Articles

Venom-gland transcriptomic, venomic, and antivenomic profiles of the spine-bellied sea snake (Hydrophis curtus) from the South China Sea

A comprehensive evaluation of the -omic profiles of venom is important for understanding the potential function and evolution of snake venom. Here, we conducted an integrated multi-omics-analysis to unveil the...

Authors: Hong-Yan Zhao, Lin Wen, Yu-Feng Miao, Yu Du, Yan Sun, Yin Yin, Chi-Xian Lin, Long-Hui Lin, Xiang Ji and Jian-Fang Gao

Amino acid transporter (AAT) gene family in foxtail millet (Setaria italica L.): widespread family expansion, functional differentiation, roles in quality formation and response to abiotic stresses

Amino acid transporters (AATs) plays an essential roles in growth and development of plants, including amino acids long-range transport, seed germination, quality formation, responsiveness to pathogenic bacter...

Authors: Yang Yang, Yongmao Chai, Jiayi Liu, Jie Zheng, Zhangchen Zhao, Aduragbemi Amo, Chunge Cui, Qiumei Lu, Liang Chen and Yin-Gang Hu

Mendelian randomization analysis identified genes pleiotropically associated with central corneal thickness

To prioritize genes that were pleiotropically or potentially causally associated with central corneal thickness (CCT).

Authors: Zhikun Yang, Jingyun Yang, Di Liu and Weihong Yu

Selection of functional EPHB2 genotypes from ENU mutated grass carp treated with GCRV

N-ethyl-N-nitrosourea (ENU) mutagenesis is a useful method for the genetic engineering of plants, and the production of functional mutants in animal models including mice and zebrafish. Grass carp reovirus (GCRV)...

Authors: Meher un Nissa, Zhu-Xiang Jiang, Guo-Dong Zheng and Shu-Ming Zou

Correction to: 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

Authors: Sonali Sachin Ranade and Ulrika Egertsdotter

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

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

Sequoia: an interactive visual analytics platform for interpretation and feature extraction from nanopore sequencing datasets

Direct-sequencing technologies, such as Oxford Nanopore’s, are delivering long RNA reads with great efficacy and convenience. These technologies afford an ability to detect post-transcriptional modifications a...

Authors: Ratanond Koonchanok, Swapna Vidhur Daulatabad, Quoseena Mir, Khairi Reda and Sarath Chandra Janga

Genomic prediction with non-additive effects in beef cattle: stability of variance component and genetic effect estimates against population size

Genomic prediction is now an essential technology for genetic improvement in animal and plant breeding. Whereas emphasis has been placed on predicting the breeding values, the prediction of non-additive geneti...

Authors: Akio Onogi, Toshio Watanabe, Atsushi Ogino, Kazuhito Kurogi and Kenji Togashi

The CCCH zinc finger family of soybean (Glycine max L.): genome-wide identification, expression, domestication, GWAS and haplotype analysis

The CCCH zinc finger (zf_CCCH) is a unique subfamily featured one or more zinc finger motif(s) comprising of three Cys and one His residues. The zf_CCCH family have been reported involving in various processes...

Authors: Xin Hu and Jianfang Zuo

Transcriptome analysis of five ovarian stages reveals gonad maturation in female Macrobrachium nipponense

Macrobrachium nipponense is an economically important species of freshwater shrimp in China. Unlike other marine shrimps, the ovaries in adult female M. nipponense can mature rapidly and periodically during the r...

Authors: Yuning Zhang, Sufei Jiang, Hui Qiao, Yiwei Xiong, Hongtuo Fu, Wenyi Zhang, Yongsheng Gong, Shubo Jin and Yan Wu

Genome-wide identification, expression analysis, and functional study of the GRAS transcription factor family and its response to abiotic stress in sorghum [Sorghum bicolor (L.) Moench]

GRAS, an important family of transcription factors, have played pivotal roles in regulating numerous intriguing biological processes in plant development and abiotic stress responses. Since the sequencing of t...

Authors: Yu Fan, Jun Yan, Dili Lai, Hao Yang, Guoxing Xue, Ailing He, Tianrong Guo, Long Chen, Xiao-bin Cheng, Da-bing Xiang, Jingjun Ruan and Jianping Cheng

Using carrot centromeric repeats to study karyotype relationships in the genus Daucus (Apiaceae)

In the course of evolution, chromosomes undergo evolutionary changes; thus, karyotypes may differ considerably among groups of organisms, even within closely related taxa. The genus Daucus seems to be a promising...

