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Genomics

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https://read.qxmd.com/read/30905613/a-proposed-core-genome-scheme-for-analyses-of-the-salmonella-genus
#1
Madison E Pearce, Marie A Chattaway, Kathie Grant, Martin C J Maiden
The salmonellae are found in a wide range of animal hosts and many food products for human consumption. Most cases of human disease are caused by S. enterica subspecies I; however as opportunistic pathogens the other subspecies (II-VI) and S. bongori are capable of causing disease. Loci that were not consistently present in all of the species and subspecies were removed from a previously proposed core genome scheme (EBcgMLSTv2.0), the removal of these 252 loci resulted in a core genus scheme (SalmcgMLSTv1.0)...
March 21, 2019: Genomics
https://read.qxmd.com/read/30902757/gene-duplication-and-deletion-not-horizontal-transfer-drove-intra-species-mosaicism-of-bartonella-henselae
#2
Rachana Banerjee, Oshina Shine, Vyshakh Rajachandran, K Govind, Michael F Minnick, Sandip Paul, Sujay Chattopadhyay
Bartonella henselae is a facultative intracellular pathogen that occurs worldwide and is responsible primarily for cat-scratch disease in young people and bacillary angiomatosis in immunocompromised patients. The principal source of genome-level diversity that contributes to B. henselae's host-adaptive features is thought to be horizontal gene transfer events. However, our analyses did not reveal the acquisition of horizontally-transferred islands in B. henselae after its divergence from other Bartonella. Rather, diversity in gene content and genome size was apparently acquired through two alternative mechanisms, including deletion and, more predominantly, duplication of genes...
March 19, 2019: Genomics
https://read.qxmd.com/read/30902756/molecular-characterization-of-bu-1-and-tlr2-gene-in-haringhata-black-chicken
#3
Aruna Pal, Abantika Pal, Amirul Islam Mallick, P Biswas, P N Chatterjee
Haringhata Black is the only registered indigenous poultry genetic resource of West Bengal till date. Molecular characterization of HB revealed that Bu-1 to be highly glycoylated transmembrane protein unlike mammalian Bu-1, whereas TLR2 of HB chicken was observed to be rich in Leucine rich repeat. HB chicken was observed to be genetically close to chicken of Japan, while distant to chicken breed of UK and Chicago. Avian species wise evolution study indicates genetic closeness of HB chicken with turkey. Differential mRNA expression profile for the immune response genes (TLR2, TLR4 and Bu1 gene) were studied for HB chicken with respect to other chicken breed and poultry birds, which reveals that HB chicken were better in terms of B cell mediated immunity and hence better response to vaccination...
March 19, 2019: Genomics
https://read.qxmd.com/read/30902755/genome-wide-sequence-analyses-of-ethnic-populations-across-russia
#4
Daria V Zhernakova, Vladimir Brukhin, Sergey Malov, Taras K Oleksyk, Klaus Peter Koepfli, Anna Zhuk, Pavel Dobrynin, Sergei Kliver, Nikolay Cherkasov, Gaik Tamazian, Mikhail Rotkevich, Ksenia Krasheninnikova, Igor Evsyukov, Sviatoslav Sidorov, Anna Gorbunova, Ekaterina Chernyaeva, Andrey Shevchenko, Sofia Kolchanova, Alexei Komissarov, Serguei Simonov, Alexey Antonik, Anton Logachev, Dmitrii E Polev, Olga A Pavlova, Andrey S Glotov, Vladimir Ulantsev, Ekaterina Noskova, Tatyana K Davydova, Tatyana M Sivtseva, Svetlana Limborska, Oleg Balanovsky, Vladimir Osakovsky, Alexey Novozhilov, Valery Puzyrev, Stephen J O'Brien
The Russian Federation is the largest and one of the most ethnically diverse countries in the world, however no centralized reference database of genetic variation exists to date. Such data are crucial for medical genetics and essential for studying population history. The Genome Russia Project aims at filling this gap by performing whole genome sequencing and analysis of peoples of the Russian Federation. Here we report the characterization of genome-wide variation of 264 healthy adults, including 60 newly sequenced samples...
March 19, 2019: Genomics
https://read.qxmd.com/read/30898611/genome-sequence-analysis-and-organization-of-the-hyphantria-cunea-granulovirus-hycugv-hc1-from-turkey
#5
Donus Gencer, Zeynep Bayramoglu, Remziye Nalcacioglu, Zihni Demirbag, Ismail Demir
The fall webworm (Hyphantria cunea) impacts a wide variety of crops and cultivated broadleaf plant species. The pest is native to North America, was introduced to Europe and has since spread further as far as central Asia. Despite several attempts to control its distribution, the pest continues to spread causing damage all over the world. A naturally occurring baculovirus, Hyphantria cunea granulovirus (HycuGV-Hc1), isolated from the larvae of H. cunea in Turkey appears to have a potential as microbial control agent against this pest...
