Articles

Transcriptional expression changes during compensatory plasticity in the terminal ganglion of the adult cricket Gryllus bimaculatus

Damage to the adult central nervous system often leads to long-term disruptions in function due to the limited capacity for neurological recovery. The central nervous system of the Mediterranean field cricket, Gr...

Authors: Meera P. Prasad, Donald K. E. Detchou, Felicia Wang, Lisa L. Ledwidge, Sarah E. Kingston and Hadley Wilson Horch

Genome-wide DNA methylation profile changes associated with shell colouration in the Yesso scallop (Patinopecten yessoensis) as measured by whole-genome bisulfite sequencing

Mollusca, a phylum of highly rich species, possess vivid shell colours, but the underlying molecular mechanism remains to be elucidated. DNA methylation, one of the most common epigenetic modifications in euka...

Authors: Changzi Yuan, Junxia Mao, Hongyan Sun, Yiying Wang, Ming Guo, Xubo Wang, Ying Tian, Zhenlin Hao, Jun Ding and Yaqing Chang

Genome-wide scans for signatures of selection in Mangalarga Marchador horses using high-throughput SNP genotyping

The detection of signatures of selection in genomic regions provides insights into the evolutionary process, enabling discoveries regarding complex phenotypic traits. In this research, we focused on identifyin...

Authors: Wellington B. Santos, Gustavo P. Schettini, Amanda M. Maiorano, Fernando O. Bussiman, Júlio C. C. Balieiro, Guilherme C. Ferraz, Guilherme L. Pereira, Welder Angelo Baldassini, Otávio R. M. Neto, Henrique N. Oliveira and Rogério A. Curi

Breed-specific reference sequence optimized mapping accuracy of NGS analyses for pigs

Reference sequences play a vital role in next-generation sequencing (NGS), impacting mapping quality during genome analyses. However, reference genomes usually do not represent the full range of genetic divers...

Authors: Dan Wang, Liu Yang, Chao Ning, Jian-Feng Liu and Xingbo Zhao

The genetic impact of an Ebola outbreak on a wild gorilla population

Numerous Ebola virus outbreaks have occurred in Equatorial Africa over the past decades. Besides human fatalities, gorillas and chimpanzees have also succumbed to the fatal virus. The 2004 outbreak at the Odza...

Authors: Claudia Fontsere, Peter Frandsen, Jessica Hernandez-Rodriguez, Jonas Niemann, Camilla Hjorth Scharff-Olsen, Dominique Vallet, Pascaline Le Gouar, Nelly Ménard, Arcadi Navarro, Hans R. Siegismund, Christina Hvilsom, M. Thomas P. Gilbert, Martin Kuhlwilm, David Hughes and Tomas Marques-Bonet

Comparative transcriptomic analysis of races 1, 2, 5 and 6 of Fusarium oxysporum f.sp. pisi in a susceptible pea host identifies differential pathogenicity profiles

The fungal pathogen Fusarium oxysporum f.sp. pisi (Fop) causes Fusarium wilt in peas. There are four races globally: 1, 2, 5 and 6 and all of these races are present in Australia. Molecular infection mechanisms h...

Authors: Saidi R. Achari, Jacqueline Edwards, Ross C. Mann, Jatinder K. Kaur, Tim Sawbridge and Brett A. Summerell

Manual Annotation Studio (MAS): a collaborative platform for manual functional annotation of viral and microbial genomes

Functional genome annotation is the process of labelling functional genomic regions with descriptive information. Manual curation can produce higher quality genome annotations than fully automated methods. Man...

Authors: Matthew R. Lueder, Regina Z. Cer, Miles Patrick, Logan J. Voegtly, Kyle A. Long, Gregory K. Rice and Kimberly A. Bishop-Lilly

Combined nanopore adaptive sequencing and enzyme-based host depletion efficiently enriched microbial sequences and identified missing respiratory pathogens

Enzyme-based host depletion significantly improves the sensitivity of clinical metagenomics. Recent studies found that real-time adaptive sequencing of DNA molecules was achieved using a nanopore sequencing ma...

