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https://www.readbyqxmd.com/read/29054864/heterogeneous-patterns-of-genetic-diversity-and-differentiation-in-european-and-siberian-chiffchaff-phylloscopus-collybita-abietinus-p-tristis
#1
Venkat Talla, Faheema Kalsoom, Daria Shipilina, Irina Marova, Niclas Backström
Identification of candidate genes for trait variation in diverging lineages and characterization of mechanistic underpinnings of genome differentiation are key steps towards understanding the processes underlying the formation of new species. Hybrid zones provide a valuable resource for such investigations since they allow for studying how genomes evolve as species exchange genetic material and for associating particular genetic regions with phenotypic traits of interest. Here we use whole-genome resequencing of both allopatric and hybridising populations of the European (Phylloscopus collybita abietinus) and the Siberian chiffchaff (P...
October 20, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29054765/characterization-of-germline-mutations-in-familial-lung-cancer-from-the-chinese-population
#2
Madiha Kanwal, Xiao-Jie Ding, Zhans-Han Ma, Lian-Wei Li, Ping Wang, Ying Chen, Yun-Chao Huang, Yi Cao
Compared with numerous studies of somatic mutations using sporadic lung cancer, the research into germline mutations using familial lung cancer (FLC) is limited. In the present study, we used FLC samples obtained from the Chinese population in highly air-polluted regions to screen for novel germline mutations in lung cancer. Through a whole genome sequencing (WGS) analysis of the nine subjects (four lung cancer patients and five normal family members of FLC), we obtained a whole genome dataset of DNA alterations in FLC samples...
October 17, 2017: Gene
https://www.readbyqxmd.com/read/29053721/xx-disorder-of-sex-development-is-associated-with-an-insertion-on-chromosome-9-and-downregulation-of-rspo1-in-dogs-canis-lupus-familiaris
#3
Vicki N Meyers-Wallen, Adam R Boyko, Charles G Danko, Jennifer K Grenier, Jason G Mezey, Jessica J Hayward, Laura M Shannon, Chuan Gao, Afrah Shafquat, Edward J Rice, Shashikant Pujar, Stefanie Eggers, Thomas Ohnesorg, Andrew H Sinclair
Remarkable progress has been achieved in understanding the mechanisms controlling sex determination, yet the cause for many Disorders of Sex Development (DSD) remains unknown. Of particular interest is a rare XX DSD subtype in which individuals are negative for SRY, the testis determining factor on the Y chromosome, yet develop testes or ovotestes, and both of these phenotypes occur in the same family. This is a naturally occurring disorder in humans (Homo sapiens) and dogs (C. familiaris). Phenotypes in the canine XX DSD model are strikingly similar to those of the human XX DSD subtype...
2017: PloS One
https://www.readbyqxmd.com/read/29053637/progress-in-genetic-studies-of-tourette-s-syndrome
#4
REVIEW
Yanjie Qi, Yi Zheng, Zhanjiang Li, Lan Xiong
Tourette's Syndrome (TS) is a complex disorder characterized by repetitive, sudden, and involuntary movements or vocalizations, called tics. Tics usually appear in childhood, and their severity varies over time. In addition to frequent tics, people with TS are at risk for associated problems including attention deficit hyperactivity disorder (ADHD), obsessive-compulsive disorder (OCD), anxiety, depression, and problems with sleep. TS occurs in most populations and ethnic groups worldwide, and it is more common in males than in females...
October 20, 2017: Brain Sciences
https://www.readbyqxmd.com/read/29052958/whole-genome-re-sequencing-reveals-evolutionary-patterns-of-sacred-lotus-nelumbo-nucifera
#5
Longyu Huang, Mei Yang, Ling Li, Hui Li, Dong Yang, Tao Shi, Pingfang Yang
Sacred lotus (Nelumbo nucifera or lotus) is an important aquatic plant in horticulture and ecosystem. As a foundation for exploring genomic variationand evolution among different germplasms, we re-sequenced 19 individuals from three cultivated temperate lotus subgroups (rhizome lotus, seed lotus and flower lotus),one wild temperate lotus subgroup (wild lotus), one tropical lotus group (Thai lotus) and outgroup (Nelumbo lutea). Through genetic diversity and polymorphism analysis by non-missing SNP sites widely distributed in the whole genome, weconfirmed that wild lotus and Thai lotus exhibited greater differentiation with a higher genomic diversity compared to cultivated lotus...
