Articles

Spatial variation in gene expression of Tasmanian devil facial tumors despite minimal host transcriptomic response to infection

Transmissible cancers lie at the intersection of oncology and infectious disease, two traditionally divergent fields for which gene expression studies are particularly useful for identifying the molecular basi...

Authors: Christopher P. Kozakiewicz, Alexandra K. Fraik, Austin H. Patton, Manuel Ruiz-Aravena, David G. Hamilton, Rodrigo Hamede, Hamish McCallum, Paul A. Hohenlohe, Mark J. Margres, Menna E. Jones and Andrew Storfer

Morphological, physiological, and transcriptional responses to low nitrogen stress in Populus deltoides Marsh. clones with contrasting nitrogen use efficiency

Nitrogen (N) is one of the main factors limiting the wood yield in poplar cultivation. Understanding the molecular mechanism of N utilization could play a guiding role in improving the nitrogen use efficiency ...

Authors: Cun Chen, Yanguang Chu, Qinjun Huang, Weixi Zhang, Changjun Ding, Jing Zhang, Bo Li, Tengqian Zhang, Zhenghong Li and Xiaohua Su

Accelerated hematopoietic mitotic aging measured by DNA methylation, blood cell lineage, and Parkinson’s disease

Aging and inflammation are important components of Parkinson’s disease (PD) pathogenesis and both are associated with changes in hematopoiesis and blood cell composition. DNA methylation (DNAm) presents a mech...

Authors: Kimberly C Paul, Alexandra M Binder, Steve Horvath, Cynthia Kusters, Qi Yan, Irish Del Rosario, Yu Yu, Jeff Bronstein and Beate Ritz

The taxonomic distribution of histamine-secreting bacteria in the human gut microbiome

Biogenic histamine plays an important role in immune response, neurotransmission, and allergic response. Although endogenous histamine production has been extensively studied, the contributions of histamine pr...

Authors: Zhongyu Mou, Yiyan Yang, A. Brantley Hall and Xiaofang Jiang

Genetic changes involving the coral gastrovascular system support the transition between colonies and bailed-out polyps: evidence from a Pocillopora acuta transcriptome

A coral colony is composed of physiologically integrated polyps. In stony corals, coloniality adopts a wide diversity of forms and involves complex ontogenetic dynamics. However, molecular mechanisms underlyin...

Authors: Po-Shun Chuang and Satoshi Mitarai

Comparison of the transcriptome in circulating leukocytes in early lactation between primiparous and multiparous cows provides evidence for age-related changes

Previous studies have identified many immune pathways which are consistently altered in humans and model organisms as they age. Dairy cows are often culled at quite young ages due to an inability to cope adequ...

Authors: Laura Buggiotti, Zhangrui Cheng, Mazdak Salavati and Claire D. Wathes

CAMPAREE: a robust and configurable RNA expression simulator

The accurate interpretation of RNA-Seq data presents a moving target as scientists continue to introduce new experimental techniques and analysis algorithms. Simulated datasets are an invaluable tool to accura...

Authors: Nicholas F. Lahens, Thomas G. Brooks, Dimitra Sarantopoulou, Soumyashant Nayak, Cris Lawrence, Antonijo Mrčela, Anand Srinivasan, Jonathan Schug, John B. Hogenesch, Yoseph Barash and Gregory R. Grant

Unveiling the transcriptomic complexity of Miscanthus sinensis using a combination of PacBio long read- and Illumina short read sequencing platforms

Miscanthus sinensis Andersson is a perennial grass that exhibits remarkable lignocellulose characteristics suitable for sustainable bioenergy production. However, knowledge of the genetic resources of this specie...

Authors: Yongli Wang, Xia Li, Congsheng Wang, Lu Gao, Yanfang Wu, Xingnan Ni, Jianzhong Sun and Jianxiong Jiang

SCReadCounts: estimation of cell-level SNVs expression from scRNA-seq data

Recent studies have demonstrated the utility of scRNA-seq SNVs to distinguish tumor from normal cells, characterize intra-tumoral heterogeneity, and define mutation-associated expression signatures. In additio...

Authors: N. M. Prashant, Nawaf Alomran, Yu Chen, Hongyu Liu, Pavlos Bousounis, Mercedeh Movassagh, Nathan Edwards and Anelia Horvath

A single chromosome strain of S. cerevisiae exhibits diminished ethanol metabolism and tolerance

Eukaryotic organisms, like the model yeast S. cerevisiae, have linear chromosomes that facilitate organization and protection of nuclear DNA. A recent work described a stepwise break/repair method that enabled fu...

Authors: Tyler W. Doughty, Rosemary Yu, Lucy Fang-I Chao, Zhongjun Qin, Verena Siewers and Jens Nielsen

Transcriptional profiling reveals changes in gene regulation and signaling transduction pathways during temperature stress in wucai (Brassica campestris L.)

Wucai (Brassica campestris L. ssp. chinensis var. rosularis Tsen) is a cold-tolerant plant that is vulnerable to high temperature. This study explored the response mechanism of wucai to low temperature. In this s...

