Articles

The effect of methanol fixation on single-cell RNA sequencing data

Single-cell RNA sequencing (scRNA-seq) has led to remarkable progress in our understanding of tissue heterogeneity in health and disease. Recently, the need for scRNA-seq sample fixation has emerged in many sc...

Authors: Xinlei Wang, Lei Yu and Angela Ruohao Wu

TMT-based quantitative proteomics analysis reveals the key proteins related with the differentiation process of goat intramuscular adipocytes

Intramuscular adipocytes differentiation is a complex process, which is regulated by various transcription factor, protein factor regulators and signal transduction pathways. However, the proteins and signal p...

Authors: Yu Du, Yong Wang, Qing Xu, Jiangjiang Zhu and Yaqiu Lin

Transcriptome analysis provides insights into copper toxicology in piebald naked carp (Gymnocypris eckloni)

Copper was used for many years in aquaculture operations as an effective algaecide or a parasite treatment of fish. It is an essential nutrient with numerous functions in organisms, but is toxic at high concen...

Authors: Wenjie Jin, Zixuan Li, Fengxia Ran, Shen Huang, Kefan Huo, Jianjuan Li, Qingshuo Han, Guojie Wang, Zhenji Wang, Shenlong Jian, Kemao Li and Changzhong Li

SnoRNA copy regulation affects family size, genomic location and family abundance levels

Small nucleolar RNAs (snoRNAs) are an abundant class of noncoding RNAs present in all eukaryotes and best known for their involvement in ribosome biogenesis. In mammalian genomes, many snoRNAs exist in multipl...

Authors: Danny Bergeron, Cédric Laforest, Stacey Carpentier, Annabelle Calvé, Étienne Fafard-Couture, Gabrielle Deschamps-Francoeur and Michelle S. Scott

Exposure to hypoxia causes stress erythropoiesis and downregulates immune response genes in spleen of mice

The spleen is the largest secondary lymphoid organ and the main site where stress erythropoiesis occurs. It is known that hypoxia triggers the expansion of erythroid progenitors; however, its effects on spleni...

Authors: Haijing Wang, Daoxin Liu, Pengfei Song, Feng Jiang, Xiangwen Chi and Tongzuo Zhang

Long non-coding RNA exploration for mesenchymal stem cell characterisation

The development of RNA sequencing (RNAseq) and the corresponding emergence of public datasets have created new avenues of transcriptional marker search. The long non-coding RNAs (lncRNAs) constitute an emergin...

Authors: Sébastien Riquier, Marc Mathieu, Chloé Bessiere, Anthony Boureux, Florence Ruffle, Jean-Marc Lemaitre, Farida Djouad, Nicolas Gilbert and Thérèse Commes

Transcriptomic analysis of caecal tissue in inbred chicken lines that exhibit heritable differences in resistance to Campylobacter jejuni

Campylobacter jejuni is the leading cause of bacterial gastroenteritis in humans and the handling or consumption of contaminated poultry meat is a key source of infection. Selective breeding of poultry that exhib...

Authors: Kay M. Russell, Jacqueline Smith, Abi Bremner, Cosmin Chintoan-Uta, Lonneke Vervelde, Androniki Psifidi and Mark P. Stevens

Transcriptional dynamics of transposable elements when converting fibroblast cells of Macaca mulatta to neuroepithelial stem cells

Transposable elements (TE) account for more than 50% of human genome. It has been reported that some types of TEs are dynamically regulated in the reprogramming of human cell lines. However, it is largely unkn...

Authors: Dahai Liu, Li Liu, Kui Duan, Junqiang Guo, Shipeng Li, Zhigang Zhao, Xiaotuo Zhang, Nan Zhou and Yun Zheng

Historical genomics reveals the evolutionary mechanisms behind multiple outbreaks of the host-specific coffee wilt pathogen Fusarium xylarioides

Nearly 50% of crop yields are lost to pests and disease, with plants and pathogens locked in an amplified co-evolutionary process of disease outbreaks. Coffee wilt disease, caused by Fusarium xylarioides, decimat...

Authors: Lily D. Peck, Reuben W. Nowell, Julie Flood, Matthew J. Ryan and Timothy G. Barraclough

Distinctive gene expression patterns and imprinting signatures revealed in reciprocal crosses between cattle sub-species

There are two genetically distinct subspecies of cattle, Bos taurus taurus and Bos taurus indicus, which arose from independent domestication events. The two types of cattle show substantial phenotypic difference...