March 18, 2019: Genomics
https://read.qxmd.com/read/30898470/the-mitochondrial-genomes-of-three-skippers-insights-into-the-evolution-of-the-family-hesperiidae-lepidoptera
#6
Luyao Ma, Fangfang Liu, Hideyuki Chiba, Xiangqun Yuan
We sequenced the mitogenomes of Astictopterus jama, Isoteinon lamprospilus and Notocrypta curvifascia to obtain further insight into the mitogenomic architecture evolution and performed phylogenetic reconstruction using 29 Hesperiidae mitogenome sequences. The complete mitogenome sequences of A. jama, I. lamprospilus and N. curvifascia are 15,430, 15,430 and 15,546 bp in size, respectively. All contain 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and an A + T-rich region. Nucleotide composition is A + T biased, and the majority of the protein-coding genes exhibit a negative AT-skew, which is reflected in the nucleotide composition, codon, and amino acid usage...
March 18, 2019: Genomics
https://read.qxmd.com/read/30880114/expression-of-the-bovine-klf6-gene-polymorphisms-and-their-association-with-carcass-and-body-measures-in-qinchuan-cattle-bos-taurus
#7
Sayed Haidar Abbas Raza, Rajwali Khan, Nicola M Schreurs, Hongfang Guo, Lin-Sheng Gui, Chugang Mei, Linsen Zan
Kruppel-like factor 6 (KLF6) genes plays a significant role in the regulation of cell differentiation, proliferation and muscle development. The aim of this study is to investigate the genetic variation and the haplotype combination of the KLF6 gene in Qinchuan cattle and verify its contribution to bovine carcass traits and body measurements. The data were analyzed by real-time quantitative PCR (qPCR) to detect the expression profile of the KLF6 gene in the various tissues of Qinchuan cattle. PCR amplicons sequencing explored three novel SNPs at loci 3332C > G; 3413C > T and 3521G > A in the 2nd exon region of the KLF6 gene...
March 14, 2019: Genomics
https://read.qxmd.com/read/30876925/abiotic-stress-induced-mirna-tf-gene-regulatory-network-a-structural-perspective
#8
Rinku Sharma, Shashankaditya Upadhyay, Basharat Bhat, Garima Singh, Sudeepto Bhattacharya, Ashutosh Singh
MicroRNAs (miRNAs) and transcription factors (TFs) are the largest families of trans-acting gene regulatory species, which are pivotal players in a complex regulatory network. Recently, extensive research on miRNAs and TFs in agriculture has identified these trans-acting regulatory species, as an effective tool for engineering new crop cultivars to increase yield and quality as well tolerance to environmental stresses but our knowledge of regulatory network is still not sufficient to decipher the exact mechanism...
March 12, 2019: Genomics
https://read.qxmd.com/read/30853596/identification-of-deleterious-snps-and-their-effects-on-bcl11a-the-master-regulator-of-fetal-hemoglobin-expression
#9
Sankha Subhra Das, Nishant Chakravorty
The B-cell lymphoma/leukemia 11A protein (encoded by BCL11A gene) is a key regulator of fetal-to-adult hemoglobin switching as seen in post-natal life. Although genetic polymorphisms like SNPs in BCL11A gene are expected to affect fetal hemoglobin (HbF) expression levels, yet their implications are poorly studied. This study utilizes a computational approach to identify the deleterious SNPs which may affect the structure and function of BCL11A protein. The study also generated a 3D structure of native and mutants...
March 7, 2019: Genomics
https://read.qxmd.com/read/30851359/grade-specific-diagnostic-and-prognostic-biomarkers-in-breast-cancer
#10
V S P K Sankara Aditya Jayanthi, Asim Bikas Das, Urmila Saxena
An integrative approach is presented to identify grade-specific biomarkers for breast cancer. Grade-specific molecular interaction networks were constructed with differentially expressed genes (DEGs) of cancer grade 1, 2, and 3. We observed that the molecular network of grade3 is predominantly associated with cancer-specific processes. Among the top ten connected DEGs in the grade3, the increase in the expression of UBE2C and CCNB2 genes was statistically significant across different grades. Along with UBE2C and CCNB2 genes, the CDK1, KIF2C, NDC80, and CCNB2 genes are also profoundly expressed in different grades and reduce the patient's survival...