Authors: Lingyun Yuan, Yushan Zheng, Libing Nie, Liting Zhang, Ying Wu, Shidong Zhu, Jinfeng Hou, Guo Lei Shan, Tong Kun Liu, Guohu Chen, Xiaoyan Tang and Chenggang Wang

Culture and genome-based analysis of four soil Clostridium isolates reveal their potential for antimicrobial production

Soil bacteria are a major source of specialized metabolites including antimicrobial compounds. Yet, one of the most diverse genera of bacteria ubiquitously present in soil, Clostridium, has been largely overlooke...

Authors: Amila S. N. W. Pahalagedara, Ruy Jauregui, Paul Maclean, Eric Altermann, Steve Flint, Jon Palmer, Gale Brightwell and Tanushree Barua Gupta

Revelation of candidate genes and molecular mechanism of reproductive seasonality in female rohu (Labeo rohita Ham.) by RNA sequencing

Carp fish, rohu (Labeo rohita Ham.) is important freshwater aquaculture species of South-East Asia having seasonal reproductive rhythm. There is no holistic study at transcriptome level revealing key candidate ge...

Authors: Sarika Jaiswal, Samiran Nandi, Mir Asif Iquebal, Rahul Singh Jasrotia, Sunita Patra, Gayatri Mishra, Uday Kumar Udit, Dinesh Kumar Sahu, U. B. Angadi, Prem Kumar Meher, Padmanav Routray, Jitendra Kumar Sundaray, Dhananjay Kumar Verma, Paramananda Das, Pallipuram Jayasankar, Anil Rai…

Transcriptome and metabolome analysis reveals anthocyanin biosynthesis pathway associated with ramie (Boehmeria nivea (L.) Gaud.) leaf color formation

The bast fiber crop ramie can be used as high-quality forage resources, especially in tropical or subtropical region where there is lack of high-quality protein feed. Hongxuan No.1 (HX_1) is a unique ramie var...

Authors: Xinkang Feng, Gang Gao, Chunming Yu, Aiguo Zhu, Jikang Chen, Kunmei Chen, Xiaofei Wang, Aminu Shehu Abubakar and Ping Chen

Characterization of the chicken T cell receptor γ repertoire by high-throughput sequencing

As one of “γδ-high” species, chicken is an excellent model for the study of γδ T cells in non-mammalian animals. However, a comprehensive characterization of the TCRγδ repertoire is still missing in chicken. The ...

Authors: Tongtong Zhang, Qian Li, Xiaoqing Li, Li Kang, Yunliang Jiang and Yi Sun

Genome-wide identification and characterization of the BES/BZR gene family in wheat and foxtail millet

BES/BZR family genes have vital roles in plant growth, development, and adaptation to environmental stimuli. However, they have not yet been characterized and systematically analyzed in wheat and foxtail millet.

Authors: Dan Liu, Yanjiao Cui, Zilong Zhao, Suying Li, Dan Liang, Conglei Wang, Gang Feng, Jianhe Wang and Zhengli Liu

Transcriptome profiling of Malus sieversii under freezing stress after being cold-acclimated

Freezing temperatures are an abiotic stress that has a serious impact on plant growth and development in temperate regions and even threatens plant survival. The wild apple tree (Malus sieversii) needs to undergo...

Authors: Ping Zhou, Xiaoshuang Li, Xiaojie Liu, Xuejing Wen, Yan Zhang and Daoyuan Zhang

Genome sequencing of the neotype strain CBS 554.65 reveals the MAT1–2 locus of Aspergillus niger

Aspergillus niger is a ubiquitous filamentous fungus widely employed as a cell factory thanks to its abilities to produce a wide range of organic acids and enzymes. Its genome was one of the first Aspergillus gen...

Authors: Valeria Ellena, Sjoerd J. Seekles, Gabriel A. Vignolle, Arthur F. J. Ram and Matthias G. Steiger

Runs of homozygosity analysis reveals consensus homozygous regions affecting production traits in Chinese Simmental beef cattle

Genomic regions with a high frequency of runs of homozygosity (ROH) are related to important traits in farm animals. We carried out a comprehensive analysis of ROH and evaluated their association with producti...

Authors: Guoyao Zhao, Yuqiang Liu, Qunhao Niu, Xu Zheng, Tianliu Zhang, Zezhao Wang, Lei Xu, Bo Zhu, Xue Gao, Lupei Zhang, Huijiang Gao, Junya Li and Lingyang Xu

The molecular interplay of the establishment of an infection – gene expression of Diaphorina citri gut and Candidatus Liberibacter asiaticus

Candidatus Liberibacter asiaticus (CLas) is one the causative agents of greening disease in citrus, an unccurable, devastating disease of citrus worldwide. CLas is vectored by Diaphorina citri, and the understand...

Authors: Flavia Moura Manoel Bento, Josiane Cecília Darolt, Bruna Laís Merlin, Leandro Penã, Nelson Arno Wulff and Fernando Luis Cônsoli

Elevated transcription of transposable elements is accompanied by het-siRNA-driven de novo DNA methylation in grapevine embryogenic callus

Somatic variation is a valuable source of trait diversity in clonally propagated crops. In grapevine, which has been clonally propagated worldwide for centuries, important phenotypes such as white berry colour...