Authors: Ruijie Liu, Rick Tearle, Wai Yee Low, Tong Chen, Dana Thomsen, Timothy P. L. Smith, Stefan Hiendleder and John L. Williams

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

Diapause is a seasonal dormancy that allows organisms to survive unfavorable conditions and optimizes the timing of reproduction and growth. Emergence from diapause reverses the state of arrested development a...

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

The global gene expression outline of the bovine blastocyst: reflector of environmental conditions and predictor of developmental capacity

Morphological evaluation of embryos has been used to screen embryos for transfer. However, the repeatability and accuracy of this method remains low. Thus, evaluation of an embryo’s gene expression signature w...

Authors: Dessie Salilew-Wondim, Dawit Tesfaye, Franca Rings, Eva Held-Hoelker, Dennis Miskel, Marc-Andre Sirard, Ernst Tholen, Karl Schellander and Michael Hoelker

Cruxome: a powerful tool for annotating, interpreting and reporting genetic variants

Next-generation sequencing (NGS) is an efficient tool used for identifying pathogenic variants that cause Mendelian disorders. However, the lack of bioinformatics training of researchers makes the interpretati...

Authors: Qingmei Han, Ying Yang, Shengyang Wu, Yingchun Liao, Shuang Zhang, Hongbin Liang, David S. Cram and Yu Zhang

Metagenomic diagnosis of severe psittacosis using multiple sequencing platforms

Chlamydia psittaci is an avian pathogen that can cause lethal human infections. Diagnosis of C. psittaci pneumonia is often delayed due to nonspecific clinical presentations and limited laboratory diagnostic tech...

Authors: Kaiying Wang, Xiong Liu, Huiying Liu, Peihan Li, Yanfeng Lin, Dongdong Yin, Lang Yang, Jinhui Li, Shenlong Li, Leili Jia, Changqing Bai, Yongqiang Jiang, Peng Li and Hongbin Song

Complete genome sequence of Arthrobacter sp. PAMC25564 and its comparative genome analysis for elucidating the role of CAZymes in cold adaptation

The Arthrobacter group is a known set of bacteria from cold regions, the species of which are highly likely to play diverse roles at low temperatures. However, their survival mechanisms in cold regions such as An...

Authors: So-Ra Han, Byeollee Kim, Jong Hwa Jang, Hyun Park and Tae-Jin Oh

Mendelian randomization studies of brain MRI yield insights into the pathogenesis of neuropsychiatric disorders

Observational studies have identified various associations between neuroimaging alterations and neuropsychiatric disorders. However, whether such associations could truly reflect causal relations remains still...

Authors: Weichen Song, Wei Qian, Weidi Wang, Shunying Yu and Guan Ning Lin

Identifying genomic islands with deep neural networks

Horizontal gene transfer is the main source of adaptability for bacteria, through which genes are obtained from different sources including bacteria, archaea, viruses, and eukaryotes. This process promotes the...

Authors: Rida Assaf, Fangfang Xia and Rick Stevens

Characterizing the oligogenic architecture of plant growth phenotypes informs genomic selection approaches in a common wheat population

Genetic variation in growth over the course of the season is a major source of grain yield variation in wheat, and for this reason variants controlling heading date and plant height are among the best-characte...

Authors: Noah DeWitt, Mohammed Guedira, Edwin Lauer, J. Paul Murphy, David Marshall, Mohamed Mergoum, Jerry Johnson, James B. Holland and Gina Brown-Guedira

Whole-genome resequencing provides insights into the population structure and domestication signatures of ducks in eastern China

Duck is an ancient domesticated animal with high economic value, used for its meat, eggs, and feathers. However, the origin of indigenous Chinese ducks remains elusive. To address this question, we performed w...

Authors: Peishi Feng, Tao Zeng, Hua Yang, Guohong Chen, Jinping Du, Li Chen, Junda Shen, Zhenrong Tao, Ping Wang, Lin Yang and Lizhi Lu

The holobiont transcriptome of teneral tsetse fly species of varying vector competence

Tsetse flies are the obligate vectors of African trypanosomes, which cause Human and Animal African Trypanosomiasis. Teneral flies (newly eclosed adults) are especially susceptible to parasite establishment an...

Authors: Miguel Medina Munoz, Caitlyn Brenner, Dylan Richmond, Noah Spencer and Rita V. M. Rio

Comparative neurotranscriptomics reveal widespread species differences associated with bonding

Pair bonding with a reproductive partner is rare among mammals but is an important feature of human social behavior. Decades of research on monogamous prairie voles (Microtus ochrogaster), along with comparative ...

