Articles

Genome-wide analysis of Claviceps paspali: insights into the secretome of the main species causing ergot disease in Paspalum spp

The phytopatogen Claviceps paspali is the causal agent of Ergot disease in Paspalum spp., which includes highly productive forage grasses such as P. dilatatum. This disease impacts dairy and beef production by af...

Authors: H. Oberti, G. Spangenberg, N. Cogan, R. Reyno, M. Feijoo, S. Murchio and M. Dalla-Rizza

piRNA-IPdb: a PIWI-bound piRNAs database to mining NGS sncRNA data and beyond

PIWI-interacting RNAs (piRNAs) are an abundant single-stranded type of small non-coding RNAs (sncRNAs), which initially were discovered in gonadal cells, with a role as defenders of genomic integrity in the ge...

Authors: Odei Barreñada, Eduardo Larriba, Miguel A. Brieño-Enriquez and Jesús del Mazo

Circadian miR-449c-5p regulates uterine Ca²⁺ transport during eggshell calcification in chickens

miRNAs regulate circadian patterns by modulating the biological clocks of animals. In our previous study, we found that the clock gene exhibited a cosine expression pattern in the fallopian tube of chicken ute...

Authors: Zhifu Cui, Zhichao Zhang, Felix Kwame Amevor, Xiaxia Du, Liang Li, Yaofu Tian, Xincheng Kang, Gang Shu, Qing Zhu, Yan Wang, Diyan Li, Yao Zhang and Xiaoling Zhao

Comparative genomics reveals molecular mechanisms underlying health and reproduction in cryptorchid mammals

Mammals have wide variations in testicular position, with scrotal testes in some species and ascrotal testes in others. Although cryptorchidism is hazardous to human health, some mammalian taxa are natural cry...

Authors: Simin Chai, Xin Huang, Tianzhen Wu, Shixia Xu, Wenhua Ren and Guang Yang

Alternative splicing during fruit development among fleshy fruits

Alternative splicing (AS) is an important mechanism of posttranscriptional modification and dynamically regulates multiple physiological processes in plants, including fruit ripening. However, little is known ...

Authors: Xiaomin Yan, Dan Bai, Hongtao Song, Kui Lin and Erli Pang

Identification and response analysis of xyloglucan endotransglycosylase/hydrolases (XTH) family to fluoride and aluminum treatment in Camellia sinensis

Xyloglucan endotransglycosylase/hydrolases (XTH) can disrupt and reconnect the xyloglucan chains, modify the cellulose-xyloglucan complex structure in the cell wall to reconstruct the cell wall. Previous studi...

Authors: Zichen Wu, Chuanlei Cui, Anqi Xing, Xiaohan Xu, Yi Sun, Zhiqiang Tian, Xuyan Li, Jiangyuan Zhu, Genmei Wang and Yuhua Wang

Comparative phenotypic and transcriptomic analyses unravel conserved and distinct mechanisms underlying shade avoidance syndrome in Brassicaceae vegetables

Plants grown under shade are exposed to low red/far-red ratio, thereby triggering an array of altered phenotypes called shade avoidance syndrome (SAS). Shade negatively influences plant growth, leading to a re...

Authors: Nguyen Hoai Nguyen, Benny Jian Rong Sng, Hock Chuan Yeo and In-Cheol Jang

Application of the 3′ mRNA-Seq using unique molecular identifiers in highly degraded RNA derived from formalin-fixed, paraffin-embedded tissue

Archival formalin-fixed, paraffin-embedded (FFPE) tissue samples with clinical and histological data are a singularly valuable resource for developing new molecular biomarkers. However, transcriptome analysis ...

Authors: Jin Sung Jang, Eileen Holicky, Julie Lau, Samantha McDonough, Mark Mutawe, Matthew J. Koster, Kenneth J. Warrington and Julie M. Cuninngham

Long-read sequencing-based in silico phage typing of vancomycin-resistant Enterococcus faecium

Vancomycin-resistant enterococci (VRE) are successful nosocomial pathogens able to cause hospital outbreaks. In the Netherlands, core-genome MLST (cgMLST) based on short-read sequencing is often used for molec...

Authors: Paola Lisotto, Erwin C. Raangs, Natacha Couto, Sigrid Rosema, Mariëtte Lokate, Xuewei Zhou, Alexander W. Friedrich, John W. A. Rossen, Hermie J. M. Harmsen, Erik Bathoorn and Monika A. Chlebowicz-Fliss

Genome-wide association analyses of carcass traits using copy number variants and raw intensity values of single nucleotide polymorphisms in cattle

The carcass value of cattle is a function of carcass weight and quality. Given the economic importance of carcass merit to producers, it is routinely included in beef breeding objectives. A detailed understand...

Authors: Pierce Rafter, Isobel Claire Gormley, Deirdre Purfield, Andrew C. Parnell, Saeid Naderi and Donagh P. Berry

Transcriptome dynamics during metamorphosis of imaginal discs into wings and thoracic dorsum in Apis mellifera castes

Much of the complex anatomy of a holometabolous insect is built from disc-shaped epithelial structures found inside the larva, i.e., the imaginal discs, which undergo a rapid differentiation during metamorphos...