October 20, 2017: Journal of Integrative Plant Biology
https://www.readbyqxmd.com/read/29052202/identification-of-parent-of-origin-dependent-qtls-using-bulk-segregant-sequencing-bulk-seq
#6
Nuno D Pires, Ueli Grossniklaus
Parent-of-origin effects play important roles in plant reproduction and are often mediated by epigenetic modifications at the histone or DNA level. However, the genetic basis underlying these modifications can be challenging to identify. Here, we describe an approach (Bulk-Seq) that can be used to map loci mediating parent-of-origin-dependent effects using whole-genome sequencing of pools of DNA.
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29052184/bisulfite-sequencing-using-small-dna-amounts
#7
Susanne Edelmann, Stefan Scholten
Bisulfite sequencing (BS-seq) enables the detection of DNA methylation at cytosine residues (5mC) at single-nucleotide resolution. For many applications, a limiting factor of conventional BS-seq protocols is the high amount of DNA required, since the treatment with bisulfite causes severe DNA fragmentation. Here, we describe a post-bisulfite tagging method that accounts for this problem. Illumina-compatible BS-seq libraries can be obtained from as little as five single haploid maize cells, enabling whole genome BS-seq (WGBS) for the generation of genome-wide, cell-type specific DNA methylation profiles...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29052098/comparative-transcriptome-analysis-reveals-whole-genome-duplications-and-gene-selection-patterns-in-cultivated-and-wild-chrysanthemum-species
#8
So Youn Won, Soo-Jin Kwon, Tae-Ho Lee, Jae-A Jung, Jung Sun Kim, Sang-Ho Kang, Seong-Han Sohn
Comparative transcriptome analysis of wild and cultivated chrysanthemums provides valuable genomic resources and helps uncover common and divergent patterns of genome and gene evolution in these species. Plants are unique in that they employ polyploidy (or whole-genome duplication, WGD) as a key process for speciation and evolution. The Chrysanthemum genus is closely associated with hybridization and polyploidization, with Chrysanthemum species exhibiting diverse ploidy levels. The commercially important species, C...
October 19, 2017: Plant Molecular Biology
https://www.readbyqxmd.com/read/29051971/fine-mapping-of-the-brassica-napus-bnsdt1-gene-associated-with-determinate-growth-habit
#9
Kaixiang Li, Yanmei Yao, Lu Xiao, Zhigang Zhao, Shaomin Guo, Zhong Fu, Dezhi Du
The newly discovered determinate plant growth habit of Brassica napus is a potential trait that might contribute to the genetic improvement of rapeseed. Brassica napus is an important species of rapeseed and has an indeterminate growth habit. However, a determinate inflorescence strain (4769) has been discovered among doubled haploid (DH) lines obtained from a spring B. napus × winter B. napus cross. We assessed the effect of the determinate growth habit on agronomic traits. The results showed that determinacy is beneficial for reducing plant height and flowering time, advancing maturity and maintaining productivity...
October 19, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29051922/hidden-heritability-due-to-heterogeneity-across-seven-populations
#10
Felix C Tropf, S Hong Lee, Renske M Verweij, Gert Stulp, Peter J van der Most, Ronald de Vlaming, Andrew Bakshi, Daniel A Briley, Charles Rahal, Robert Hellpap, Anastasia Nyman, Tõnu Esko, Andres Metspalu, Sarah E Medland, Nicholas G Martin, Nicola Barban, Harold Snieder, Matthew R Robinson, Melinda C Mills
Meta-analyses of genome-wide association studies (GWAS), which dominate genetic discovery are based on data from diverse historical time periods and populations. Genetic scores derived from GWAS explain only a fraction of the heritability estimates obtained from whole-genome studies on single populations, known as the 'hidden heritability' puzzle. Using seven sampling populations (N=35,062), we test whether hidden heritability is attributed to heterogeneity across sampling populations and time, showing that estimates are substantially smaller from across compared to within populations...