March 6, 2019: Genomics
https://read.qxmd.com/read/30851358/identification-of-male-specific-snp-markers-and-development-of-pcr-based-genetic-sex-identification-technique-in-crucifix-crab-charybdis-feriatus-with-implication-of-an-xx-xy-sex-determination-system
#11
Shaobin Fang, Yin Zhang, Xi Shi, Huaiping Zheng, Shengkang Li, Yueling Zhang, Hanafiah Fazhan, Khor Waiho, Huaqiang Tan, Mhd Ikhwanuddin, Hongyu Ma
In this study, we first identified male-specific SNP markers using restriction site-associated DNA sequencing, and further developed a PCR-based sex identification technique for Charybdis feriatus. A total of 296.96 million clean reads were obtained, with 114.95 and 182.01 million from females and males. After assembly and alignment, 10 SNP markers were identified being heterozygous in males but homozygous in females. Five markers were further confirmed to be male-specific in a large number of individuals. Moreover, two male-specific sense primers and a common antisense primer were designed, using which, a PCR-based genetic sex identification method was successfully developed and used to identify the sex of 103 individuals, with a result of 49 females and 54 males...
March 6, 2019: Genomics
https://read.qxmd.com/read/30826444/accurate-prediction-of-maize-grain-yield-using-its-contributing-genes-for-gene-based-breeding
#12
Meiping Zhang, Yanru Cui, Yun-Hua Liu, Wenwei Xu, Sing-Hoi Sze, Seth C Murray, Shizhong Xu, Hong-Bin Zhang
Accurately predicting the phenotypes of complex traits is crucial to enhanced breeding in plants and livestock, and to enhanced medicine in humans. Here we reports the first study accurately predicting complex traits using their contributing genes, especially their number of favorable alleles (NFAs), genotypes and transcript expressions, with the grain yield of maize, Zea mays L. When the NFAs or genotypes of only 27 SNP/InDel-containing grain yield genes were used, a prediction accuracy of r = 0.52 or 0...
February 28, 2019: Genomics
https://read.qxmd.com/read/30826443/peripheral-blood-gene-expression-signatures-associated-with-epilepsy-and-its-etiologic-classification
#13
Chitra Rawat, Suman Kushwaha, Achal K Srivastava, Ritushree Kukreti
Heterogeneity in epilepsy often interferes with its diagnosis as well as treatment. To examine this heterogeneity at transcriptomic level, we performed whole-genome mRNA expression profiling in whole blood samples from 34 patients with epilepsy (PWE) (idiopathic, n = 13; cryptogenic, n = 9; and symptomatic, n = 12) and 41 healthy controls (HC) using Illumina HT-12 Expression Beadchip v4 microarray. In silico analysis using R software identified 165 genes to be significantly differentially expressed in PWE compared to HC (fold change>1...
February 28, 2019: Genomics
https://read.qxmd.com/read/30826442/comparative-phylogenetic-analysis-of-aquaporins-provides-insight-into-the-gene-family-expansion-and-evolution-in-plants-and-their-role-in-drought-tolerant-and-susceptible-chickpea-cultivars
#14
Athar Hussain, Rabbia Tanveer, Ghulam Mustafa, Muhammed Farooq, Imran Amin, Shahid Mansoor
Aquaporins (AQPs) are water channel proteins that play a significant role in drought stress. Although the AQPs identified in multiple plant species, there is no detailed evolutionary and comparative study of AQPs regarding chickpea plant. The current study involved evolutionary analyses coupled with promoter and expression analyses of chickpea AQPs (CaAQPs). A total of 924 non-redundant AQPs were studied in 24 plant species including algae, mosses, lycophytes, monocots and dicots. Phylogenetic analysis demonstrated a clear divergence of eight AQP subfamilies (LIPs, SIPs, GIPs, NIPs, XIPs, PIPs, HIPs and TIPs)...
February 28, 2019: Genomics
https://read.qxmd.com/read/30822468/muscle-transcriptome-signature-and-gene-regulatory-network-analysis-in-two-divergent-lines-of-a-hilly-bovine-species-mithun-bos-frontalis
#15
Sabyasachi Mukherjee, Anupama Mukherjee, Rahul Singh Jasrotia, Sarika Jaiswal, M A Iquebal, Imsusosang Longkumer, Moonmoon Mech, Kezhavituo Vüpru, Kobu Khate, Chandan Rajkhowa, Anil Rai, Dinesh Kumar
A massive bovine, Bos frontalis, also known as Mithun or Gayal, found at higher altitude is very promising meat and milk animal. For candidate gene and marker discovery, RNA-seq data was generated from longissimus dorsi muscle tissues with Illumina-HiSeq. Such markers can be used in future for genetic gain of traits like feed conversion efficiency (FCE) and average daily gain (ADG). Analysis revealed 297differentially expressed genes (DEGs) having 173 up and 124 down-regulated unigenes. Extensive conservation was found in genic region while comparing with Bos taurus...