Authors: Joel A. Tripp, Alejandro Berrio, Lisa A. McGraw, Mikhail V. Matz, Jamie K. Davis, Kiyoshi Inoue, James W. Thomas, Larry J. Young and Steven M. Phelps

Conformational epitope matching and prediction based on protein surface spiral features

A conformational epitope (CE) is composed of neighboring amino acid residues located on an antigenic protein surface structure. CEs bind their complementary paratopes in B-cell receptors and/or antibodies. An ...

Authors: Ying-Tsang Lo, Tao-Chuan Shih, Tun-Wen Pai, Li-Ping Ho, Jen-Leih Wu and Hsin-Yiu Chou

Detection of copy number variants in African goats using whole genome sequence data

Copy number variations (CNV) are a significant source of variation in the genome and are therefore essential to the understanding of genetic characterization. The aim of this study was to develop a fine-scaled...

Authors: Wilson Nandolo, Gábor Mészáros, Maria Wurzinger, Liveness J. Banda, Timothy N. Gondwe, Henry A. Mulindwa, Helen N. Nakimbugwe, Emily L. Clark, M. Jennifer Woodward-Greene, Mei Liu, George E. Liu, Curtis P. Van Tassell, Benjamin D. Rosen and Johann Sölkner

LncRNA:DNA triplex-forming sites are positioned at specific areas of genome organization and are predictors for Topologically Associated Domains

Chromosomes are organized into units called topologically associated domains (TADs). TADs dictate regulatory landscapes and other DNA-dependent processes. Even though various factors that contribute to the spe...

Authors: Benjamin Soibam and Ayzhamal Zhamangaraeva

RNA-Seq analysis of blood meal induced gene-expression changes in Aedes aegypti ovaries

Transmission of pathogens by vector mosquitoes is intrinsically linked with mosquito’s reproductive strategy because anautogenous mosquitoes require vertebrate blood to develop a batch of eggs. Each cycle of e...

Authors: Dilip K. Nag, Constentin Dieme, Pascal Lapierre, Erica Lasek-Nesselquist and Laura D. Kramer

Genome-wide identification of the DUF668 gene family in cotton and expression profiling analysis of GhDUF668 in Gossypium hirsutum under adverse stress

Domain of unknown function 668 (DUF668) may play a crucial role in the plant growth and developmental response to adverse stress. However, our knowledge of the function of the DUF668 gene family is limited.

Authors: Jieyin Zhao, Peng Wang, Wenju Gao, Yilei Long, Yuxiang Wang, Shiwei Geng, Xuening Su, Yang Jiao, Quanjia Chen and Yanying Qu

Transcriptomic insights into the effects of CytCo, a novel nematotoxic protein, on the pine wood nematode Bursaphelenchus xylophilus

The pine wood nematode Bursaphelenchus xylophilus is a destructive pest of Pinus trees worldwide and lacks effective control measures. Screening for nematotoxic proteins has been undertaken to develop new strateg...

Authors: Ye Chen, Xiang Zhou, Kai Guo, Sha-Ni Chen and Xiu Su

Rapid sequence evolution driven by transposable elements at a virulence locus in a fungal wheat pathogen

Plant pathogens cause substantial crop losses in agriculture production and threaten food security. Plants evolved the ability to recognize virulence factors and pathogens have repeatedly escaped recognition d...

Authors: Nikhil Kumar Singh, Thomas Badet, Leen Abraham and Daniel Croll

In silico characterization of putative gene homologues involved in somatic embryogenesis suggests that some conifer species may lack LEC2, one of the key regulators of initiation of the process

Somatic embryogenesis (SE) is the process in which somatic embryos develop from somatic tissue in vitro on medium in most cases supplemented with growth regulators. Knowledge of genes involved in regulation of...

Authors: Sonali Sachin Ranade and Ulrika Egertsdotter

Growth inhibition of Spodoptera frugiperda larvae by camptothecin correlates with alteration of the structures and gene expression profiles of the midgut

Spodoptera frugiperda is a serious pest that causes devastating losses to many major crops, including corn, rice, sugarcane, and peanut. Camptothecin (CPT) is a bioactive secondary metabolite of the woody plant C...

Authors: Benshui Shu, Yan Zou, Haikuo Yu, Wanying Zhang, Xiangli Li, Liang Cao and Jintian Lin

Identification of cis-regulatory motifs in first introns and the prediction of intron-mediated enhancement of gene expression in Arabidopsis thaliana

Intron mediated enhancement (IME) is the potential of introns to enhance the expression of its respective gene. This essential function of introns has been observed in a wide range of species, including fungi,...

