Articles

Developmentally regulated activation of defense allows for rapid inhibition of infection in age-related resistance to Phytophthora capsici in cucumber fruit

Age-related resistance (ARR) is a developmentally regulated phenomenon conferring resistance to pathogens or pests. Although ARR has been observed in several host-pathogen systems, the underlying mechanisms ar...

Authors: Ben N. Mansfeld, Marivi Colle, Chunqiu Zhang, Ying-Chen Lin and Rebecca Grumet

Reduced phosphorus intake throughout gestation and lactation of sows is mitigated by transcriptional adaptations in kidney and intestine

The environmental impact of pig farming need to be reduced, with phosphorus (P) being of particular interest. Specified dietary regimens and management systems contribute to meet environmental concerns and red...

Authors: Aisanjiang Wubuli, Christian Gerlinger, Henry Reyer, Michael Oster, Eduard Muráni, Nares Trakooljul, Siriluck Ponsuksili, Petra Wolf and Klaus Wimmers

The expansion of the TRB and TRG genes in domestic goats (Capra hircus) is characteristic of the ruminant species

Goats (Capra hircus), one of the first domesticated species, are economically important for milk and meat production, and their broad geographical distribution reflects their successful adaptation to diverse envi...

Authors: Francesco Giannico, Serafina Massari, Anna Caputi Jambrenghi, Adriano Soriano, Angela Pala, Giovanna Linguiti, Salvatrice Ciccarese and Rachele Antonacci

Analysis of six chloroplast genomes provides insight into the evolution of Chrysosplenium (Saxifragaceae)

Chrysosplenium L. (Saxifragaceae) is a genus of plants widely distributed in Northern Hemisphere and usually found in moist, shaded valleys and mountain slopes. This genus is ideal for studying plant adaptation t...

Authors: Zhihua Wu, Rui Liao, Tiange Yang, Xiang Dong, Deqing Lan, Rui Qin and Hong Liu

Parallel analysis of miRNAs and mRNAs suggests distinct regulatory networks in Crassostrea gigas infected by Ostreid herpesvirus 1

Since 2008, the aquaculture production of Crassostrea gigas was heavily affected by mass mortalities associated to Ostreid herpesvirus 1 (OsHV-1) microvariants worldwide. Transcriptomic studies revealed the major...

Authors: Umberto Rosani, Miriam Abbadi, Timothy Green, Chang-Ming Bai, Edoardo Turolla, Giuseppe Arcangeli, K. Mathias Wegner and Paola Venier

GMIEC: a shiny application for the identification of gene-targeted drugs for precision medicine

Precision medicine is a medical approach that takes into account individual genetic variability and often requires Next Generation Sequencing data in order to predict new treatments. Here we present GMIEC, Genomi...

Authors: Guidantonio Malagoli Tagliazucchi and Cristian Taccioli

Genomics and Systems Biology at the “Century of Human Population Genetics” conference

Authors: Tatiana V. Tatarinova, Ancha V. Baranova, Anastasia A. Anashkina and Yuriy L. Orlov

Differences between human and chimpanzee genomes and their implications in gene expression, protein functions and biochemical properties of the two species

Chimpanzees are the closest living relatives of humans. The divergence between human and chimpanzee ancestors dates to approximately 6,5–7,5 million years ago. Genetic features distinguishing us from chimpanze...

Authors: Maria V. Suntsova and Anton A. Buzdin

De novo sequencing, assembly and functional annotation of Armillaria borealis genome

Massive forest decline has been observed almost everywhere as a result of negative anthropogenic and climatic effects, which can interact with pests, fungi and other phytopathogens and aggravate their effects....

Authors: Vasilina S. Akulova, Vadim V. Sharov, Anastasiya I. Aksyonova, Yuliya A. Putintseva, Natalya V. Oreshkova, Sergey I. Feranchuk, Dmitry A. Kuzmin, Igor N. Pavlov, Yulia A. Litovka and Konstantin V. Krutovsky

A comparison of BeadChip and WGS genotyping outputs using partial validation by sanger sequencing

Head-to-head comparison of BeadChip and WGS/WES genotyping techniques for their precision is far from straightforward. A tool for validation of high-throughput genotyping calls such as Sanger sequencing is nei...

Authors: Kirill A. Danilov, Dimitri A. Nikogosov, Sergey V. Musienko and Ancha V. Baranova

Optimizing the genetic prediction of the eye and hair color for North Eurasian populations

Predicting the eye and hair color from genotype became an established and widely used tool in forensic genetics, as well as in studies of ancient human populations. However, the accuracy of this tool has been ...