Authors: Mingyu Gan, Bingbing Wu, Gangfeng Yan, Gang Li, Li Sun, Guoping Lu and Wenhao Zhou

Genome-wide investigation and expression profiling of polyphenol oxidase (PPO) family genes uncover likely functions in organ development and stress responses in Populus trichocarpa

Trees such as Populus are planted extensively for reforestation and afforestation. However, their successful establishment greatly depends upon ambient environmental conditions and their relative resistance to ab...

Authors: Fang He, Yu-Jie Shi, Qian Zhao, Kuang-Ji Zhao, Xing-Lei Cui, Liang-Hua Chen, Han-Bo Yang, Fan Zhang, Jia-Xuan Mi, Jin-Liang Huang and Xue-Qin Wan

Impact of human gene annotations on RNA-seq differential expression analysis

Differential expression (DE) analysis of RNA-seq data typically depends on gene annotations. Different sets of gene annotations are available for the human genome and are continually updated–a process complica...

Authors: Yu Hamaguchi, Chao Zeng and Michiaki Hamada

Population genomics provides insights into the population structure and temperature-driven adaptation of Collichthys lucidus

Understanding the genetic structure and local adaptive evolutionary mechanisms of marine organisms is crucial for the management of biological resources. As the ecologically and commercially important small-si...

Authors: Linlin Zhao, Fangyuan Qu, Na Song, Zhiqiang Han, Tianxiang Gao and Zhaohui Zhang

Transcriptomic analysis of the seminal vesicle response to the reproductive toxicant acrylamide

The seminal vesicles synthesise bioactive factors that support gamete function, modulate the female reproductive tract to promote implantation, and influence developmental programming of offspring phenotype. D...

Authors: David A. Skerrett-Byrne, Brett Nixon, Elizabeth G. Bromfield, James Breen, Natalie A. Trigg, Simone J. Stanger, Ilana R. Bernstein, Amanda L. Anderson, Tessa Lord, R. John Aitken, Shaun D. Roman, Sarah A. Robertson and John E. Schjenken

Genome-wide identification, genomic organization, and expression profiling of the CONSTANS-like (COL) gene family in petunia under multiple stresses

CONSTANS-like (CO-like, COL) are putative zinc-finger transcription factors known to play vital role in various plant biological processes such as control of flowering time, regulation of plant growth and deve...

Authors: Khadiza Khatun, Sourav Debnath, Arif Hasan Khan Robin, Antt Htet Wai, Ujjal Kumar Nath, Do-Jin Lee, Chang-Kil Kim and Mi-Young Chung

The mitochondrial genome and Epigenome of the Golden lion Tamarin from fecal DNA using Nanopore adaptive sequencing

The golden lion tamarin (Leontopithecus rosalia) is an endangered Platyrrhine primate endemic to the Atlantic coastal forests of Brazil. Despite ongoing conservation efforts, genetic data on this species remains ...

Authors: Nicole Wanner, Peter A. Larsen, Adam McLain and Christopher Faulk

Genomic diversity of Areca Palm Velarivirus 1 (APV1) in Areca palm (Areca catechu) plantations in Hainan, China

Areca palm (Areca catechu L.) is an important commercial crop in southeast Asia, but its cultivation is threatened by yellowing leaf disease (YLD). Areca palm velarivirus 1 (APV1) was recently associated with YLD...

Authors: Xianmei Cao, Ruibai Zhao, Hongxing Wang, Huaiwen Zhang, Xue Zhao, Latif Ullah Khan and Xi Huang

Integrated analysis of lncRNA-miRNA-mRNA ceRNA network in human aortic dissection

Many studies on long chain non-coding RNAs (lncRNAs) are published in recent years. But the roles of lncRNAs in aortic dissection (AD) are still unclear and should be further examined. The present work focused...

