Articles

Genome-wide identification and expression patterns analysis of the RPD3/HDA1 gene family in cotton

Histone deacetylases (HDACs) catalyze histone deacetylation and suppress gene transcription during various cellular processes. Within the superfamily of HDACs, RPD3/HDA1-type HDACs are the most studied, and it is...

Authors: Jingjing Zhang, Aimin Wu, Hengling Wei, Pengbo Hao, Qi Zhang, Miaomiao Tian, Xu Yang, Shuaishuai Cheng, Xiaokang Fu, Liang Ma, Hantao Wang and Shuxun Yu

Skeletal muscle and cardiac transcriptomics of a regionally endothermic fish, the Pacific bluefin tuna, Thunnus orientalis

The Pacific bluefin tuna (Thunnus orientalis) is a regionally endothermic fish that maintains temperatures in their swimming musculature, eyes, brain and viscera above that of the ambient water. Within their skel...

Authors: Adam Ciezarek, Luke Gardner, Vincent Savolainen and Barbara Block

Gene expression within the periaqueductal gray is linked to vocal behavior and early-onset parkinsonism in Pink1 knockout rats

Parkinson’s disease (PD) is a degenerative disease with early-stage pathology hypothesized to manifest in brainstem regions. Vocal deficits, including soft, monotone speech, result in significant clinical and ...

Authors: Cynthia A. Kelm-Nelson and Stephen Gammie

Full-length genome sequence of segmented RNA virus from ticks was obtained using small RNA sequencing data

In 2014, a novel tick-borne virus of the Flaviviridae family was first reported in the Mogiana region of Brazil and named the Mogiana tick virus (MGTV). Thereafter, the Jingmen tick virus (JMTV), Kindia tick viru...

Authors: Xiaofeng Xu, Jinlong Bei, Yibo Xuan, Jiayuan Chen, Defu Chen, Stephen C. Barker, Samuel Kelava, Xiaoai Zhang, Shan Gao and Ze Chen

Long-read sequencing and de novo genome assembly of marine medaka (Oryzias melastigma)

Marine medaka (Oryzias melastigma) is considered as an important ecotoxicological indicator to study the biochemical, physiological and molecular responses of marine organisms towards increasing amount of polluta...

Authors: Pingping Liang, Hafiz Sohaib Ahmed Saqib, Xiaomin Ni and Yingjia Shen

Comparative transcriptome analysis of root, stem, and leaf tissues of Entada phaseoloides reveals potential genes involved in triterpenoid saponin biosynthesis

Entada phaseoloides (L.) Merr. is an important traditional medicinal plant. The stem of Entada phaseoloides is popularly used as traditional medicine because of its significance in dispelling wind and dampness an...

Authors: Weifang Liao, Zhinan Mei, Lihong Miao, Pulin Liu and Ruijie Gao

Transcriptome response comparison between vector and non-vector aphids after feeding on virus-infected wheat plants

Plant viruses maintain intricate interactions with their vector and non-vector insects and can impact the fitness of insects. However, the details of their molecular and cellular mechanisms have not been studi...

Authors: Dandan Li, Chi Zhang, Zeqian Tong, Dan Su, Gaisheng Zhang, Shize Zhang, Huiyan Zhao and Zuqing Hu

CrustyBase: an interactive online database for crustacean transcriptomes

Transcriptome sequencing has opened the field of genomics to a wide variety of researchers, owing to its efficiency, applicability across species and ability to quantify gene expression. The resulting datasets...

Authors: Cameron J. Hyde, Quinn P. Fitzgibbon, Abigail Elizur, Gregory G. Smith and Tomer Ventura

Integrated analysis of lncRNA, miRNA and mRNA reveals novel insights into the fertility regulation of large white sows

Improving sow fertility is extremely important as it can lead to increased reproductive efficiency and thus profitability for swine producers. There are considerable differences in fertility rates among indivi...

Authors: Huiyan Hu, Qing Jia, Jianzhong Xi, Bo Zhou and Zhiqiang Li

The wild strawberry kinome: identification, classification and transcript profiling of protein kinases during development and in response to gray mold infection

Protein kinases (PKs) play an important role in signaling cascades and are one of the largest and most conserved protein super families in plants. Despite their importance, the woodland strawberry (Fragaria vesca

Authors: Hui Liu, Wei Qu, Kaikai Zhu and Zong-Ming ( Max) Cheng

Differences in midgut transcriptomes between resistant and susceptible strains of Chilo suppressalis to Cry1C toxin

Chilo suppressalis is a widespread rice pest that poses a major threat to food security in China. This pest can develop resistance to Cry toxins from Bacillus thuringiensis (Bt), threatening the sustainable use o...

