Articles

Genome-wide association study reveals the genetic architecture of root hair length in maize

Root hair, a special type of tubular-shaped cell, outgrows from root epidermal cell and plays important roles in the acquisition of nutrients and water, as well as interactions with biotic and abiotic stress. ...

Authors: Lin Liu, Lu-Guang Jiang, Jin-Hong Luo, Ai-Ai Xia, Li-Qun Chen and Yan He

PathFams: statistical detection of pathogen-associated protein domains

A substantial fraction of genes identified within bacterial genomes encode proteins of unknown function. Identifying which of these proteins represent potential virulence factors, and mapping their key virulen...

Authors: Briallen Lobb, Benjamin Jean-Marie Tremblay, Gabriel Moreno-Hagelsieb and Andrew C. Doxey

Genomic variation in captive deer mouse (Peromyscus maniculatus) populations

Deer mice (genus Peromyscus) are the most common rodents in North America. Despite the availability of reference genomes for some species, a comprehensive database of polymorphisms, especially in those maintained...

Authors: Matthew D. Lucius, Hao Ji, Diego Altomare, Robert Doran, Ben Torkian, Amanda Havighorst, Vimala Kaza, Youwen Zhang, Alexander V. Gasparian, Joseph Magagnoli, Vijay Shankar, Michael Shtutman and Hippokratis Kiaris

Choice of pre-processing pipeline influences clustering quality of scRNA-seq datasets

Single-cell RNA sequencing (scRNA-seq) has quickly become one of the most dominant techniques in modern transcriptome assessment. In particular, 10X Genomics’ Chromium system, with its high throughput approach...

Authors: Inbal Shainer and Manuel Stemmer

Dual RNA-seq transcriptome analysis of caecal tissue during primary Eimeria tenella infection in chickens

Coccidiosis is an infectious disease with large negative impact on the poultry industry worldwide. It is an enteric infection caused by unicellular Apicomplexan parasites of the genus Eimeria. The present study a...

Authors: Arnar K. S. Sandholt, Eva Wattrang, Tobias Lilja, Harri Ahola, Anna Lundén, Karin Troell, Staffan G. Svärd and Robert Söderlund

Correction to: Post-diapause transcriptomic restarts: insight from a high-latitude copepod

Authors: Vittoria Roncalli, Matthew C. Cieslak, Ann M. Castelfranco, Russell R. Hopcroft, Daniel K. Hartline and Petra H. Lenz

Gene co-expression network analysis in zebrafish reveals chemical class specific modules

Zebrafish is a popular animal model used for high-throughput screening of chemical hazards, however, investigations of transcriptomic mechanisms of toxicity are still needed. Here, our goal was to identify gen...

Authors: Prarthana Shankar, Ryan S. McClure, Katrina M. Waters and Robyn L. Tanguay

Correction to: Genome-wide development of insertiondeletion (InDel) markers for Cannabis and its uses in genetic structure analysis of Chinese germplasm and sex-linked marker identification

Authors: Gen Pan, Zheng Li, Siqi Huang, Jie Tao, Yaliang Shi, Anguo Chen, Jianjun Li, Huijuan Tang, Li Chang, Yong Deng, Defang Li and Lining Zhao

Correction to: Multi-ethnic genome-wide association analyses of white blood cell and platelet traits in the Population Architecture using Genomics and Epidemiology (PAGE) Study

Authors: Yao Hu, Stephanie A. Bien, Katherine K. Nishimura, Jeffrey Haessler, Chani J. Hodonsky, Antoine R. Baldassari, Heather M. Highland, Zhe Wang, Michael Preuss, Colleen M. Sitlani, Genevieve L. Wojcik, Ran Tao, Mariaelisa Graff, Laura M. Huckins, Quan Sun, Ming-Huei Chen…

Complete genome sequence and identification of polyunsaturated fatty acid biosynthesis genes of the myxobacterium Minicystis rosea DSM 24000^T

Myxobacteria harbor numerous biosynthetic gene clusters that can produce a diverse range of secondary metabolites. Minicystis rosea DSM 24000^T is a soil-dwelling myxobacterium belonging to the suborderSorangiinea...

Authors: Shilpee Pal, Gaurav Sharma and Srikrishna Subramanian

Morphological characteristics and transcriptome analysis at different anther development stages of the male sterile mutant MS7–2 in Wucai (Brassica campestris L.)

The discovery of male sterile materials is of great significance for the development of plant fertility research. Wucai (Brassica campestris L. ssp. chinensis var. rosularis Tsen) is a variety of non-heading Chin...

