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Genomics

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https://www.readbyqxmd.com/read/29684432/intraspecific-mitochondrial-genome-comparison-identified-cytb-as-a-high-resolution-population-marker-in-a-new-pest-athetis-lepigone
#1
Lei Chen, Jian-Rong Huang, Jun Dai, Yan-Fei Guo, Jing-Tao Sun, Xiao-Yue Hong
A new outbreak pest, Athetis lepigone (Möschler) (Lepidoptera: Noctuidae), has caused severe economic loss in maize crops in China. In order to conduct population genetics study with a more polymorphic and scientific mitochondrial marker, we sequenced the complete mitochondrial genomes of 13 different A. lepigone individuals. Intraspecific comparison of all PCGs showed that the NADH dehydrogenase and cytochrome b genes had the highest nucleotide diversity. We also found evidence of episodic positive selection on two amino acids, which are encoded by NADH dehydrogenase genes (ND3 and ND4L), against a background of widespread neutral selection of all other mitochondrial PCGs...
April 20, 2018: Genomics
https://www.readbyqxmd.com/read/29679643/classification-and-experimental-identification-of-plant-long-non-coding-rnas
#2
Muneeza I Rai, Maheen Alam, David A Lightfoot, Priyatansh Gurha, Ahmed J Afzal
Our understanding of gene regulation is constantly evolving. It is now clear that the majority of cellular transcripts are non-coding RNAs. The spectrum of non-coding RNAs is diverse and includes short (<200 nt) and long non-coding RNAs (lncRNAs) (>200 nt). LncRNAs regulate gene expression through diverse mechanisms. In this review, we describe the emerging roles of lncRNA mediated plant gene regulation. We discuss the current classification of lncRNAs and their role in genome organization and gene regulation...
April 18, 2018: Genomics
https://www.readbyqxmd.com/read/29678683/long-term-affected-flat-oyster-ostrea-edulis-haemocytes-show-differential-gene-expression-profiles-from-na%C3%A3-ve-oysters-in-response-to-bonamia-ostreae
#3
P Ronza, A Cao, D Robledo, A Gómez-Tato, J A Álvarez-Dios, A F M Hasanuzzaman, M I Quiroga, A Villalba, B G Pardo, P Martínez
European flat oyster (Ostrea edulis) production has suffered a severe decline due to bonamiosis. The responsible parasite enters in oyster haemocytes, causing an acute inflammatory response frequently leading to death. We used an immune-enriched oligo-microarray to understand the haemocyte response to Bonamia ostreae by comparing expression profiles between naïve (NS) and long-term affected (AS) populations along a time series (1 d, 30 d, 90 d). AS showed a much higher response just after challenge, which might be indicative of selection for resistance...
April 17, 2018: Genomics
https://www.readbyqxmd.com/read/29678682/where-are-we-going-with-genomics-in-plant-pathogenic-bacteria
#4
REVIEW
Jin Xu, Nian Wang
Genome sequencing is commonly used in research laboratories right now thanks to the rise of high-throughput sequencing with higher speed and output-to-cost ratios. Here, we summarized the application of genomics in different aspects of plant pathosystems. Genomics has been used in studying the mechanisms of plant bacterial interactions, and host specificity. It also helps with taxonomy, study of non-cultured bacteria, identification of causal agent, single cell sequencing, population genetics, and meta-transcriptomic...
April 17, 2018: Genomics
https://www.readbyqxmd.com/read/29678681/genome-wide-meta-analysis-identifies-novel-gender-specific-loci-associated-with-thyroid-antibodies-level-in-croatians
#5
Antonela Matana, Marijana Popović, Thibaud Boutin, Vesela Torlak, Dubravka Brdar, Ivana Gunjača, Ivana Kolčić, Vesna Boraska Perica, Ante Punda, Ozren Polašek, Caroline Hayward, Maja Barbalić, Tatijana Zemunik
Autoimmune thyroid diseases (AITD) are multifactorial endocrine diseases most frequently accompanied by Tg and TPO autoantibodies. Both antibodies have a higher prevalence in females and act under a strong genetic influence. To identify novel variants underlying thyroid antibody levels, we performed GWAS meta-analysis on the plasma levels of TgAb and TPOAb in three Croatian cohorts, as well as gender specific GWAS and a bivariate analysis. No significant association was detected with the level of TgAb and TPOAb in the meta-analysis of GWAS or bivariate results for all individuals...