Authors: Hao Zhang, Ce Bian, Simei Tu, Fanxing Yin, Panpan Guo, Jian Zhang, Xiaotong Song, Qingyang Liu, Chen Chen and Yanshuo Han

Identification of ABC transporter G subfamily in white lupin and functional characterization of L.albABGC29 in phosphorus use

White lupin (Lupinus albus) is a leguminous crop with elite adaptive ability in phosphorus-deficient soil and used as a model plant for studying phosphorus (P) use. However, the genetic basis of its adaptation to...

Authors: Mehtab Muhammad Aslam, Muhammad Waseem, Qian Zhang, Wang Ke, Jianhua Zhang and Weifeng Xu

Construction of a ceRNA network in glioma and analysis of its clinical significance

Glioma is the most common central nervous system tumor with a poor survival rate and prognosis. Previous studies have found that long non-coding RNA (lncRNA) and competitive endogenous RNA (ceRNA) play importa...

Authors: Guangdong Liu, Haihong Li, Wenyang Ji, Haidong Gong, Yan Jiang, Guomin Ji and Guangyao Liu

AutoCNV: a semiautomatic CNV interpretation system based on the 2019 ACMG/ClinGen Technical Standards for CNVs

The American College of Medical Genetics and Genomics (ACMG) and the Clinical Genome Resource (ClinGen) presented technical standards for interpretation and reporting of constitutional copy-number variants in ...

Authors: Chunna Fan, Zhonghua Wang, Yan Sun, Jun Sun, Xi Liu, Licheng Kang, Yingshuo Xu, Manqiu Yang, Wentao Dai, Lijie Song, Xiaoming Wei, Jiale Xiang, Hui Huang, Meizhen Zhou, Fanwei Zeng, Lin Huang…

Multi-tiered analyses of honey bees that resist or succumb to parasitic mites and viruses

Varroa destructor mites, and the numerous viruses they vector to their honey bee hosts, are among the most serious threats to honey bee populations, causing mortality and morbidity to both the individual honey be...

Authors: Daniel B. Weaver, Brandi L. Cantarel, Christine G. Elsik, Dawn L. Boncristiani and Jay D. Evans

Repertoire analysis of γδ T cells in the chicken enables functional annotation of the genomic region revealing highly variable pan-tissue TCR gamma V gene usage as well as identifying public and private repertoires

Despite increasing interest in γδ T cells and their non-classical behaviour, most studies focus on animals with low numbers of circulating γδ T cells, such as mice and humans. Arguably, γδ T cell functions mig...

Authors: Robert Dixon, Stephen G. Preston, Stefan Dascalu, Patrik G. Flammer, Steven R. Fiddaman, Kirstie McLoughlin, Amy Boyd, Jiri Volf, Ivan Rychlik, Michael B. Bonsall, Bernd Kaspers and Adrian L. Smith

Exon and intron sharing in opposite direction-an undocumented phenomenon in human genome-between Pou5f1 and Tcf19 genes

Overlapping genes share same genomic regions in parallel (sense) or anti-parallel (anti-sense) orientations. These gene pairs seem to occur in all domains of life and are best known from viruses. However, the ...

Authors: Majid Mehravar, Fatemeh Ghaemimanesh and Ensieh M. Poursani

Genome-wide associations for immune traits in two maternal pig lines

In recent years, animal welfare and health has become more and more important in pig breeding. So far, numerous parameters have been considered as important biomarkers, especially in the immune reaction and in...

Authors: Christina M. Dauben, Maren J. Pröll-Cornelissen, Esther M. Heuß, Anne K. Appel, Hubert Henne, Katharina Roth, Karl Schellander, Ernst Tholen and Christine Große-Brinkhaus

The mitochondrial genome of Faughnia haani (Stomatopoda): novel organization of the control region and phylogenetic position of the superfamily Parasquilloidea

Stomatopod crustaceans are aggressive marine predators featuring complex compound eyes and powerful raptorial appendages used for “smashing” or “spearing” prey and/or competitors. Among them, parasquilloids (s...