Authors: Jian Wang, Yitao Yang, Lei Zhang, Shaoxing Wang, Lingyun Yuan, Guohu Chen, Xiaoyan Tang, Jinfeng Hou, Shidong Zhu and Chenggang Wang

Integrated analysis of lncRNA and mRNA in liver of Megalobrama amblycephala post Aeromonas hydrophila infection

As non-coding RNA molecules of more than 200 bp in length, long non-coding RNAs (lncRNAs) play a variety of roles in biological processes, including regulating the immune responses to bacterial infections. In ...

Authors: Qianhui Sun, Jixiu Wang, Guowen Wang, Huanling Wang and Hong Liu

Genome-resolved metagenome and metatranscriptome analyses of thermophilic composting reveal key bacterial players and their metabolic interactions

Composting is an important technique for environment-friendly degradation of organic material, and is a microbe-driven process. Previous metagenomic studies of composting have presented a general description o...

Authors: Lucas Palma Perez Braga, Roberta Verciano Pereira, Layla Farage Martins, Livia Maria Silva Moura, Fabio Beltrame Sanchez, José Salvatore Leister Patané, Aline Maria da Silva and João Carlos Setubal

Transcriptome analysis reveals the molecular mechanisms of heterosis on thermal resistance in hybrid abalone

Heterosis has been exploited for decades in different animals and crops due to it resulting in dramatic increases in yield and adaptability. Hybridization is a classical breeding method that can effectively im...

Authors: Qizhen Xiao, Zekun Huang, Yawei Shen, Yang Gan, Yi Wang, Shihai Gong, Yisha Lu, Xuan Luo, Weiwei You and Caihuan Ke

Correction to: epidemiological and genomic characteristics of A. baumannii from different infection sites using comparative genomics

Authors: Xingchen Bian, Xiaofen Liu, Xuefei Zhang, Xin Li, Jing Zhang, Huajun Zheng, Sichao Song, Xiang Li and Meiqing Feng

Redox proteomic study of Bacillus cereus thiol proteome during fermentative anaerobic growth

Bacillus cereus is a notorious foodborne pathogen, which can grow under anoxic conditions. Anoxic growth is supported by endogenous redox metabolism, for which the thiol redox proteome serves as an interface. Her...

Authors: Fella Hamitouche, Jean-Charles Gaillard, Philippe Schmitt, Jean Armengaud, Catherine Duport and Luc Dedieu

A tetraploidization event shaped the Aquilaria sinensis genome and contributed to the ability of sesquiterpenes synthesis

Agarwood, generated from the Aquilaria sinensis, has high economic and medicinal value. Although its genome has been sequenced, the ploidy of A. sinensis paleopolyploid remains unclear. Moreover, the expression c...

Authors: Fanbo Meng, Tianzhe Chu, Qiang Tang and Wei Chen

Comparative analysis of the complete mitochondrial genome sequences and anther development cytology between maintainer and Ogura-type cytoplasm male-sterile cabbage (B. oleracea Var. capitata)

Cytoplasmic male sterility (CMS) has been widely used for commercial F1 hybrid seeds production. CMS is primarily caused by chimeric genes in mitochondrial genomes. However, which specific stages of anther dev...

Authors: Xionghui Zhong, Denghui Chen, Jian Cui, Hailong Li, Yuxin Huang and Jungen Kang

The chloroplast genome of Amygdalus L. (Rosaceae) reveals the phylogenetic relationship and divergence time

Limited access to genetic information has greatly hindered our understanding of the molecular evolution, phylogeny, and differentiation time of subg. Amygdalus. This study reported complete chloroplast (cp) genom...

Authors: Zhongyu Du, Ke Lu, Kai Zhang, Yiming He, Haitao Wang, Guaiqiang Chai, Jianguo Shi and Yizhong Duan

Inter-chromosomal k-mer distances

Inversion Symmetry is a generalization of the second Chargaff rule, stating that the count of a string of k nucleotides on a single chromosomal strand equals the count of its inverse (reverse-complement) k-mer...

Authors: Alon Kafri, Benny Chor and David Horn

High contiguity de novo genome assembly and DNA modification analyses for the fungus fly, Sciara coprophila, using single-molecule sequencing

The lower Dipteran fungus fly, Sciara coprophila, has many unique biological features that challenge the rule of genome DNA constancy. For example, Sciara undergoes paternal chromosome elimination and maternal X ...