Authors: Elena Balanovska, Elena Lukianova, Janet Kagazezheva, Andrey Maurer, Natalia Leybova, Anastasiya Agdzhoyan, Igor Gorin, Valeria Petrushenko, Maxat Zhabagin, Vladimir Pylev, Elena Kostryukova and Oleg Balanovsky

Tracing the genetic history of the ‘Cañaris’ from Ecuador and Peru using uniparental DNA markers

According to history, in the pre-Hispanic period, during the conquest and Inka expansion in Ecuador, many Andean families of the Cañar region would have been displaced to several places of Tawantinsuyu, including...

Authors: José R. Sandoval, Daniela R. Lacerda, Marilza M. S. Jota, Paulo Robles-Ruiz, Pierina Danos, César Paz-y-Miño, Spencer Wells, Fabrício R. Santos and Ricardo Fujita

Analysis of two mechanisms of telomere maintenance based on the theory of g-Networks and stochastic automata networks

Background Telomeres, which are composed of repetitive nucleotide sequences at the end of chromosomes, behave as a division clock that measures replicative senescence. Under the normal physiological condition,...

Authors: Kyung Hyun Lee and Marek Kimmel

ComHapDet: a spatial community detection algorithm for haplotype assembly

Haplotypes, the ordered lists of single nucleotide variations that distinguish chromosomal sequences from their homologous pairs, may reveal an individual’s susceptibility to hereditary and complex diseases an...

Authors: Abishek Sankararaman, Haris Vikalo and François Baccelli

Bayesian gamma-negative binomial modeling of single-cell RNA sequencing data

Single-cell RNA sequencing (scRNA-seq) is a powerful profiling technique at the single-cell resolution. Appropriate analysis of scRNA-seq data can characterize molecular heterogeneity and shed light into the u...

Authors: Siamak Zamani Dadaneh, Paul de Figueiredo, Sing-Hoi Sze, Mingyuan Zhou and Xiaoning Qian

GLaMST: grow lineages along minimum spanning tree for b cell receptor sequencing data

B cell affinity maturation enables B cells to generate high-affinity antibodies. This process involves somatic hypermutation of B cell immunoglobulin receptor (BCR) genes and selection by their ability to bind...

Authors: Xingyu Yang, Christopher M. Tipton, Matthew C. Woodruff, Enlu Zhou, F. Eun-Hyung Lee, Inãki Sanz and Peng Qiu

MAPK cascade gene family in Camellia sinensis: In-silico identification, expression profiles and regulatory network analysis

Mitogen Activated Protein Kinase (MAPK) cascade is a fundamental pathway in organisms for signal transduction. Though it is well characterized in various plants, there is no systematic study of this cascade in...

Authors: Archita Chatterjee, Abhirup Paul, G. Meher Unnati, Ruchika Rajput, Trisha Biswas, Tamalika Kar, Srijita Basak, Neelam Mishra, Ashutosh Pandey and Anurag Prakash Srivastava

Genome-wide identification of lysin motif containing protein family genes in eight rosaceae species, and expression analysis in response to pathogenic fungus Botryosphaeria dothidea in Chinese white pear

Lysin motif-containing proteins (LYP), which act as pattern-recognition receptors, play central roles in growth, node formation, and responses to biotic stresses. The sequence of Chinese white pear genome (cv....

Authors: Qiming Chen, Qionghou Li, Xin Qiao, Hao Yin and Shaoling Zhang

Metabolome and transcriptome analyses of the molecular mechanisms of flower color mutation in tobacco

Anthocyanins determinate the flower color of many plants. Tobacco is a model plant for studying the molecular regulation of flower coloration. We investigated the mechanism underlying flower coloration in toba...

Authors: Fangchan Jiao, Lu Zhao, Xingfu Wu, Zhongbang Song and Yongping Li

Integrating binding and expression data to predict transcription factors combined function

Transcription factor binding to the regulatory region of a gene induces or represses its gene expression. Transcription factors share their binding sites with other factors, co-factors and/or DNA-binding prote...

Authors: Mahmoud Ahmed, Do Sik Min and Deok Ryong Kim

Selected Research Articles from the 2019 International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC)

Authors: Byung-Jun Yoon, Xiaoning Qian, Tamer Kahveci and Ranadip Pal

Genome-wide analysis of lncRNA and mRNA expression and endogenous hormone regulation during tension wood formation in Catalpa bungei

Phytohormones are the key factors regulating vascular development in plants, and they are also involved in tension wood (TW) formation. Although the theory of hormone distribution in TW formation is widely sup...