Authors: Dariusz Kadluczka and Ewa Grzebelus

Two homologous Salmonella serogroup C1-specific genes are required for flagellar motility and cell invasion

Salmonella is a major bacterial pathogen associated with a large number of outbreaks of foodborne diseases. Many highly virulent serovars that cause human illness belong to Salmonella serogroup C1, and Salmonella

Authors: Xiujuan Zhou, Bin Liu, Yanhong Liu, Chunlei Shi, Pina M. Fratamico, Lida Zhang, Dapeng Wang, Jianhua Zhang, Yan Cui, Ping Xu and Xianming Shi

Transcriptomics unravels molecular players shaping dorsal lip hypertrophy in the vacuum cleaner cichlid, Gnathochromis permaxillaris

Teleosts display a spectacular diversity of craniofacial adaptations that often mediates ecological specializations. A considerable amount of research has revealed molecular players underlying skeletal craniof...

Authors: Laurène Alicia Lecaudey, Pooja Singh, Christian Sturmbauer, Anna Duenser, Wolfgang Gessl and Ehsan Pashay Ahi

Genotyping and lipid profiling of 601 cultivated sunflower lines reveals novel genetic determinants of oil fatty acid content

Sunflower is an important oilseed crop domesticated in North America approximately 4000 years ago. During the last century, oil content in sunflower was under strong selection. Further improvement of oil prope...

Authors: Alina I. Chernova, Rim F. Gubaev, Anupam Singh, Katrina Sherbina, Svetlana V. Goryunova, Elena U. Martynova, Denis V. Goryunov, Stepan V. Boldyrev, Anna A. Vanyushkina, Nikolay A. Anikanov, Elena A. Stekolshchikova, Ekaterina A. Yushina, Yakov N. Demurin, Zhanna M. Mukhina, Vera A. Gavrilova, Irina N. Anisimova…

Genome-wide identification and characterization of caffeoyl-coenzyme A O-methyltransferase genes related to the Fusarium head blight response in wheat

Lignin is one of the main components of the cell wall and is directly associated with plant development and defence mechanisms in plants, especially in response to Fusarium graminearum (Fg) infection. Caffeoyl-co...

Authors: Guang Yang, Wenqiu Pan, Ruoyu Zhang, Yan Pan, Qifan Guo, Weining Song, Weijun Zheng and Xiaojun Nie

Comparative analyses of the Hymenoscyphus fraxineus and Hymenoscyphus albidus genomes reveals potentially adaptive differences in secondary metabolite and transposable element repertoires

The dieback epidemic decimating common ash (Fraxinus excelsior) in Europe is caused by the invasive fungus Hymenoscyphus fraxineus. In this study we analyzed the genomes of H. fraxineus and H. albidus, its native...

Authors: Malin Elfstrand, Jun Chen, Michelle Cleary, Sandra Halecker, Katarina Ihrmark, Magnus Karlsson, Kateryna Davydenko, Jan Stenlid, Marc Stadler and Mikael Brandström Durling

Identification of long noncoding RNAs reveals the effects of dinotefuran on the brain in Apis mellifera (Hymenopptera: Apidae)

Dinotefuran (CAS No. 165252–70-0), a neonicotinoid insecticide, has been used to protect various crops against invertebrate pests and has been associated with numerous negative sublethal effects on honey bees....

Authors: Minjie Huang, Jie Dong, Haikun Guo, Minghui Xiao and Deqian Wang

Analysis of merged whole blood transcriptomic datasets to identify circulating molecular biomarkers of feed efficiency in growing pigs

Improving feed efficiency (FE) is an important goal due to its economic and environmental significance for farm animal production. The FE phenotype is complex and based on the measurements of the individual fe...

Authors: Farouk Messad, Isabelle Louveau, David Renaudeau, Hélène Gilbert and Florence Gondret

Maternal cold exposure induces distinct transcriptome changes in the placenta and fetal brown adipose tissue in mice

Brown adipose tissue (BAT) is specialized to dissipate energy in the form of heat. BAT-mediated heat production in rodents and humans is critical for effective temperature adaptation of newborns to the extraut...

Authors: Sujoy Ghosh, Chul-Hong Park, Jisu Lee, Nathan Lee, Rui Zhang, Clara Huesing, Dorien Reijnders, Jennifer Sones, Heike Münzberg, Leanne Redman and Ji Suk Chang

TAD cliques predict key features of chromatin organization

Mechanisms underlying genome 3D organization and domain formation in the mammalian nucleus are not completely understood. Multiple processes such as transcriptional compartmentalization, DNA loop extrusion and...