Authors: John M. Urban, Michael S. Foulk, Jacob E. Bliss, C. Michelle Coleman, Nanyan Lu, Reza Mazloom, Susan J. Brown, Allan C. Spradling and Susan A. Gerbi

C-terminal domain phosphatase-like 1 (CPL1) is involved in floral transition in Arabidopsis

RNA polymerase II plays critical roles in transcription in eukaryotic organisms. C-terminal Domain Phosphatase-like 1 (CPL1) regulates the phosphorylation state of the C-terminal domain of RNA polymerase II su...

Authors: Chen Yuan, Jingya Xu, Qianqian Chen, Qinggang Liu, Yikai Hu, Yicheng Jin and Cheng Qin

Ischemic stroke induces cardiac dysfunction and alters transcriptome profile in mice

Stroke can induce cardiac dysfunction in the absence of primary cardiac disease; however, the mechanisms underlying the interaction between the neurological deficits and the heart are poorly understood. The ob...

Authors: Jie Chen, Jiahong Gong, Haili Chen, Xuqing Li, Li Wang, Xiaoli Qian, Kecheng Zhou, Ting Wang, Songhe Jiang, Lei Li and Shengcun Li

Proteome analysis identified proteins associated with mitochondrial function and inflammation activation crucially regulating the pathogenesis of fatty liver disease

Fatty liver disease prevalently occurs in commercial postpartum dairies, resulting in a worldwide high culling rate because of their subsequent limitations of production and reproduction performance.

Authors: Letian Zhang, Tingjun Liu, Chengzhang Hu, Xuan Zhang, Qin Zhang and Kerong Shi

Up-regulation of apoptotic- and cell survival-related gene pathways following exposures of western corn rootworm to B. thuringiensis crystalline pesticidal proteins in transgenic maize roots

Resistance of pest insect species to insecticides, including B. thuringiensis (Bt) pesticidal proteins expressed by transgenic plants, is a threat to global food security. Despite the western corn rootworm, Diabr...

Authors: Brad S. Coates, Emeline Deleury, Aaron J. Gassmann, Bruce E. Hibbard, Lance J. Meinke, Nicholas J. Miller, Jennifer Petzold-Maxwell, B. Wade French, Thomas W. Sappington, Blair D. Siegfried and Thomas Guillemaud

Integrative lncRNA landscape reveals lncRNA-coding gene networks in the secondary cell wall biosynthesis pathway of moso bamboo (Phyllostachys edulis)

LncRNAs are extensively involved in plant biological processes. However, the lack of a comprehensive lncRNA landscape in moso bamboo has hindered the molecular study of lncRNAs. Moreover, the role of lncRNAs i...

Authors: Jiongliang Wang, Yinguang Hou, Yu Wang and Hansheng Zhao

Transcriptome analysis provides genome annotation and expression profiles in the central nervous system of Lymnaea stagnalis at different ages

The pond snail, Lymnaea stagnalis (L. stagnalis), has served as a valuable model organism for neurobiology studies due to its simple and easily accessible central nervous system (CNS). L. stagnalis has been widel...

Authors: Martina Rosato, Brittany Hoelscher, Zhenguo Lin, Chidera Agwu and Fenglian Xu

Genome-wide association studies for canine hip dysplasia in single and multiple populations – implications and potential novel risk loci

Association mapping studies of quantitative trait loci (QTL) for canine hip dysplasia (CHD) can contribute to the understanding of the genetic background of this common and debilitating disease and might contr...

Authors: Shizhi Wang, Erling Strandberg, Per Arvelius, Dylan N. Clements, Pamela Wiener and Juliane Friedrich

The genome of the extremophile Artemia provides insight into strategies to cope with extreme environments

Brine shrimp Artemia have an unequalled ability to endure extreme salinity and complete anoxia. This study aims to elucidate its strategies to cope with these stressors.

Authors: Stephanie De Vos, Stephane Rombauts, Louis Coussement, Wannes Dermauw, Marnik Vuylsteke, Patrick Sorgeloos, James S. Clegg, Ziro Nambu, Filip Van Nieuwerburgh, Parisa Norouzitallab, Thomas Van Leeuwen, Tim De Meyer, Gilbert Van Stappen, Yves Van de Peer and Peter Bossier

Altered synthesis of genes associated with short-chain fatty acids in the gut of patients with atrial fibrillation

The gut microbiota provides health benefits in humans by producing short-chain fatty acids (SCFAs), whose deficiency causes multiple disorders and inflammatory diseases. However, gut bacteria producing SCFAs i...