Authors: Geng Chen, Yanhui Wang, Yanmin Liu, Fajun Chen and Lanzhi Han

RNA-seq analysis of galaninergic neurons from ventrolateral preoptic nucleus identifies expression changes between sleep and wake

Previous studies show that galanin neurons in ventrolateral preoptic nucleus (VLPO-Gal) are essential for sleep regulation. Here, we explored the transcriptional regulation of the VLPO-Gal neurons in sleep by ...

Authors: Xiaofeng Guo, Xiaoling Gao, Brendan T. Keenan, Jingxu Zhu, Dimitra Sarantopoulou, Jie Lian, Raymond J. Galante, Gregory R. Grant and Allan I. Pack

MasterPATH: network analysis of functional genomics screening data

Functional genomics employs several experimental approaches to investigate gene functions. High-throughput techniques, such as loss-of-function screening and transcriptome profiling, allow to identify lists of...

Authors: Natalia Rubanova, Guillaume Pinna, Jeremie Kropp, Anna Campalans, Juan Pablo Radicella, Anna Polesskaya, Annick Harel-Bellan and Nadya Morozova

Benchmarking hybrid assembly approaches for genomic analyses of bacterial pathogens using Illumina and Oxford Nanopore sequencing

We benchmarked the hybrid assembly approaches of MaSuRCA, SPAdes, and Unicycler for bacterial pathogens using Illumina and Oxford Nanopore sequencing by determining genome completeness and accuracy, antimicrob...

Authors: Zhao Chen, David L. Erickson and Jianghong Meng

Genome-wide characterization and expression profiling of MAPK cascade genes in Salvia miltiorrhiza reveals the function of SmMAPK3 and SmMAPK1 in secondary metabolism

The contribution of mitogen-activated protein kinase (MAPK) cascades to plant growth and development has been widely studied, but this knowledge has not yet been extended to the medicinal plant Salvia miltiorrhiz...

Authors: Yongfeng Xie, Meiling Ding, Bin Zhang, Jie Yang, Tianlin Pei, Pengda Ma and Juane Dong

Understanding seasonal weight loss tolerance in dairy goats: a transcriptomics approach

Seasonal weight loss (SWL) is a very important limitation to the production of ruminants in the Mediterranean and Tropical regions. In these areas, long dry seasons lead to poor pastures with low nutritional v...

Authors: José Ricardo Parreira, Lorenzo Enrique Hernández-Castellano, Anastasio Argüello, Juan Capote, Noemí Castro, Susana de Sousa Araújo and André Martinho de Almeida

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

Accurate prediction of DNA N⁴-methylcytosine sites via boost-learning various types of sequence features

DNA N4-methylcytosine (4mC) is a critical epigenetic modification and has various roles in the restriction-modification system. Due to the high cost of experimental laboratory detection, computational methods ...

Authors: Zhixun Zhao, Xiaocai Zhang, Fang Chen, Liang Fang and Jinyan Li

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

Genome-wide detection of signatures of selection in indicine and Brazilian locally adapted taurine cattle breeds using whole-genome re-sequencing data

The cattle introduced by European conquerors during the Brazilian colonization period were exposed to a process of natural selection in different types of biomes throughout the country, leading to the developm...

Authors: Elisa Peripolli, Christian Reimer, Ngoc-Thuy Ha, Johannes Geibel, Marco Antonio Machado, João Cláudio do Carmo Panetto, Andréa Alves do Egito, Fernando Baldi, Henner Simianer and Marcos Vinícius Gualberto Barbosa da Silva

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

Using genomic resources for linkage analysis in Peromyscus with an application for characterizing Dominant Spot

Peromyscus are the most common mammalian species in North America and are widely used in both laboratory and field studies. The deer mouse, P. maniculatus and the old-field mouse, P. polionotus, are closely relat...

Authors: Zhenhua Shang, David J. Horovitz, Ronald H. McKenzie, Jessica L. Keisler, Michael R. Felder and Shannon W. Davis

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

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