Authors: Yao Xiao, Fei Yi, Juanjuan Ling, Guijuan Yang, Na Lu, Zirui Jia, Junchen Wang, Kun Zhao, Junhui Wang and Wenjun Ma

Leishmania infection induces a limited differential gene expression in the sand fly midgut

Sand flies are the vectors of Leishmania parasites. To develop in the sand fly midgut, Leishmania multiplies and undergoes various stage differentiations giving rise to the infective form, the metacyclic promasti...

Authors: Iliano V. Coutinho-Abreu, Tiago Donatelli Serafim, Claudio Meneses, Shaden Kamhawi, Fabiano Oliveira and Jesus G. Valenzuela

Disrupted architecture and fast evolution of the mitochondrial genome of Argeia pugettensis (Isopoda): implications for speciation and fitness

Argeia pugettensis is an isopod species that parasitizes other crustaceans. Its huge native geographic range spans the Pacific from China to California, but molecular data are available only for a handful of spec...

Authors: Jianmei An, Wanrui Zheng, Jielong Liang, Qianqian Xi, Ruru Chen, Junli Jia, Xia Lu and Ivan Jakovlić

Nucleotide diversity of functionally different groups of immune response genes in Old World camels based on newly annotated and reference-guided assemblies

Immune-response (IR) genes have an important role in the defense against highly variable pathogens, and therefore, diversity in these genomic regions is essential for species’ survival and adaptation. Although...

Authors: Sara Lado, Jean P. Elbers, Mark F. Rogers, José Melo-Ferreira, Adiya Yadamsuren, Jukka Corander, Petr Horin and Pamela A. Burger

Effect of recent and ancient inbreeding on production and fertility traits in Canadian Holsteins

Phenotypic performances of livestock animals decline with increasing levels of inbreeding, however, the noticeable decline known as inbreeding depression, may not be due only to the total level of inbreeding, ...

Authors: Bayode O. Makanjuola, Christian Maltecca, Filippo Miglior, Flavio S. Schenkel and Christine F. Baes

Transcriptomic analyses of Aedes aegypti cultured cells and ex vivo midguts in response to an excess or deficiency of heme: a quest for transcriptionally-regulated heme transporters

Aedes aegypti is the principle vector of many arboviruses, including dengue virus and Zika virus, which are transmitted when an infected female mosquito takes a blood meal in order to initiate vitellogenesis. Dur...

Authors: Heather Eggleston and Zach N. Adelman

Dynamic transcriptome and metabolome analyses of two types of rice during the seed germination and young seedling growth stages

Seed germination and young seedling growth are important agricultural traits for developing populations of both irrigated and directly seeded rice. Previous studies have focused on the identification of QTLs. ...

Authors: Jing Yang, Ling Su, Dandan Li, Lixin Luo, Kai Sun, Meng Yang, Fengwei Gu, Aoyun Xia, Yongzhu Liu, Hui Wang, Zhiqiang Chen and Tao Guo

Expression profiling of WD40 family genes including DDB1- and CUL4- associated factor (DCAF) genes in mice and human suggests important regulatory roles in testicular development and spermatogenesis

The WD40-repeat containing proteins, including DDB1–CUL4-associated factors (DCAFs), are abundant and conserved proteins that play important roles in different cellular processes including spermatogenesis. DCA...

Authors: Bhavesh V. Mistry, Maha Alanazi, Hanae Fitwi, Olfat Al-Harazi, Mohamed Rajab, Abdullah Altorbag, Falah Almohanna, Dilek Colak and Abdullah M. Assiri

Comparative transcriptome combined with metabolome analyses revealed key factors involved in nitric oxide (NO)-regulated cadmium stress adaptation in tall fescue

It has been reported that nitric oxide (NO) could ameliorate cadmium (Cd) toxicity in tall fescue; however, the underlying mechanisms of NO mediated Cd detoxification are largely unknown. In this study, we inv...

Authors: Huihui Zhu, Honglian Ai, Zhengrong Hu, Dongyun Du, Jie Sun, Ke Chen and Liang Chen

Genome-wide analysis of long non-coding RNAs in adult tissues of the melon fly, Zeugodacus cucurbitae (Coquillett)

Long non-coding RNAs (lncRNAs) are involved in many fundamental biological processes, such as transcription regulation, protein degradation, and cell differentiation. Information on lncRNA in the melon fly, Zeugo...