Authors: Darrell Lizamore, Ross Bicknell and Chris Winefield

Characterization and genomic analysis of the first Oceanospirillum phage, vB_OliS_GJ44, representing a novel siphoviral cluster

Marine bacteriophages play key roles in the community structure of microorganisms, biogeochemical cycles, and the mediation of genetic diversity through horizontal gene transfer. Recently, traditional isolatio...

Authors: Wenjing Zhang, Yantao Liang, Kaiyang Zheng, Chengxiang Gu, Yundan Liu, Ziyue Wang, Xinran Zhang, Hongbing Shao, Yong Jiang, Cui Guo, Hui He, Hualong Wang, Yeong Yik Sung, Wen Jye Mok, Yuzhong Zhang, Andrew McMinn…

Genome-wide identification and expression profile under abiotic stress of the barley non-specific lipid transfer protein gene family and its Qingke Orthologues

Plant non-specific lipid transfer proteins (nsLTPs), a group of small, basic ubiquitous proteins to participate in lipid transfer, cuticle formation and stress response, are involved in the regulation of plant...

Authors: Jiecuo Duo, Huiyan Xiong, Xiongxiong Wu, Yuan Li, Jianping Si, Chao Zhang and Ruijun Duan

Recombination mapping of the Brazilian stingless bee Frieseomelitta varia confirms high recombination rates in social hymenoptera

Meiotic recombination is a fundamental genetic process that shuffles allele combinations and promotes accurate segregation of chromosomes. Analyses of the ubiquitous variation of recombination rates within and...

Authors: Prashant Waiker, Fabiano Carlos Pinto de Abreu, Danielle Luna-Lucena, Flávia Cristina Paula Freitas, Zilá Luz Paulino Simões and Olav Rueppell

A complete mitochondrial genome for fragrant Chinese rosewood (Dalbergia odorifera, Fabaceae) with comparative analyses of genome structure and intergenomic sequence transfers

Dalbergia odorifera is an economically and culturally important species in the Fabaceae because of the high-quality lumber and traditional Chinese medicines made from this plant, however, overexploitation has inc...

Authors: Zhou Hong, Xuezhu Liao, Yuanjun Ye, Ningnan Zhang, Zengjiang Yang, Weidong Zhu, Wei Gao, Joel Sharbrough, Luke R. Tembrock, Daping Xu and Zhiqiang Wu

Altered expression of microRNAs in the rat diaphragm in a model of ventilator-induced diaphragm dysfunction after controlled mechanical ventilation

Ventilator-induced diaphragm dysfunction (VIDD) is a common complication of life support by mechanical ventilation observed in critical patients in clinical practice and may predispose patients to severe compl...

Authors: Pengcheng Wang, Xianlong Zhou, Gang Li, Haoli Ma, Ruining Liu and Yan Zhao

Integrative analyses of targeted metabolome and transcriptome of Isatidis Radix autotetraploids highlighted key polyploidization-responsive regulators

Isatidis Radix, the root of Isatis indigotica Fort. (Chinese woad) can produce a variety of efficacious compound with medicinal properties. The tetraploid I. indigotica plants exhibit superior phenotypic traits, ...

Authors: Zixuan Zhang, Mingpu Tan, Yingying Zhang, Yue Jia, Shuxian Zhu, Jiang Wang, Jiajing Zhao, Yueyue Liao and Zengxu Xiang

DNA damage repair system in C57BL/6 J mice is evolutionarily stable

DNA damage repair (DDR) system is vital in maintaining genome stability and survival. DDR consists of over 160 genes in 7 different pathways to repair specific type of DNA damage caused by external and interna...

Authors: Xiaoyu Wang and San Ming Wang

Brain-derived neurotrophic factor gene variants and obesity in former smokers

From genome-wide association studies, brain-derived neurotrophic factor (BDNF) locus on chromosome 11 was the only SNP associated with both smoking and body mass index (BMI) in European, African and Asian populat...

Authors: Shan-shan Yang, Yao He, Lin Xu, Yali Jin, Wei-sen Zhang, Chao-qiang Jiang, Kar Keung Cheng and Tai Hing Lam

Microbial trend analysis for common dynamic trend, group comparison, and classification in longitudinal microbiome study

The human microbiome is inherently dynamic and its dynamic nature plays a critical role in maintaining health and driving disease. With an increasing number of longitudinal microbiome studies, scientists are e...

Authors: Chan Wang, Jiyuan Hu, Martin J. Blaser and Huilin Li

Genome collinearity analysis illuminates the evolution of donkey chromosome 1 and horse chromosome 5 in perissodactyls: A comparative study

It is important to resolve the evolutionary history of species genomes as it has affected both genome organization and chromosomal architecture. The rapid innovation in sequencing technologies and the improvem...

Authors: Shaohua Li, Gaoping Zhao, Hongmei Han, Yunxia Li, Jun Li, Jinfeng Wang, Guifang Cao and Xihe Li

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