October 2017: Nature Human Behaviour
https://www.readbyqxmd.com/read/29051752/icesag37-a-novel-integrative-and-conjugative-element-carrying-antimicrobial-resistance-genes-and-potential-virulence-factors-in-streptococcus-agalactiae
#11
Kaixin Zhou, Lianyan Xie, Lizhong Han, Xiaokui Guo, Yong Wang, Jingyong Sun
ICESag37, a novel integrative and conjugative element carrying multidrug resistance and potential virulence factors, was characterized in a clinical isolate of Streptococcus agalactiae. Two clinical strains of S. agalactiae, Sag37 and Sag158, were isolated from blood samples of new-borns with bacteremia. Sag37 was highly resistant to erythromycin and tetracycline, and susceptible to levofloxacin and penicillin, while Sag158 was resistant to tetracycline and levofloxacin, and susceptible to erythromycin. Transfer experiments were performed and selection was carried out with suitable antibiotic concentrations...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29051525/virulence-characteristics-of-carbapenem-resistant-klebsiella-pneumoniae-strains-from-patients-with-necrotizing-skin-and-soft-tissue-infections
#12
Fiorella Krapp, Andrew R Morris, Egon A Ozer, Alan R Hauser
Two types of Klebsiella pneumoniae (KP) strains are currently emerging: hypervirulent (hvKP) strains and carbapenem-resistant (CR-KP) strains. To date, these two strain types rarely overlap. Recent reports, however, suggest that CR-KP strains are increasing in virulence. hvKP strains frequently present as highly invasive infections, such as necrotizing skin and soft tissue infections (NSSTI). To examine whether CR-KP strains with features of hvKP were present in our U.S. hospital, we retrospectively identified four cases of CR-KP NSSTI diagnosed between January 2012 and January 2016...
October 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29051505/large-scale-genomic-analyses-reveal-the-population-structure-and-evolutionary-trends-of-streptococcus-agalactiae-strains-in-brazilian-fish-farms
#13
Gustavo M Barony, Guilherme C Tavares, Felipe L Pereira, Alex F Carvalho, Fernanda A Dorella, Carlos A G Leal, Henrique C P Figueiredo
Streptococcus agalactiae is a major pathogen and a hindrance on tilapia farming worldwide. The aims of this work were to analyze the genomic evolution of Brazilian strains of S. agalactiae and to establish spatial and temporal relations between strains isolated from different outbreaks of streptococcosis. A total of 39 strains were obtained from outbreaks and their whole genomes were sequenced and annotated for comparative analysis of multilocus sequence typing, genomic similarity and whole genome multilocus sequence typing (wgMLST)...
October 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29051239/whole-genome-sequencing-of-a-human-clinical-isolate-of-the-novel-species-klebsiella-quasivariicola-sp-nov
#14
S Wesley Long, Sarah E Linson, Matthew Ojeda Saavedra, Concepcion Cantu, James J Davis, Thomas Brettin, Randall J Olsen
In a study of 1,777 Klebsiella strains, we discovered KPN1705, which was distinct from all recognized Klebsiella spp. We closed the genome of strain KPN1705 using a hybrid of Illumina short-read and Oxford Nanopore long-read technologies. For this novel species, we propose the name Klebsiella quasivariicola sp. nov.
October 19, 2017: Genome Announcements
https://www.readbyqxmd.com/read/29051237/whole-genome-sequence-of-a-megasphaera-elsdenii-strain-isolated-from-the-gut-of-a-healthy-indian-adult-subject
#15
Satyabrata Bag, Tarini Shankar Ghosh, Bhabatosh Das
Megasphaera elsdenii has been previously reported in the gut of ruminating animals. Its role as an animal probiotic is being investigated, specifically from the perspective of enhancing animal productivity. Herein, we report the draft genome sequence of M. elsdenii strain indica isolated from the stool sample of a healthy Indian subject.