Authors: Jing Zhang, Kun Zuo, Chen Fang, Xiandong Yin, Xiaoqing Liu, Jiuchang Zhong, Kuibao Li, Jing Li, Li Xu and Xinchun Yang

Distribution and diversity of dimetal-carboxylate halogenases in cyanobacteria

Halogenation is a recurring feature in natural products, especially those from marine organisms. The selectivity with which halogenating enzymes act on their substrates renders halogenases interesting targets ...

Authors: Nadia Eusebio, Adriana Rego, Nathaniel R. Glasser, Raquel Castelo-Branco, Emily P. Balskus and Pedro N. Leão

Genome-wide identification, characterization and expression analysis of MATE family genes in apple (Malus × domestica Borkh)

As an important group of the multidrug efflux transporter family, the multidrug and toxic compound extrusion (MATE) family has a wide range of functions and is distributed in all kingdoms of living organisms. ...

Authors: Weihan Zhang, Liao Liao, Jinsheng Xu, Yuepeng Han and Li Li

A validated generally applicable approach using the systematic assessment of disease modules by GWAS reveals a multi-omic module strongly associated with risk factors in multiple sclerosis

There exist few, if any, practical guidelines for predictive and falsifiable multi-omic data integration that systematically integrate existing knowledge. Disease modules are popular concepts for interpreting ...

Authors: Tejaswi V. S. Badam, Hendrik A. de Weerd, David Martínez-Enguita, Tomas Olsson, Lars Alfredsson, Ingrid Kockum, Maja Jagodic, Zelmina Lubovac-Pilav and Mika Gustafsson

Genome-wide association study for deoxynivalenol production and aggressiveness in wheat and rye head blight by resequencing 92 isolates of Fusarium culmorum

Fusarium culmorum is an important pathogen causing head blight of cereals in Europe. This disease is of worldwide importance leading to reduced yield, grain quality, and contamination by mycotoxins. These mycotox...

Authors: Thomas Miedaner, Andrea Vasquez, Valheria Castiblanco, Hilda Elena Castillo, Nora Foroud, Tobias Würschum and Willmar Leiser

Comparative genomic analysis of a naturally born serpentized pig reveals putative mutations related to limb and bone development

It is believed that natural selection acts on the phenotypical changes caused by mutations. Phenotypically, from fishes to amphibians to reptiles, the emergence of limbs greatly facilitates the landing of anci...

Authors: Yankai Jiang, Xinyue Cao and Haibin Wang

Correction to: Genome wide effects of oleic acid on cultured bovine granulosa cells: evidence for the activation of pathways favoring folliculo-luteal transition

Authors: Vengala Rao Yenuganti, Dirk Koczan and Jens Vanselow

Whole genome sequence based capsular typing and antimicrobial resistance prediction of Group B streptococcal isolates from colonized pregnant women in Nigeria

Streptococcus agalactiae (Group B Streptococcus, GBS) is one of the major bacterial pathogens responsible for neonatal sepsis. Whole genome sequencing has, in recent years, emerged as a reliable tool for capsular...

Authors: Mienye Bob-Manuel, Lesley McGee, Jeremiah A Igunma, Mary A Alex-Wele, Orikomaba K Obunge and Kennedy T Wariso

A graphical, interactive and GPU-enabled workflow to process long-read sequencing data

Long-read sequencing has great promise in enabling portable, rapid molecular-assisted cancer diagnoses. A key challenge in democratizing long-read sequencing technology in the biomedical and clinical community...

Authors: Shishir Reddy, Ling-Hong Hung, Olga Sala-Torra, Jerald P. Radich, Cecilia CS Yeung and Ka Yee Yeung

Facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencing

Genome-wide data are invaluable to characterize differentiation and adaptation of natural populations. Reduced representation sequencing (RRS) subsamples a genome repeatedly across many individuals. However, R...

Authors: Henrik Christiansen, Franz M. Heindler, Bart Hellemans, Quentin Jossart, Francesca Pasotti, Henri Robert, Marie Verheye, Bruno Danis, Marc Kochzius, Frederik Leliaert, Camille Moreau, Tasnim Patel, Anton P. Van de Putte, Ann Vanreusel, Filip A. M. Volckaert and Isa Schön

CeTF: an R/Bioconductor package for transcription factor co-expression networks using regulatory impact factors (RIF) and partial correlation and information (PCIT) analysis

Finding meaningful gene-gene interaction and the main Transcription Factors (TFs) in co-expression networks is one of the most important challenges in gene expression data mining.