Authors: Hee-seung Hwang, Jongwoo Jung and Juan Antonio Baeza

Transcriptome profile of the sinoatrial ring reveals conserved and novel genetic programs of the zebrafish pacemaker

Sinoatrial Node (SAN) is part of the cardiac conduction system, which controls the rhythmic contraction of the vertebrate heart. The SAN consists of a specialized pacemaker cell population that has the potenti...

Authors: Rashid Minhas, Henry Loeffler-Wirth, Yusra H. Siddiqui, Tomasz Obrębski, Shikha Vashisht, Karim Abu Nahia, Alexandra Paterek, Angelika Brzozowska, Lukasz Bugajski, Katarzyna Piwocka, Vladimir Korzh, Hans Binder and Cecilia Lanny Winata

The chloroplast genomes of four Bupleurum (Apiaceae) species endemic to Southwestern China, a diversity center of the genus, as well as their evolutionary implications and phylogenetic inferences

As one of the largest genera in Apiaceae, Bupleurum L. is well known for its high medicinal value. The genus has frequently attracted the attention of evolutionary biologist and taxonomist for its distinctive cha...

Authors: Rong Huang, Xuena Xie, Aimin Chen, Fang Li, Enwei Tian and Zhi Chao

Metagenomic investigation of potential abortigenic pathogens in foetal tissues from Australian horses

Abortion in horses leads to economic and welfare losses to the equine industry. Most cases of equine abortions are sporadic, and the cause is often unknown. This study aimed to detect potential abortigenic pat...

Authors: Rumana Akter, Charles M. El-Hage, Fiona M. Sansom, Joan Carrick, Joanne M. Devlin and Alistair R. Legione

Privacy-preserving storage of sequenced genomic data

The current and future applications of genomic data may raise ethical and privacy concerns. Processing and storing of this data introduce a risk of abuse by potential offenders since the human genome contains ...

Authors: Rastislav Hekel, Jaroslav Budis, Marcel Kucharik, Jan Radvanszky, Zuzana Pös and Tomas Szemes

Neurogenomic divergence during speciation by reinforcement of mating behaviors in chorus frogs (Pseudacris)

Species interactions can promote mating behavior divergence, particularly when these interactions are costly due to maladaptive hybridization. Selection against hybridization can indirectly cause evolution of ...

Authors: Oscar E. Ospina, Alan R. Lemmon, Mysia Dye, Christopher Zdyrski, Sean Holland, Daniel Stribling, Michelle L. Kortyna and Emily Moriarty Lemmon

Genome-wide association mapping uncovers sex-associated copy number variation markers and female hemizygous regions on the W chromosome in Salix viminalis

Sex chromosomes are in some species largely undifferentiated (homomorphic) with restricted sex determination regions. Homomorphic but different sex chromosomes are found in the closely related genera Populus and

Authors: Henrik R. Hallingbäck, Pascal Pucholt, Pär K. Ingvarsson, Ann Christin Rönnberg-Wästljung and Sofia Berlin

A high-density linkage map and sex-linked markers for the Amazon Tambaqui Colossoma macropomum

Tambaqui (Colossoma macropomum, Cuvier, 1818) is the most economically important native freshwater fish species in Brazil. It can reach a total length of over 1 m and a weight of over 40 kg. The species displays ...

Authors: Eduardo Sousa Varela, Michaël Bekaert, Luciana Nakaghi Ganeco-Kirschnik, Lucas Simon Torati, Luciana Shiotsuki, Fernanda Loureiro de Almeida, Luciana Cristine Vasques Villela, Fabrício Pereira Rezende, Aurisan da Silva Barroso, Luiz Eduardo Lima de Freitas, John Bernard Taggart and Herve Migaud

Genomic analysis of the nomenclatural type strain of the nematode-associated entomopathogenic bacterium Providencia vermicola

Enterobacteria of the genus Providencia are mainly known as opportunistic human pathogens but have been isolated from highly diverse natural environments. The species Providencia vermicola comprises insect pathog...