Authors: Tharvesh M. Liyakat Ali, Annaël Brunet, Philippe Collas and Jonas Paulsen

Genome sequencing identified novel mechanisms underlying virescent mutation in upland cotton Gossypiuma hirsutum

Virescent mutation broadly exists in plants and is an ideal experimental material to investigate regulatory mechanisms underlying chlorophyll synthesis, photosynthesis and plant growth. Up to date, the molecul...

Authors: Jin Gao, Yang Shi, Wei Wang, Yong-Hui Wang, Hua Yang, Qing-Hua Shi, Jian-Ping Chen, Yan-Ru Sun and Li-Wang Cai

A functional map of genomic HIF1α-DNA complexes in the eye lens revealed through multiomics analysis

During eye lens development the embryonic vasculature regresses leaving the lens without a direct oxygen source. Both embryonically and throughout adult life, the lens contains a decreasing oxygen gradient fro...

Authors: Joshua Disatham, Lisa Brennan, Daniel Chauss, Jason Kantorow, Behdad Afzali and Marc Kantorow

Modelling segmental duplications in the human genome

Segmental duplications (SDs) are long DNA sequences that are repeated in a genome and have high sequence identity. In contrast to repetitive elements they are often unique and only sometimes have multiple copi...

Authors: Eldar T. Abdullaev, Iren R. Umarova and Peter F. Arndt

Female-specific genomic regions and molecular sex identification of the clearhead icefish (Protosalanx hyalocranius)

The clearhead icefish, Protosalanx hyalocranius, is an economically important fishery species in China. Since 1980s, P. hyalocranius was widely introduced into lakes and reservoirs of northern China for aquacultu...

Authors: Teng-Fei Xing, Yu-Long Li and Jin-Xian Liu

De novo transcriptome analysis of white teak (Gmelina arborea Roxb) wood reveals critical genes involved in xylem development and secondary metabolism

Gmelina arborea Roxb is a fast-growing tree species of commercial importance for tropical countries due to multiple industrial uses of its wood. Wood is primarily composed of thick secondary cell walls of xylem c...

Authors: Mary Luz Yaya Lancheros, Krishan Mohan Rai, Vimal Kumar Balasubramanian, Lavanya Dampanaboina, Venugopal Mendu and Wilson Terán

Genome-wide profiling of long noncoding RNAs involved in wheat spike development

Long noncoding RNAs (lncRNAs) have been shown to play important roles in the regulation of plant growth and development. Recent transcriptomic analyses have revealed the gene expression profiling in wheat spik...

Authors: Pei Cao, Wenjuan Fan, Pengjia Li and Yuxin Hu

Insertion of an endogenous Jaagsiekte sheep retrovirus element into the BCO2 - gene abolishes its function and leads to yellow discoloration of adipose tissue in Norwegian Spælsau (Ovis aries)

The accumulation of carotenoids in adipose tissue leading to yellow fat is, in sheep, a heritable recessive trait that can be attributed to a nonsense mutation in the beta-carotene oxygenase 2 (BCO2) gene. Howeve...

Authors: Matthew Kent, Michel Moser, Inger Anne Boman, Kristine Lindtveit, Mariann Árnyasi, Kristil Kindem Sundsaasen and Dag Inge Våge

Severe pantothenic acid deficiency induces alterations in the intestinal mucosal proteome of starter Pekin ducks

Pantothenic acid deficiency (PAD) results in growth depression and intestinal hypofunction of animals. However, the underlying molecular mechanisms remain to be elucidated. Mucosal proteome might reflect dieta...

Authors: Jing Tang, Yulong Feng, Bo Zhang, Yongbao Wu, Zhanbao Guo, Suyun Liang, Zhengkui Zhou, Ming Xie and Shuisheng Hou

Temporal dynamics of teleost populations during the Pleistocene: a report from publicly available genome data

Global climate oscillation, as a selection dynamic, is an ecologically important element resulting in global biodiversity. During the glacial geological periods, most organisms suffered detrimental selection p...

Authors: Jia Li, Chao Bian, Yunhai Yi, Hui Yu, Xinxin You and Qiong Shi

Validation of reference genes for whole blood gene expression analysis in cord blood of preterm and full-term neonates and peripheral blood of healthy adults

Preterm birth is the leading cause of neonatal morbidity and mortality, but research efforts in neonatology are complicated due to the unavailability of large volume blood samples. Whole blood assays can be us...

Authors: Kristin Hieronymus, Benjamin Dorschner, Felix Schulze, Neeta L. Vora, Joel S. Parker, Jennifer Lucia Winkler, Angela Rösen-Wolff and Stefan Winkler

Embryonic thermal manipulation impacts the postnatal transcriptome response of heat-challenged Japanese quails

The thermal-manipulation (TM) during egg incubation is a cyclic exposure to hot or cold temperatures during embryogenesis that is associated to long-lasting effects on growth performance, physiology, metabolis...