April 17, 2018: Genomics
https://www.readbyqxmd.com/read/29674165/identification-expression-and-function-of-myosin-heavy-chain-family-genes-in-tribolium-castaneum
#6
Chengjun Li, Juanjuan Liu, Peng Lü, Shangshang Ma, Keming Zhu, Lu Gao, Bin Li, Keping Chen
Functions of myosin heavy chain (myosin) family genes are poorly understood in some insects. To address this, we determined the expression and function of myosin family genes in Tribolium castaneum. TcMyo15 is predominantly expressed in early embryos, late larvae and early adults, but TcMyo7B transcripts significantly increased in late larvae. TcMyo20 transcripts are abundant in pre-adults, whereas TcMhc1 is highly expressed in post-embryonic stages. TcMhc2 shows peak expression in late pupae. TcMyo9 transcripts reached their highest levels in late pupae...
April 16, 2018: Genomics
https://www.readbyqxmd.com/read/29665418/a-continuous-genome-assembly-of-the-corkwing-wrasse-symphodus-melops
#7
Morten Mattingsdal, Sissel Jentoft, Ole K Tørresen, Halvor Knutsen, Michael M Hansen, Joana I Robalo, Zuzanna Zagrodzka, Carl André, Enrique Blanco Gonzalez
The wrasses (Labridae) are one of the most successful and species-rich families of the Perciformes order of teleost fish. Its members display great morphological diversity, and occupy distinct trophic levels in coastal waters and coral reefs. The cleaning behaviour displayed by some wrasses, such as corkwing wrasse (Symphodus melops), is of particular interest for the salmon aquaculture industry to combat and control sea lice infestation as an alternative to chemicals and pharmaceuticals. There are still few genome assemblies available within this fish family for comparative and functional studies, despite the rapid increase in genome resources generated during the past years...
April 14, 2018: Genomics
https://www.readbyqxmd.com/read/29665417/glaucoma-pred-glaucoma-prediction-based-on-myocilin-genotype-and-phenotype-information
#8
K Rangachari, Namrata Bankoti, N Shyamala, Daliah Michael, Z Sameer Ahmed, P Chandrasekaran, K Sekar
Glaucoma is the second leading cause of blindness after cataract and is heterogeneous in nature. Employing a genetic approach for the detection of the diseased condition provides an advantage that the gene responsible for the disease can be identified by genetic test. The availability of predictive tests based on the published literature would provide a mechanism for early detection and treatment. The genotype and phenotype information could be a valuable source for predicting the risk of the disease. To this end, a web server has been developed, based on the genotype and phenotype of myocilin mutation, which were identified by familial linkage analysis and case studies...
April 14, 2018: Genomics
https://www.readbyqxmd.com/read/29660477/gene-selection-using-hybrid-binary-black-hole-algorithm-and-modified-binary-particle-swarm-optimization
#9
Elnaz Pashaei, Elham Pashaei, Nizamettin Aydin
In cancer classification, gene selection is an important data preprocessing technique, but it is a difficult task due to the large search space. Accordingly, the objective of this study is to develop a hybrid meta-heuristic Binary Black Hole Algorithm (BBHA) and Binary Particle Swarm Optimization (BPSO) (4-2) model that emphasizes gene selection. In this model, the BBHA is embedded in the BPSO (4-2) algorithm to make the BPSO (4-2) more effective and to facilitate the exploration and exploitation of the BPSO (4-2) algorithm to further improve the performance...
April 13, 2018: Genomics
https://www.readbyqxmd.com/read/29660476/the-first-mitochondrial-genome-of-the-model-echinoid-lytechinus-variegatus-and-insights-into-odontophoran-phylogenetics
#10
Omri Bronstein, Andreas Kroh
Assembly of publically available next-generation sequence data facilitated the generation of three camarodont echinoid mitogenomes: two for the Green Urchin (Lytechinus variegatus) and one for the Red Urchin (Mesocentrotus franciscanus). The data generated are exploited in a phylogenomic analysis of the superfamily Odontophora, originally proposed for echinoids with tooth supports on the epiphyses of the jaw. The analysis highly supports this taxon and its current subdivision into three families: the Echinometridae, Toxopneustidae, and Strongylocentrotidae...