Authors: Giuseppe Andolfo, Christina Schuster, Haifa Ben Gharsa, Michelina Ruocco and Andreas Leclerque

Chloroplast genomes of five Oedogonium species: genome structure, phylogenetic analysis and adaptive evolution

The order Oedogoniales within the single family Oedogoniaceae comprised of three genera, Oedogonium, Oedocladium, and Bulbochaete based on traditional morphological criteria. While several molecular phylogenetic ...

Authors: Qian Xiong, Yuxin Hu, Wenqi Lv, Qinghua Wang, Guoxiang Liu and Zhengyu Hu

Genetic identification and characterization of chromosomal regions for kernel length and width increase from tetraploid wheat

Improvement of wheat gercTriticum aestivum L.) yield could relieve global food shortages. Kernel size, as an important component of 1000-kernel weight (TKW), is always a significant consideration to improve yield...

Authors: Jieguang Zhou, Cong Li, Jianing You, Huaping Tang, Yang Mu, Qiantao Jiang, Yaxi Liu, Guoyue Chen, Jirui Wang, Pengfei Qi, Jun Ma, Yutian Gao, Ahsan Habib, Yuming Wei, Youliang Zheng, Xiujin Lan…

Correction to: Deploying new generation sequencing for the study of flesh color depletion in Atlantic Salmon (Salmo salar)

Authors: Thu Thi Minh Vo, Tuan Viet Nguyen, Gianluca Amoroso, Tomer Ventura and Abigail Elizur

Global identification of long non-coding RNAs involved in the induction of spinach flowering

Spinach is a beneficial annual vegetable species and sensitive to the bolting or early flowering, which causes a large reduction in quality and productivity. Indeed, bolting is an event induced by the coordina...

Authors: Fatemeh Ghorbani, Reza Abolghasemi, Maryam Haghighi, Nematollah Etemadi, Shui Wang, Marzieh Karimi and Aboozar Soorni

Exploration of the lactation function of protein phosphorylation sites in goat mammary tissues by phosphoproteome analysis

Protein phosphorylation plays an important role in lactation. Differentially modified phosphorylation sites and phosphorylated proteins between peak lactation (PL, 90 days postpartum) and late lactation (LL, 2...

Authors: Chao Zhu, Junru Zhu, Quyu Duan, Yue Jiang, Hao Yin, Yonglong He, Fu Li and Xiao-Peng An

Genome-wide association study and transcriptome of olecranon-type traits in peach (Prunus persica L.) germplasm

The top of the olecranon honey peach (Prunus persica L.) fruit appears similar to an eagle’s beak. In this study, a single olecranon honey peach with a round-type fruit was observed in our fruit orchard. To explo...

Authors: Jianliang Liu, Yao Bao, Yuming Zhong, Qin Wang and Huifan Liu

Early life and adult stress promote sex dependent changes in hypothalamic miRNAs and environmental enrichment prevents stress-induced miRNA and gene expression changes in rats

The hypothalamus plays a key role in the stress response. While early life stress (ELS) increases susceptibility to psychiatric disorders including major depressive disorder (MDD), acute stress during adulthoo...

Authors: Lauren Allen McKibben and Yogesh Dwivedi

A systematic bioinformatics approach for large-scale identification and characterization of host-pathogen shared sequences

Biology has entered the era of big data with the advent of high-throughput omics technologies. Biological databases provide public access to petabytes of data and information facilitating knowledge discovery. ...

Authors: Stephen Among James, Hui San Ong, Ranjeev Hari and Asif M. Khan

Female developmental environment delays development of male honeybee (Apis mellifera)

Nutrition and cell size play an important role in the determination of caste differentiation in queen and worker of honeybees (Apis mellifera), whereas the haploid genome dominates the differentiation of drones. ...

Authors: Yi Bo Liu, Yao Yi, Amal Abdelmawla, Yun Lin Zheng, Zhi Jiang Zeng and Xu Jiang He

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

Predicting metabolic pathway membership with deep neural networks by integrating sequential and ontology information

Inference of protein’s membership in metabolic pathways has become an important task in functional annotation of protein. The membership information can provide valuable context to the basic functional annotat...

Authors: Imam Cartealy and Li Liao

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

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