Authors: Carlos Alberto Oliveira de Biagi Jr, Ricardo Perecin Nociti, Danielle Barbosa Brotto, Breno Osvaldo Funicheli, Patrícia de Cássia Ruy, João Paulo Bianchi Ximenez, David Livingstone Alves Figueiredo and Wilson Araújo Silva Jr

First core microsatellite panel identification in Apennine brown bears (Ursus arctos marsicanus): a collaborative approach

The low cost and rapidity of microsatellite analysis have led to the development of several markers for many species. Because in non-invasive genetics it is recommended to genotype individuals using few loci, ...

Authors: Erminia Scarpulla, Alessio Boattini, Mario Cozzo, Patrizia Giangregorio, Paolo Ciucci, Nadia Mucci, Ettore Randi and Francesca Davoli

Genome-wide analysis of R2R3-MYB transcription factors family in the autopolyploid Saccharum spontaneum: an exploration of dominance expression and stress response

Sugarcane (Saccharum) is the most critical sugar crop worldwide. As one of the most enriched transcription factor families in plants, MYB genes display a great potential to contribute to sugarcane improvement by ...

Authors: Yuan Yuan, Xiping Yang, Mengfan Feng, Hongyan Ding, Muhammad Tahir Khan, Jisen Zhang and Muqing Zhang

Dysregulated long noncoding RNAs in the brainstem of the DBA/1 mouse model of SUDEP

Long noncoding RNAs (lncRNAs) play an important role in many neurological diseases. This study aimed to investigate differentially expressed lncRNAs and messenger RNAs (mRNAs) in the susceptibility gaining pro...

Authors: Deng Chen, Lina Zhu, Xin Lin, Dong Zhou and Ling Liu

Transcriptomic analysis to elucidate the effects of high stocking density on grass carp (Ctenopharyngodon idella)

Grass carp (Ctenopharyngodon idella) is one of the most widely cultivated fishes in China. High stocking density can reportedly affect fish growth and immunity. Herein we performed PacBio long-read single-molecul...

Authors: Yan He, Hongyan Yu, Honggang Zhao, Hua Zhu, Qingjing Zhang, Anqi Wang, Yubang Shen, Xiaoyan Xu and Jiale Li

Experimental Babesia rossi infection induces hemolytic, metabolic, and viral response pathways in the canine host

Babesia rossi is a leading cause of morbidity and mortality among the canine population of sub-Saharan Africa, but pathogenesis remains poorly understood. Previous studies of B. rossi infection were derived from ...

Authors: Rachel L. Smith, Amelia Goddard, Arun Boddapati, Steven Brooks, Johan P. Schoeman, Justin Lack, Andrew Leisewitz and Hans Ackerman

Expanding the potential genes of inborn errors of immunity through protein interactions

Inborn errors of immunity (IEI) are a group of genetic disorders that impair the immune system, with over 400 genes described so far, and hundreds more to be discovered. To facilitate the search for new genes,...

Authors: Humza A. Khan and Manish J. Butte

Transcriptome sequencing and differential expression analysis of seed starch accumulation in Chinese chestnut Metaxenia

Chestnut seeds are important kinds of edible nuts rich in starch and protein. The characteristics and nutrient contents of chestnut have been found to show obvious metaxenia effects in previous studies. To imp...

Authors: Shengxing Li, Zhuogong Shi, Qiurong Zhu, Liang Tao, Wenhui Liang and Zhiheng Zhao

Genome analyses of four Wolbachia strains and associated mitochondria of Rhagoletis cerasi expose cumulative modularity of cytoplasmic incompatibility factors and cytoplasmic hitchhiking across host populations

The endosymbiont Wolbachia can manipulate arthropod reproduction and invade host populations by inducing cytoplasmic incompatibility (CI). Some host species are coinfected with multiple Wolbachia strains which ma...

Authors: Jennifer L. Morrow and Markus Riegler

Mapping of quantitative trait loci underlying a magic trait in ongoing ecological speciation

Telmatochromis temporalis is a cichlid fish endemic to Lake Tanganyika. The normal and dwarf morphs of this fish are a clear example of ongoing ecological speciation, and body size plays an important role in this...

Authors: Tetsumi Takahashi, Atsushi J. Nagano and Teiji Sota

Quantitative analysis of the blood transcriptome of young healthy pigs and its relationship with subsequent disease resilience

Disease resilience, which is the ability of an animal to maintain performance under disease, is important for pigs in commercial herds, where they are exposed to various pathogens. Our objective was to investi...

Authors: Kyu-Sang Lim, Jian Cheng, Austin Putz, Qian Dong, Xuechun Bai, Hamid Beiki, Christopher K. Tuggle, Michael K. Dyck, Pig Gen Canada, Frederic Fortin, John C. S. Harding, Graham S. Plastow and Jack C. M. Dekkers