February 26, 2019: Genomics
https://read.qxmd.com/read/30818063/analysis-of-synonymous-codon-usage-patterns-of-hprt1-gene-across-twelve-mammalian-species
#16
Surajit De Mandal, Tarikul Huda Mazumder, Amrita Kumari Panda, Nachimuthu Senthil Kumar, Fengliang Jin
Genetic changes in Hypoxanthine guanine phosphoribosyltransferace (HPRT1) gene can alter the expression of the dopamine neurotransmitter leads to abnormal neuron function, a disease called Lesch-Nyhan syndrome (LNS). Although different studies were conducted on LNS, information on codon usage bias (CUB) of HPRT1 gene is limited. The present study examines the genetic determinants of CUB in HPRT1 gene using twelve mammalian species. In the coding sequence of HPRT1 genes, A/T ending codons was most frequently used...
February 25, 2019: Genomics
https://read.qxmd.com/read/30818062/genome-wide-association-study-of-the-level-of-blood-components-in-pekin-ducks
#17
Feng Zhu, Qian-Qian Cui, Yu-Ze Yang, Jin-Ping Hao, Fang-Xi Yang, Zhuo-Cheng Hou
Blood components are considered to reflect nutrient metabolism and immune activity in both humans and animals. In this study, we measured 12 blood components in Pekin ducks and performed genome-wide association analysis to identify the QTLs (quantitative trait locus) using a genotyping-by-sequencing strategy. A total of 54 QTLs were identified for blood components. One genome-wide significant QTL for alkaline phosphatase was identified within the intron-region of the OTOG gene (P = 1.31E-07). Moreover, 21 genome-wide significant SNPs for the level of serum cholinesterase were identified on six different scaffolds...
February 25, 2019: Genomics
https://read.qxmd.com/read/30818061/identification-characterization-and-expression-profiling-of-cation-proton-antiporter-superfamily-in-triticum-aestivum-l-and-functional-analysis-of-tanhx4b
#18
Himanshu Sharma, Mehak Taneja, Santosh Kumar Upadhyay
The monovalent cation proton antiporter (CPA) superfamily comprises Na+ /H+ exchanger (NHX), K+ efflux antiporter (KEA), and cation/H+ exchanger (CHX) family proteins, which play vital functions in plants. A total of 107 TaCPA proteins were identified in Triticum aestivum, and phylogenetically classified into 35 TaNHX, 24 TaKEA and 48 TaCHX proteins. These families had representatives derived from all three sub-genomes. TaKEA genes consisted of higher number of exons, followed by TaNHXs and TaCHXs. The occurrence of about 10 transmembrane regions and higher composition of helices and coils support their membrane-bound and hydrophobic nature...
February 25, 2019: Genomics
https://read.qxmd.com/read/30807818/comparative-profiling-of-ovarian-and-testicular-pirnas-in-the-mud-crab-scylla-paramamosain
#19
Khor Waiho, Hanafiah Fazhan, Yin Zhang, Shengkang Li, Yueling Zhang, Huaiping Zheng, Mhd Ikhwanuddin, Hongyu Ma
PIWI-interacting RNAs (piRNAs) are abundantly found in germ cells and involved in gametogenesis and gonadal development. Information on the regulatory roles of piRNAs in crustacean reproduction, however, is scarce. Thus, we identified gonadal piRNAs of mud crab Scylla paramamosain. Of the 115,491 novel piRNAs, 596 were differentially expressed. Subsequently, 389,887 potential piRNA-target genes were predicted. The expression of 4 piRNAs and 9 genes with high piRNA interactions were validated with the inclusion of additional immature specimens, including LRP2 that is involved in growth and reproduction, MDN1 in ribosome biogenesis pathway and gametogenesis, and PRKDC, a DNA repair gene involved in gonadal differentiation and maturation...
February 23, 2019: Genomics
https://read.qxmd.com/read/30802599/genome-wide-characterization-revealed-role-of-nbs-lrr-genes-during-powdery-mildew-infection-in-vitis-vinifera
#20
Neetu Goyal, Garima Bhatia, Shailesh Sharma, Naina Garewal, Anuradha Upadhyay, Santosh Kumar Upadhyay, Kashmir Singh
NBS-LRR comprises a large class of disease resistance (R) proteins that play a widespread role in plant protection against pathogens. In grapevine, powdery mildew cause significant losses in its productivity and efforts are being directed towards finding of resistance loci or genes imparting resistance/tolerance against such fungal diseases. In the present study, we performed genome wide analysis of NBS-LRR genes during PM infection in grapevine. We identified 18, 23, 12, 16, 10, 10, 9, 20 and 14 differentially expressed NBS-LRR genes in response to PM infection in seven partially PM-resistant (DVIT3351...
February 22, 2019: Genomics
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