Authors: Anaïs Vitorino Carvalho, Christelle Hennequet-Antier, Aurélien Brionne, Sabine Crochet, Justine Jimenez, Nathalie Couroussé, Anne Collin and Vincent Coustham

Integrative analysis of histomorphology, transcriptome and whole genome resequencing identified DIO2 gene as a crucial gene for the protuberant knob located on forehead in geese

During domestication, remarkable changes in behavior, morphology, physiology and production performance have taken place in farm animals. As one of the most economically important poultry, goose owns a unique ...

Authors: Yan Deng, Shenqiang Hu, Chenglong Luo, Qingyuan Ouyang, Li Li, Jiaming Ma, Zhenping Lin, Junpeng Chen, Hehe Liu, Jiwei Hu, Guohong Chen, Dingming Shu, Yuxuan Pan, Bo Hu, Hua He, Hao Qu…

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

Metabolic stress, as negative energy balance on one hand or obesity on the other hand can lead to increased levels of free fatty acids in the plasma and follicular fluid of animals and humans. In an earlier st...

Authors: Vengala Rao Yenuganti, Dirk Koczan and Jens Vanselow

Transcriptional responses in jejunum of two layer chicken strains following variations in dietary calcium and phosphorus levels

Calcium (Ca) and phosphorus (P) are essential nutrients that are linked to a large array of biological processes. Disturbances in Ca and P homeostasis in chickens are associated with a decline in growth and eg...

Authors: Henry Reyer, Michael Oster, Siriluck Ponsuksili, Nares Trakooljul, Adewunmi O. Omotoso, Muhammad A. Iqbal, Eduard Muráni, Vera Sommerfeld, Markus Rodehutscord and Klaus Wimmers

DNA methylation-based sex classifier to predict sex and identify sex chromosome aneuploidy

Sex is an important covariate of epigenome-wide association studies due to its strong influence on DNA methylation patterns across numerous genomic positions. Nevertheless, many samples on the Gene Expression ...

Authors: Yucheng Wang, Eilis Hannon, Olivia A. Grant, Tyler J. Gorrie-Stone, Meena Kumari, Jonathan Mill, Xiaojun Zhai, Klaus D. McDonald-Maier and Leonard C. Schalkwyk

Reproductive developmental transcriptome analysis of Tripidium ravennae (Poaceae)

Tripidium ravennae is a cold-hardy, diploid species in the sugarcane complex (Poaceae subtribe Saccharinae) with considerable potential as a genetic resource for developing improved bioenergy and ornamental grass...

Authors: Nathan Maren, Fangzhou Zhao, Rishi Aryal, Darren Touchell, Wusheng Liu, Thomas Ranney and Hamid Ashrafi

UniBind: maps of high-confidence direct TF-DNA interactions across nine species

Transcription factors (TFs) bind specifically to TF binding sites (TFBSs) at cis-regulatory regions to control transcription. It is critical to locate these TF-DNA interactions to understand transcriptional re...

Authors: Rafael Riudavets Puig, Paul Boddie, Aziz Khan, Jaime Abraham Castro-Mondragon and Anthony Mathelier

Construction of a high-density linkage map and graphical representation of the arrangement of transcriptome-based unigene markers on the chromosomes of onion, Allium cepa L.

Genomic information for Allium cepa L. is limited as it is heterozygous and its genome is very large. To elucidate potential SNP markers obtained by NGS, we used a complete set of A. fistulosum L.-A. cepa monosom...

Authors: Satoshi Fujito, Turgut Yigit Akyol, Takuya Mukae, Tadayuki Wako, Ken-ichiro Yamashita, Hikaru Tsukazaki, Hideki Hirakawa, Keisuke Tanaka, Yoko Mine, Shusei Sato and Masayoshi Shigyo

Buffalo sperm surface proteome profiling reveals an intricate relationship between innate immunity and reproduction

Low conception rate (CR) despite insemination with morphologically normal spermatozoa is a common reproductive restraint that limits buffalo productivity. This accounts for a significant loss to the farmers an...

Authors: Vipul Batra, Vanya Bhushan, Syed Azmal Ali, Parul Sarwalia, Ankit Pal, Seema Karanwal, Subhash Solanki, Arumugam Kumaresan, Rakesh Kumar and Tirtha Kumar Datta

A scaling-free minimum enclosing ball method to detect differentially expressed genes for RNA-seq data

Identifying differentially expressed genes between the same or different species is an urgent demand for biological and medical research. For RNA-seq data, systematic technical effects and different sequencing...