April 13, 2018: Genomics
https://www.readbyqxmd.com/read/29660475/transcriptome-sequencing-of-active-buds-from-populus-deltoides-cl-and-populus-%C3%A3-zhaiguanheibaiyang-reveals-phytohormones-involved-in-branching
#11
Jinnan Wang, Yanting Tian, Jihong Li, Keqiang Yang, Shiyan Xing, Xiaojiao Han, Dong Xu, Yiwei Wang
Branching in woody plants affects their ecological benefits and impacts wood formation. To obtain genome-wide insights into the transcriptome changes and regulatory mechanisms associated with branching, we performed high-throughput RNA sequencing to characterize cDNA libraries generated from active buds of Populus deltoides CL. 'zhonglin2025' (BC) and Populus × zhaiguanheibaiyang (NC). NC has more branches than BC and rapid growth. We obtained a total of 198.2 million high-quality clean reads from the NC and BC libraries...
April 13, 2018: Genomics
https://www.readbyqxmd.com/read/29655905/functional-relevance-of-synonymous-alleles-reflected-in-allele-rareness-in-the-population
#12
Eu-Hyun Im, Yoonsoo Hahn, Sun Shim Choi
We provide theoretical evidence supporting the non-neutrality of synonymous alleles by investigating the rareness of synonymous alleles in the population. We find a significantly greater number of synonymous rare alleles than conventional neutral alleles derived from noncoding regions. A permutation experiment shows that the rareness of synonymous alleles is not a byproduct of random statistical noise. We then compare the frequencies of synonymous rare alleles and common alleles in various functional contexts in which synonymous alleles are known to be involved...
April 12, 2018: Genomics
https://www.readbyqxmd.com/read/29627505/genome-analysis-of-urease-positive-serratia-marcescens-co-producing-srt-2-and-aac-6-ic-with-multidrug-efflux-pumps-for-antimicrobial-resistance
#13
Vijaya Bharathi Srinivasan, Govindan Rajamohan
In this study, we present the genome sequence of Serratia marcescens SM03, recovered from a human gut in India. The final assembly consists of 26 scaffolds (4620 coding DNA sequences, 5.08 Mb, 59.6% G + C ratio) and 79 tRNA genes. Analysis identified novel genes associated with lactose utilization, virulence, P-loop GTPases involved in urease production, CFA/I fimbriae apparatus and Yersinia - type CRISPR proteins. Antibiotic susceptibility testing indicated drug tolerant phenotype and inhibition assays demonstrated involvement of extrusion in resistance...
April 5, 2018: Genomics
https://www.readbyqxmd.com/read/29627504/prioritizing-complex-disease-risk-genes-by-integrating-multiple-data
#14
Shanshan Guo, Benliang Wei, Bingchen Dong, Wan Li, Song Wu, Yuehan He, Yahui Wang, Xilei Zhao, Lina Chen, Weiming He
Complex diseases, such as obesity, type II diabetes and chronic obstructive pulmonary disease (COPD) as metabolic disorder-related diseases are major concern for worldwide public health in the 21st century. The identification of these disease risk genes has attracted increasing interest in computational systems biology. In this paper, a novel method was proposed to prioritize disease risk genes (PDRG) by integrating functional annotations, protein interactions and gene expression information to assess similarity between genes in a disease-related metabolic network...
April 5, 2018: Genomics
https://www.readbyqxmd.com/read/29626511/rna-sequencing-analysis-of-salt-tolerance-in-soybean-glycine-max
#15
Ailan Zeng, Pengyin Chen, Ken L Korth, Jieqing Ping, Julie Thomas, Chengjun Wu, Subodh Srivastava, Andy Pereira, Floyd Hancock, Kristofor Brye, Jianxin Ma
Salt stress causes foliar chlorosis and scorch, plant stunting, and eventually yield reduction in soybean. There are differential responses, namely tolerance (excluder) and intolerance (includer), among soybean germplasm. However, the genetic and physiological mechanisms for salt tolerance is complex and not clear yet. Based on the results from the screening of the RA-452 x Osage mapping population, two F4:6 lines with extreme responses, most tolerant and most sensitive, were selected for a time-course gene expression study in which the 250 mM NaCl treatment was initially imposed at the V1 stage and continued for 24 h (hrs)...