Authors: Georg Back and Dirk Walther

Evaluating the accuracy of Listeria monocytogenes assemblies from quasimetagenomic samples using long and short reads

Whole genome sequencing of cultured pathogens is the state of the art public health response for the bioinformatic source tracking of illness outbreaks. Quasimetagenomics can substantially reduce the amount of...

Authors: Seth Commichaux, Kiran Javkar, Padmini Ramachandran, Niranjan Nagarajan, Denis Bertrand, Yi Chen, Elizabeth Reed, Narjol Gonzalez-Escalona, Errol Strain, Hugh Rand, Mihai Pop and Andrea Ottesen

Population transcriptomic sequencing reveals allopatric divergence and local adaptation in Pseudotaxus chienii (Taxaceae)

Elucidating the effects of geography and selection on genetic variation is critical for understanding the relative importance of adaptation in driving differentiation and identifying the environmental factors ...

Authors: Li Liu, Zhen Wang, Yingjuan Su and Ting Wang

Inferring and analyzing gene regulatory networks from multi-factorial expression data: a complete and interactive suite

High-throughput transcriptomic datasets are often examined to discover new actors and regulators of a biological response. To this end, graphical interfaces have been developed and allow a broad range of users...

Authors: Océane Cassan, Sophie Lèbre and Antoine Martin

Genetic analysis of three maize husk traits by QTL mapping in a maize-teosinte population

The maize husk consists of numerous leafy layers and plays vital roles in protecting the ear from pathogen infection and dehydration. Teosinte, the wild ancestor of maize, has about three layers of small husk ...

Authors: Xiaolei Zhang, Ming Lu, Aiai Xia, Tao Xu, Zhenhai Cui, Ruiying Zhang, Wenguo Liu and Yan He

Secretome characterization of clinical isolates from the Mycobacterium abscessus complex provides insight into antigenic differences

Mycobacterium abscessus (MAB) is a widely disseminated pathogenic non-tuberculous mycobacterium (NTM). Like with the M. tuberculosis complex (MTBC), excreted / secreted (ES) proteins play an essential role for it...

Authors: Fernanda Cornejo-Granados, Thomas A. Kohl, Flor Vásquez Sotomayor, Sönke Andres, Rogelio Hernández-Pando, Juan Manuel Hurtado-Ramirez, Christian Utpatel, Stefan Niemann, Florian P. Maurer and Adrian Ochoa-Leyva

Correction to: Phenotype and multi-omics comparison of Staphylococcus and Streptococcus uncovers pathogenic traits and predicts zoonotic potential

Authors: Niels A. Zondervan, Vitor A. P. Martins dos Santos, Maria Suarez-Diez and Edoardo Saccenti

De novo transcriptome sequencing and anthocyanin metabolite analysis reveals leaf color of Acer pseudosieboldianum in autumn

Leaf color is an important ornamental trait of colored-leaf plants. The change of leaf color is closely related to the synthesis and accumulation of anthocyanins in leaves. Acer pseudosieboldianum is a colored-le...

Authors: Yu-Fu Gao, Dong-Hui Zhao, Jia-Qi Zhang, Jia-Shuo Chen, Jia-Lin Li, Zhuo Weng and Li-Ping Rong

Chromosome-level genome assembly and manually-curated proteome of model necrotroph Parastagonospora nodorum Sn15 reveals a genome-wide trove of candidate effector homologs, and redundancy of virulence-related functions within an accessory chromosome

The fungus Parastagonospora nodorum causes septoria nodorum blotch (SNB) of wheat (Triticum aestivum) and is a model species for necrotrophic plant pathogens. The genome assembly of reference isolate Sn15 was fir...

Authors: Stefania Bertazzoni, Darcy A. B. Jones, Huyen T. Phan, Kar-Chun Tan and James K. Hane

Genome-wide association analysis reveals that EDNRB2 causes a dose-dependent loss of pigmentation in ducks

Birds have various plumage color patterns, and spot is a common phenotype. Herein, we conducted genome-wide association studies (GWAS) in a population of 225 ducks with different sized black spots to reveal th...

Authors: Yang Xi, Qian Xu, Qin Huang, Shengchao Ma, Yushi Wang, Chunchun Han, Rongping Zhang, Jiwen Wang, Hehe Liu and Liang Li

Transcriptomic and metabolomic characterization of post-hatch metabolic reprogramming during hepatic development in the chicken

Artificial selection of modern meat-producing chickens (broilers) for production characteristics has led to dramatic changes in phenotype, yet the impact of this selection on metabolic and molecular mechanisms...

Authors: Heidi A. Van Every and Carl J. Schmidt

Re-examination of two diatom reference genomes using long-read sequencing

The marine diatoms Thalassiosira pseudonana and Phaeodactylum tricornutum are valuable model organisms for exploring the evolution, diversity and ecology of this important algal group. Their reference genomes, pu...