Authors: Wei-Jun Li, Yu-Jia Song, Hong-Liang Han, Hui-Qian Xu, Dong Wei, Guy Smagghe and Jin-Jun Wang

Comparative genomic analysis of Vibrios yields insights into genes associated with virulence towards C. gigas larvae

Vibriosis has been implicated in major losses of larvae at shellfish hatcheries. However, the species of Vibrio responsible for disease in aquaculture settings and their associated virulence genes are often varia...

Authors: Hanna Kehlet-Delgado, Claudia C. Häse and Ryan S. Mueller

The genetic basis of diurnal preference in Drosophila melanogaster

Most animals restrict their activity to a specific part of the day, being diurnal, nocturnal or crepuscular. The genetic basis underlying diurnal preference is largely unknown. Under laboratory conditions, Drosop...

Authors: Mirko Pegoraro, Laura M. M. Flavell, Pamela Menegazzi, Perrine Colombi, Pauline Dao, Charlotte Helfrich-Förster and Eran Tauber

Preliminary comparative analysis of the genomes of selected field reisolates of the Mycoplasma synoviae vaccine strain MS-H reveals both stable and unstable mutations after passage in vivo

Genomic comparison of Mycoplasma synoviae vaccine strain MS-H and the MS-H parental strain 86,079/7NS established a preliminary profile of genes related to attenuation of MS-H. In this study we aimed to identify ...

Authors: Somayeh Kordafshari, Pollob Shil, Marc S. Marenda, Olusola M. Olaogun, Barbara Konsak-Ilievski, Jillian Disint and Amir H. Noormohammadi

ACEP: improving antimicrobial peptides recognition through automatic feature fusion and amino acid embedding

Antimicrobial resistance is one of our most serious health threats. Antimicrobial peptides (AMPs), effecter molecules of innate immune system, can defend host organisms against microbes and most have shown a l...

Authors: Haoyi Fu, Zicheng Cao, Mingyuan Li and Shunfang Wang

Analysis of the brain transcriptome in lines of laying hens divergently selected for feather pecking

Feather pecking (FP) in laying hens reduces animal welfare and leads to economic losses for the layer industry. FP is considered a heritable condition that is influenced by dysregulation of neurotransmitter ho...

Authors: Clemens Falker-Gieske, Andrea Mott, Siegfried Preuß, Sören Franzenburg, Werner Bessei, Jörn Bennewitz and Jens Tetens

Genomic analysis of demographic history and ecological niche modeling in the endangered Chinese Grouse Tetrastes sewerzowi

The Quaternary had worldwide consequences in forming the contemporary diversity of many populations, species and communities, which is characterized by marked climatic oscillations between glacial and intergla...

Authors: Kai Song, Bin Gao, Peter Halvarsson, Yun Fang, Ying-Xin Jiang, Yue-Hua Sun and Jacob Höglund

Integrative analysis of circRNAs, miRNAs, and mRNAs profiles to reveal ceRNAs networks in chicken intramuscular and abdominal adipogenesis

Tissue-specific fat deposition is regulated by a series of complex regulatory mechanisms. Reports indicate that epigenetic regulators, such as circular RNAs (circRNAs), are crucial in diseases progression, ani...

Authors: Meng Zhang, Yu Han, Yanhui Zhai, Xiangfei Ma, Xinglan An, Sheng Zhang and Ziyi Li

Circular DNA intermediates in the generation of large human segmental duplications

Duplications of large genomic segments provide genetic diversity in genome evolution. Despite their importance, how these duplications are generated remains uncertain, particularly for distant duplicated genom...

Authors: Javier U. Chicote, Marcos López-Sánchez, Tomàs Marquès-Bonet, José Callizo, Luis A. Pérez-Jurado and Antonio García-España

A new mechanism for a familiar mutation – bovine DGAT1 K232A modulates gene expression through multi-junction exon splice enhancement

The DGAT1 gene encodes an enzyme responsible for catalysing the terminal reaction in mammary triglyceride synthesis, and underpins a well-known pleiotropic quantitative trait locus (QTL) with a large influence on...

Authors: Tania Fink, Thomas J. Lopdell, Kathryn Tiplady, Renee Handley, Thomas J. J. Johnson, Richard J. Spelman, Stephen R. Davis, Russell G. Snell and Mathew D. Littlejohn

Combined transcriptome and proteome profiling of the pancreatic β-cell response to palmitate unveils key pathways of β-cell lipotoxicity

Prolonged exposure to elevated free fatty acids induces β-cell failure (lipotoxicity) and contributes to the pathogenesis of type 2 diabetes. In vitro exposure of β-cells to the saturated free fatty acid palmi...