Authors: Yan Zhou, Bin Yang, Junhui Wang, Jiadi Zhu and Guoliang Tian

High resolution mapping and candidate gene identification of downy mildew race 16 resistance in spinach

Downy mildew, the most devastating disease of spinach (Spinacia oleracea L.), is caused by the oomycete Peronospora effusa [=P. farinosa f. sp. spinaciae]. The P. effusa shows race specificities to the resistant ...

Authors: Gehendra Bhattarai, Wei Yang, Ainong Shi, Chunda Feng, Braham Dhillon, James C. Correll and Beiquan Mou

Exome-based investigation of the genetic basis of human pigmentary glaucoma

Glaucoma is a leading cause of visual disability and blindness. Release of iris pigment within the eye, pigment dispersion syndrome (PDS), can lead to one type of glaucoma known as pigmentary glaucoma. PDS has...

Authors: Carly van der Heide, Wes Goar, Kacie J. Meyer, Wallace L. M. Alward, Erin A. Boese, Nathan C. Sears, Ben R. Roos, Young H. Kwon, Adam P. DeLuca, Owen M. Siggs, Claudia Gonzaga-Jauregui, Val C. Sheffield, Kai Wang, Edwin M. Stone, Robert F. Mullins, Michael G. Anderson…

LABRAT reveals association of alternative polyadenylation with transcript localization, RNA binding protein expression, transcription speed, and cancer survival

The sequence content of the 3′ UTRs of many mRNA transcripts is regulated through alternative polyadenylation (APA). The study of this process using RNAseq data, though, has been historically challenging.

Authors: Raeann Goering, Krysta L. Engel, Austin E. Gillen, Nova Fong, David L. Bentley and J. Matthew Taliaferro

Comparative insights into genome signatures of ferric iron oxide- and anode-stimulated Desulfuromonas spp. strains

Halotolerant Fe (III) oxide reducers affiliated in the family Desulfuromonadaceae are ubiquitous and drive the carbon, nitrogen, sulfur and metal cycles in marine subsurface sediment. Due to their possible applic...

Authors: Yong Guo, Tomo Aoyagi and Tomoyuki Hori

MicroPIPE: validating an end-to-end workflow for high-quality complete bacterial genome construction

Oxford Nanopore Technology (ONT) long-read sequencing has become a popular platform for microbial researchers due to the accessibility and affordability of its devices. However, easy and automated construction...

Authors: Valentine Murigneux, Leah W. Roberts, Brian M. Forde, Minh-Duy Phan, Nguyen Thi Khanh Nhu, Adam D. Irwin, Patrick N. A. Harris, David L. Paterson, Mark A. Schembri, David M. Whiley and Scott A. Beatson

Reliable wolf-dog hybrid detection in Europe using a reduced SNP panel developed for non-invasively collected samples

Understanding the processes that lead to hybridization of wolves and dogs is of scientific and management importance, particularly over large geographical scales, as wolves can disperse great distances. Howeve...

Authors: Jenni Harmoinen, Alina von Thaden, Jouni Aspi, Laura Kvist, Berardino Cocchiararo, Anne Jarausch, Andrea Gazzola, Teodora Sin, Hannes Lohi, Marjo K. Hytönen, Ilpo Kojola, Astrid Vik Stronen, Romolo Caniglia, Federica Mattucci, Marco Galaverni, Raquel Godinho…

Transcriptome profiling of the diaphragm in a controlled mechanical ventilation model reveals key genes involved in ventilator-induced diaphragmatic dysfunction

Ventilator-induced diaphragmatic dysfunction (VIDD) is associated with weaning difficulties, intensive care unit hospitalization (ICU), infant mortality, and poor long-term clinical outcomes. The expression pa...

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

A two-way rectification method for identifying differentially expressed genes by maximizing the co-function relationship

The identification of differentially expressed genes (DEGs) is an important task in many biological studies. The currently widely used methods often calculate a score for each gene by estimating the significan...

Authors: Bolin Chen, Li Gao and Xuequn Shang

Fusarium head blight resistance in European winter wheat: insights from genome-wide transcriptome analysis

Fusarium head blight (FHB) is a devastating disease of wheat worldwide. Resistance to FHB is quantitatively controlled by the combined effects of many small to medium effect QTL. Flowering traits, especially t...

Authors: Maria Buerstmayr, Christian Wagner, Tetyana Nosenko, Jimmy Omony, Barbara Steiner, Thomas Nussbaumer, Klaus F. X. Mayer and Hermann Buerstmayr