October 19, 2017: Genome Announcements
https://www.readbyqxmd.com/read/29051233/high-quality-whole-genome-sequences-of-the-oligo-mouse-microbiota-bacterial-community
#16
Debora Garzetti, Sandrine Brugiroux, Boyke Bunk, Rüdiger Pukall, Kathy D McCoy, Andrew J Macpherson, Bärbel Stecher
The Oligo-Mouse-Microbiota (Oligo-MM(12)) is a community of 12 mouse intestinal bacteria to be used for microbiome research in gnotobiotic mice. We present here the high-quality whole genome sequences of the Oligo-MM(12) strains, which were obtained by combining the accuracy of the Illumina platforms with the long reads of the PacBio technology.
October 19, 2017: Genome Announcements
https://www.readbyqxmd.com/read/29051054/gene-environment-interaction-and-psychiatric-disorders-review-and-future-directions
#17
REVIEW
Elham Assary, John Paul Vincent, Robert Keers, Michael Pluess
Empirical studies suggest that psychiatric disorders result from a complex interplay between genetic and environmental factors. Most evidence for such gene-environment interaction (GxE) is based on single candidate gene studies conducted from a Diathesis-Stress perspective. Recognizing the short-comings of candidate gene studies, GxE research has begun to focus on genome-wide and polygenic approaches as well as drawing on different theoretical concepts underlying GxE, such as Differential Susceptibility. After reviewing evidence from candidate GxE studies and presenting alternative theoretical frameworks underpinning GxE research, more recent approaches and findings from whole genome approaches are presented...
October 16, 2017: Seminars in Cell & Developmental Biology
https://www.readbyqxmd.com/read/29051020/draft-genome-sequences-of-three-multidrug-resistant-cutibacterium-formerly-propionibacterium-acnes-strains-isolated-from-acne-patients-china
#18
Nanxue Zhang, Zhong Lu, Ying Ma
OBJECTIVES: Cutibacterium acnes (formerly Propionibacterium acnes), an anaerobic Gram-positive bacterium, is a skin commensal and considered to be associated with acne. Here we report draft genome sequences of three multidrug-resistant C. acnes strains (CA17, CA39, and CA51), isolated from skin lesions of acne patients from China. METHODS: The whole genome of the three multidrug-resistant C. acnes strains were sequenced using an Illumina HiSeq 2500 platform. De novo assembly and annotation were performed with SPAdes-3...
October 16, 2017: Journal of Global Antimicrobial Resistance
https://www.readbyqxmd.com/read/29050774/whole-genome-sequencing-of-clinical-strains-of-mycobacterium-tuberculosis-from-mumbai-india-a-potential-tool-for-determining-drug-resistance-and-strain-lineage
#19
Anirvan Chatterjee, Kayzad Nilgiriwala, Dhananjaya Saranath, Camilla Rodrigues, Nerges Mistry
Amplification of drug resistance in Mycobacterium tuberculosis (M.tb) and its transmission are significant barriers in controlling tuberculosis (TB) globally. Diagnostic inaccuracies and delays impede appropriate drug administration, which exacerbates primary and secondary drug resistance. Increasing affordability of whole genome sequencing (WGS) and exhaustive cataloguing of drug resistance mutations is poised to revolutionise TB diagnostics and facilitate personalized drug therapy. However, application of WGS for diagnostics in high endemic areas is yet to be demonstrated...
December 2017: Tuberculosis
https://www.readbyqxmd.com/read/29050768/single-nucleotide-polymorphisms-in-efflux-pumps-genes-in-extensively-drug-resistant-mycobacterium-tuberculosis-isolates-from-pakistan
#20
Akbar Kanji, Rumina Hasan, Asho Ali, Ambreen Zaver, Ying Zhang, Kehkashan Imtiaz, Wanliang Shi, Taane G Clark, Ruth McNerney, Jody Phelan, Shoaib Rao, Samreen Shafiq, Zahra Hasan
It is challenging to understand mechanisms of drug resistance in Mycobacterium tuberculosis (MTB) due to the large variability in resistance associated genes. Efflux pump genes contribute to drug resistance and thus add to this complexity. Efflux pump gene protein superfamilies have been characterized by genome analysis of drug resistant strains and through in vitro transcriptional studies. However, there is limited information regarding efflux pump genes in extensively drug resistant (XDR) tuberculosis (TB) isolates...
December 2017: Tuberculosis
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