April 4, 2018: Genomics
https://www.readbyqxmd.com/read/29621573/genomic-molecular-evolution-and-expression-analysis-of-nox-genes-in-soybean-glycine-max
#16
Zaibao Zhang, Yilin Zhao, Xiaobing Feng, Zhaoyi Luo, Shuwei Kong, Chi Zhang, Andong Gong, Hongyu Yuan, Lin Cheng, Xiangnan Wang
Reactive oxygen species (ROS) are versatile signaling molecules in sensing stresses and play critical roles in signaling and development. Plasma membrane NADPH oxidases (NOXs) are key producers of ROS, and play important roles in the regulation of plant-pathogen interactions. Here, we performed a comprehensive analysis of the NOX gene family in the soybean genome (Glycine max) and 17 NOX (GmNOX) genes were identified. Structural analysis revealed that the GmNOX proteins in soybean were as conserved as those in other plants...
April 2, 2018: Genomics
https://www.readbyqxmd.com/read/29614347/discovery-of-novel-transcripts-of-the-human-tissue-kallikrein-klk1-and-kallikrein-related-peptidase-2-klk2-in-human-cancer-cells-exploiting-next-generation-sequencing-technology
#17
Panagiotis G Adamopoulos, Christos K Kontos, Andreas ScorilasP
Tissue kallikrein, kallikrein-related peptidases (KLKs), and plasma kallikrein form the largest group of serine proteases in the human genome, sharing many structural and functional properties. Several KLK transcripts have been found aberrantly expressed in numerous human malignancies, confirming their prognostic or/and diagnostic values. However, the process of alternative splicing can now be studied in-depth due to the development of Next-Generation Sequencing (NGS). In the present study, we used NGS to discover novel transcripts of the KLK1 and KLK2 genes, after nested touchdown PCR...
March 31, 2018: Genomics
https://www.readbyqxmd.com/read/29614346/analysis-of-time-course-microarray-data-comparison-of-common-tools
#18
Kobra Moradzadeh, Shiva Moein, Niloofar Nickaeen, Yousof Gheisari
High-throughput time-series data have a special value for studying the dynamism of biological systems. However, the interpretation of such complex data can be challenging. The aim of this study was to compare common algorithms recently developed for the detection of differentially expressed genes in time-course microarray data. Using different measures such as sensitivity, specificity, predictive values, and related signaling pathways, we found that limma, timecourse, and gprege have reasonably good performance for the analysis of datasets in which only test group is followed over time...
March 31, 2018: Genomics
https://www.readbyqxmd.com/read/29608956/detection-and-validation-of-est-ssr-markers-associated-with-sugar-related-traits-in-sugarcane-using-linkage-and-association-mapping
#19
Kittipat Ukoskit, Ganlayarat Posudsavang, Nattapat Pongsiripat, Prasert Chatwachirawong, Peeraya Klomsa-Ard, Patthinun Poomipant, Somvong Tragoonrung
Sugar-related traits are of great importance in sugarcane breeding. In the present study, quantitative trait loci (QTL) mapping validated with association mapping was used to identify expressed sequence tag-simple sequence repeats (EST-SSRs) associated with sugar-related traits. For linkage mapping, 524 EST-SSRs, 241 Amplified Fragment Length Polymorphisms, and 10 genomic SSR markers were mapped using 283 F1 progenies derived from an interspecific cross. Six regions were identified using Multiple QTL Mapping, and 14 unlinked markers using single marker analysis...
March 31, 2018: Genomics
https://www.readbyqxmd.com/read/29605634/crispcut-a-novel-tool-for-designing-optimal-sgrnas-for-crispr-cas9-based-experiments-in-human-cells
#20
Jaspreet Kaur Dhanjal, Navaneethan Radhakrishnan, Durai Sundar
The ability to direct the CRISPR/Cas9 nuclease to a unique target site within a genome would have broad use in targeted genome engineering. However, CRISPR RNA is reported to bind to other genomic locations that differ from the intended target site by a few nucleotides, demonstrating significant off-target activity. We have developed the CRISPcut tool that screens the off-targets using various parameters and predicts the ideal genomic target for -guide RNAs in human cell lines. sgRNAs for four different types of Cas9 nucleases can be designed with an option for the user to work with different PAM sequences...
March 29, 2018: Genomics
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