Authors: Gina V. Filloramo, Bruce A. Curtis, Emma Blanche and John M. Archibald

A new mouse SNP genotyping assay for speed congenics: combining flexibility, affordability, and power

Speed congenics is an important tool for creating congenic mice to investigate gene functions, but current SNP genotyping methods for speed congenics are expensive. These methods usually rely on chip or array ...

Authors: Kimberly R. Andrews, Samuel S. Hunter, Brandi K. Torrevillas, Nora Céspedes, Sarah M. Garrison, Jessica Strickland, Delaney Wagers, Gretchen Hansten, Daniel D. New, Matthew W. Fagnan and Shirley Luckhart

A comparative analysis of the intrauterine transcriptome in fertile and subfertile mares using cytobrush sampling

Subfertility is a major problem in modern horse breeding. Especially, mares without clinical signs of reproductive diseases, without known uterine pathogens and no evidence of inflammation but not becoming pre...

Authors: Katharina S. Weber, Karen Wagener, Miguel Blanco, Stefan Bauersachs and Heinrich Bollwein

The Rhododendron Plant Genome Database (RPGD): a comprehensive online omics database for Rhododendron

The genus Rhododendron L. has been widely cultivated for hundreds of years around the world. Members of this genus are known for great ornamental and medicinal value. Owing to advances in sequencing technology, g...

Authors: Ningyawen Liu, Lu Zhang, Yanli Zhou, Mengling Tu, Zhenzhen Wu, Daping Gui, Yongpeng Ma, Jihua Wang and Chengjun Zhang

Genome-wide identification and expression analysis of the WRKY transcription factor family in flax (Linum usitatissimum L.)

Members of the WRKY protein family, one of the largest transcription factor families in plants, are involved in plant growth and development, signal transduction, senescence, and stress resistance. However, li...

Authors: Hongmei Yuan, Wendong Guo, Lijuan Zhao, Ying Yu, Si Chen, Lei Tao, Lili Cheng, Qinghua Kang, Xixia Song, Jianzhong Wu, Yubo Yao, Wengong Huang, Ying Wu, Yan Liu, Xue Yang and Guangwen Wu

Transcriptome analysis reveals potential function of long non-coding RNAs in 20-hydroxyecdysone regulated autophagy in Bombyx mori

20-hydroxyecdysone (20E) plays important roles in insect molting and metamorphosis. 20E-induced autophagy has been detected during the larval–pupal transition in different insects. In Bombyx mori, autophagy is in...

Authors: Huili Qiao, Jingya Wang, Yuanzhuo Wang, Juanjuan Yang, Bofan Wei, Miaomiao Li, Bo Wang, Xiaozhe Li, Yang Cao, Ling Tian, Dandan Li, Lunguang Yao and Yunchao Kan

Genome analysis of Spiroplasma citri strains from different host plants and its leafhopper vectors

Spiroplasma citri comprises a bacterial complex that cause diseases in citrus, horseradish, carrot, sesame, and also infects a wide array of ornamental and weed species. S. citri is transmitted in a persistent pr...

Authors: Rachel Rattner, Shree Prasad Thapa, Tyler Dang, Fatima Osman, Vijayanandraj Selvaraj, Yogita Maheshwari, Deborah Pagliaccia, Andres S. Espindola, Subhas Hajeri, Jianchi Chen, Gitta Coaker, Georgios Vidalakis and Raymond Yokomi

The dissection of R genes and locus Pc5.1 in Phytophthora capsici infection provides a novel view of disease resistance in peppers

Phytophthora capsici root rot (PRR) is a disastrous disease in peppers (Capsicum spp.) caused by soilborne oomycete with typical symptoms of necrosis and constriction at the basal stem and consequent plant wiltin...

Authors: Jin-Song Du, Lin-Feng Hang, Qian Hao, Hai-Tao Yang, Siyad Ali, Radwa Salah Ezaat Badawy, Xiao-Yu Xu, Hua-Qiang Tan, Li-Hong Su, Huan-Xiu Li, Kai-Xi Zou, Yu Li, Bo Sun, Li-Jin Lin and Yun-Song Lai

Correction to: Comparative analysis of chloroplast genomes of cultivars and wild species of sweetpotato (Ipomoea batatas [L.] Lam)

Authors: Shizhuo Xiao, Pan Xu, Yitong Deng, Xibin Dai, Lukuan Zhao, Bettina Heider, An Zhang, Zhilin Zhou and Qinghe Cao