Authors: Maria Lytrivi, Kassem Ghaddar, Miguel Lopes, Victoria Rosengren, Anthony Piron, Xiaoyan Yi, Henrik Johansson, Janne Lehtiö, Mariana Igoillo-Esteve, Daniel A. Cunha, Lorella Marselli, Piero Marchetti, Henrik Ortsäter, Decio L. Eizirik and Miriam Cnop

Genomic content of chemosensory receptors in two sister blister beetles facilitates characterization of chemosensory evolution

More than 2500 species belong to the Meloidae family (Coleoptera: Tenebrionoidea), members of which produce the potent defensive blistering agent cantharidin and are commonly known as blister beetles or Spanishfl...

Authors: Yuan-Ming Wu, Yang-Yang Liu and Xiang-Sheng Chen

Genome compartmentalization predates species divergence in the plant pathogen genus Zymoseptoria

Antagonistic co-evolution can drive rapid adaptation in pathogens and shape genome architecture. Comparative genome analyses of several fungal pathogens revealed highly variable genomes, for many species chara...

Authors: Alice Feurtey, Cécile Lorrain, Daniel Croll, Christoph Eschenbrenner, Michael Freitag, Michael Habig, Janine Haueisen, Mareike Möller, Klaas Schotanus and Eva H. Stukenbrock

Features of alternative splicing in stomach adenocarcinoma and their clinical implication: a research based on massive sequencing data

Alternative splicing (AS) offers a main mechanism to form protein polymorphism. A growing body of evidence indicates the correlation between splicing disorders and carcinoma. Nevertheless, an overall analysis ...

Authors: Yuanyuan Zhang, Shengling Ma, Qian Niu, Yun Han, Xingyu Liu, Jie Jiang, Simiao Chen and Haolong Lin

Functional characterization and regulatory mechanism of wheat CPK34 kinase in response to drought stress

Drought is one of the most adverse environmental factors limiting crop productions and it is important to identify key genetic determinants for food safety. Calcium-dependent protein kinases (CPKs) are known t...

Authors: Ge-Zi Li, Han-Xiao Li, Meng-Jun Xu, Peng-Fei Wang, Xiang-Hong Xiao and Guo-Zhang Kang

Using short read sequencing to characterise balanced reciprocal translocations in pigs

A balanced constitutional reciprocal translocation (RT) is a mutual exchange of terminal segments of two non-homologous chromosomes without any loss or gain of DNA in germline cells. Carriers of balanced RTs a...

Authors: Aniek C. Bouwman, Martijn F. L. Derks, Marleen L. W. J. Broekhuijse, Barbara Harlizius and Roel F. Veerkamp

Genome-wide characterization of the GRF family and their roles in response to salt stress in Gossypium

Cotton (Gossypium spp.) is the most important world-wide fiber crop but salt stress limits cotton production in coastal and other areas. Growth regulation factors (GRFs) play regulatory roles in response to salt ...

Authors: Jun-Feng Cao, Jin-Quan Huang, Xia Liu, Chao-Chen Huang, Zi-Shou Zheng, Xiu-Fang Zhang, Xiao-Xia Shangguan, Ling-Jian Wang, Yu-Gao Zhang, Jonathan F. Wendel, Corrinne E. Grover and Zhi-Wen Chen

Global transcriptomic responses orchestrate difenoconazole resistance in Penicillium spp. causing blue mold of stored apple fruit

Blue mold is a globally important and economically impactful postharvest disease of apples caused by multiple Penicillium spp. There are currently four postharvest fungicides registered for blue mold control, and...

Authors: Franz J. Lichtner, Verneta L. Gaskins, Kerik D. Cox and Wayne M. Jurick II

Systematic analysis of the Capsicum ERF transcription factor family: identification of regulatory factors involved in the regulation of species-specific metabolites

ERF transcription factors (TFs) belong to the Apetala2/Ethylene responsive Factor (AP2/ERF) TF family and play a vital role in plant growth and development processes. Capsorubin and capsaicinoids have relative...

Authors: Jiali Song, Changming Chen, Shuanglin Zhang, Juntao Wang, Zhubing Huang, Muxi Chen, Bihao Cao, Zhangsheng Zhu and Jianjun Lei

Third-generation sequencing found LncRNA associated with heat shock protein response to heat stress in Populus qiongdaoensis seedlings

As air temperatures increase globally, more and more plants are exposed to heat-stress conditions. Although many studies have explored regulation networks in plants with the aim of improving their heat-stress ...

Authors: Jiahong Xu, Yao Zheng, Shouqin Pu, Xiujie Zhang, Zhihao Li and Jinhui Chen