae species from genera Castanea, Fagus and Quercus. The assessment of genetic diversity, relationships and structure, as well as taxonomic classification of Fagaceae based on molecular data is important for definition of conservation, forestry management strategies and discrimination among natural hybrids and their parents since natural hybridization may increase with the climate changes...
January 18, 2018: Molecular Biology Reports
https://www.readbyqxmd.com/read/29348295/tuning%C3%A2-crispr-cas9-gene-drives-in-saccharomyces-cerevisiae
#17
Emily Roggenkamp, Rachael M Giersch, Madison N Schrock, Emily Turnquist, Megan Halloran, Gregory C Finnigan
Control of biological populations is an ongoing challenge in many fields including agriculture, biodiversity, ecological preservation, pest control, and the spread of disease. In some cases, such as insects that harbor human pathogens (e.g. malaria), elimination or reduction of a small number of species would have a dramatic impact across the globe. Given the recent discovery and development of the CRISPR/Cas9 gene editing technology, a unique arrangement of this system-a nuclease based "gene drive"-allows for the Super-Mendelian spread and forced propagation of a genetic element through a population...
January 18, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29348261/complement-receptor-c5ar1-plays-an-evolutionarily-conserved-role-in-successful-cardiac-regeneration
#18
Niranjana Natarajan, Yamen Abbas, Donald M Bryant, Juan Manuel Gonzalez-Rosa, Michka Sharpe, Aysu Uygur, Lucas H Cocco-Delgado, Nhi Ngoc Ho, Norma P Gerard, Craig J Gerard, Calum A Macrae, Caroline E Burns, C Geoffrey Burns, Jessica L Whited, Richard T Lee
Background -Defining conserved molecular pathways in animal models of successful cardiac regeneration could yield insight into why adult mammals have inadequate cardiac regeneration after injury. Insight into the transcriptomic landscape of early cardiac regeneration from model organisms will shed light on evolutionarily conserved pathways in successful cardiac regeneration. Methods -Here we describe a cross-species transcriptomic screen in three model organisms for cardiac regeneration -axolotl, neonatal mice and zebrafish...
January 18, 2018: Circulation
https://www.readbyqxmd.com/read/29348176/contribution-of-the-trnaile-4317a-g-mutation-to-the-phenotypic-manifestation-of-the-deafness-associated-mitochondrial-12s-rrna-1555a-g-mutation
#19
Feilong Meng, Zheyun He, Xiaowen Tang, Jing Zheng, Xiaofen Jin, Yi Zhu, Xiaoyan Ren, Mi Zhou, Meng Wang, Shasha Gong, Jun Qin Mo, Qiang Shu, Min-Xin Guan
The 1555A>G mutation in mitochondrial 12S rRNA has been associated with aminoglycoside-induced and nonsyndromic deafness in many individuals worldwide. Mitochondrial genetic modifiers are proposed to influence the phenotypic expression of m.1555A>G mutation. Here, we report that a deafness-susceptibility allele (m.4317A>G) in the tRNAIle gene modulates the phenotype expression of m.1555A>G mutation. Strikingly, a large Han Chinese pedigree carrying both m.4317A>G and m.1555A>G mutations exhibited much higher penetrance of deafness than those carrying only m...
January 18, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29343863/genetic-analyses-favour-an-ancient-and-natural-origin-of-elephants-on-borneo
#20
Reeta Sharma, Benoit Goossens, Rasmus Heller, Rita Rasteiro, Nurzhafarina Othman, Michael W Bruford, Lounès Chikhi
The origin of the elephant on the island of Borneo remains elusive. Research has suggested two alternative hypotheses: the Bornean elephant stems either from a recent introduction in the 17th century or from an ancient colonization several hundreds of thousands years ago. Lack of elephant fossils has been interpreted as evidence for a very recent introduction, whereas mtDNA divergence from other Asian elephants has been argued to favor an ancient colonization. We investigated the demographic history of Bornean elephants using full-likelihood and approximate Bayesian computation analyses...
January 17, 2018: Scientific Reports
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