Authors: Michelle Prioli Miranda Soares, Daniel Guariz Pinheiro, Flávia Cristina de Paula Freitas, Zilá Luz Paulino Simões and Márcia Maria Gentile Bitondi

The mitochondrial genomes of Tortricidae: nucleotide composition, gene variation and phylogenetic performance

Mitochondrial genomes (mitogenomes) have greatly improved our understanding of the backbone phylogeny of Lepidoptera, but few studies on comparative mitogenomics below the family level have been conducted. Her...

Authors: Mingsheng Yang, Junhao Li, Silin Su, Hongfei Zhang, Zhengbing Wang, Weili Ding and Lili Li

Epigenetic interplay between methylation and miRNA in bladder cancer: focus on isoform expression

Various epigenetic factors are responsible for the non-genetic regulation on gene expression. The epigenetically dysregulated oncogenes or tumor suppressors by miRNA and/or DNA methylation are often observed i...

Authors: Manu Shivakumar, Seonggyun Han, Younghee Lee and Dokyoon Kim

Complete genomes of the eukaryotic poultry parasite Histomonas meleagridis: linking sequence analysis with virulence / attenuation

Histomonas meleagridis is a protozoan parasite and the causative agent of histomonosis, an important poultry disease whose significance is underlined by the absence of any treatment and prophylaxis. The recent su...

Authors: Nicola Palmieri, Marcelo de Jesus Ramires, Michael Hess and Ivana Bilic

Conserved and breed-specific differences in the cervical transcriptome of sheep with divergent fertility at the follicular phase of a natural oestrus cycle

The outcome of cervical artificial insemination (AI) with frozen-thawed semen in sheep is limited by the inability of sperm to traverse the cervix of some ewe breeds. Previous research has demonstrated that ce...

Authors: Laura Abril-Parreño, Kieran G. Meade, Anette Kristine Krogenæs, Xavier Druart, Sean Fair and Paul Cormican

Identification and prediction of developmental enhancers in sea urchin embryos

The transcription of developmental regulatory genes is often controlled by multiple cis-regulatory elements. The identification and functional characterization of distal regulatory elements remains challenging...

Authors: César Arenas-Mena, Sofija Miljovska, Edward J. Rice, Justin Gurges, Tanvi Shashikant, Zihe Wang, Sevinç Ercan and Charles G. Danko

Evolution and structural variations in chloroplast tRNAs in gymnosperms

Chloroplast transfer RNAs (tRNAs) can participate in various vital processes. Gymnosperms have important ecological and economic value, and they are the dominant species in forest ecosystems in the Northern He...

Authors: Yu-He Zhao, Tong Zhou, Jiu-Xia Wang, Yan Li, Min-Feng Fang, Jian-Ni Liu and Zhong-Hu Li

Non-coding RNA in raw and commercially processed milk and putative targets related to growth and immune-response

Bovine milk contains extracellular vesicles (EVs) that play a role in cellular communication, acting in either an autocrine, paracrine, or an exocrine manner. The unique properties of the EVs protect the cargo...

Authors: S. Shome, R. L. Jernigan, D. C. Beitz, S. Clark and E. D. Testroet

Genome-wide identification, phylogeny and expression analysis of AP2/ERF transcription factors family in sweet potato

In recent years, much attention has been given to AP2/ERF transcription factors because they play indispensable roles in many biological processes, such as plant development and biotic and abiotic stress response...

Authors: Shutao He, Xiaomeng Hao, Shuli He, Xiaoge Hao and Xiaonan Chen

Genome-wide selection signatures detection in Shanghai Holstein cattle population identified genes related to adaption, health and reproduction traits

Over several decades, a wide range of natural and artificial selection events in response to subtropical environments, intensive pasture and intensive feedlot systems have greatly changed the customary behavio...

Authors: Dengying Liu, Zhenliang Chen, Wei Zhao, Longyu Guo, Hao Sun, Kai Zhu, Guanglei Liu, Xiuping Shen, Xiaoduo Zhao, Qishan Wang, Peipei Ma and Yuchun Pan

Comparative analysis of full-length mitochondrial genomes of five Skeletonema species reveals conserved genome organization and recent speciation

Skeletonema species are prominent primary producers, some of which can also cause massive harmful algal blooms (HABs) in coastal waters under specific environmental conditions. Nevertheless, genomic information o...

Authors: Shuya Liu, Yichao Wang, Qing Xu, Mengjia Zhang and Nansheng Chen

Correction to: Expanding the potential genes of inborn errors of immunity through protein interactions

Authors: Humza A. Khan and Manish J. Butte

A comparative analysis of differentially expressed mRNAs, miRNAs and circRNAs provides insights into the key genes involved in the high-altitude adaptation of yaks

Yaks that inhabit the Tibetan Plateau exhibit striking phenotypic and physiological differences from cattle and have adapted well to the extreme conditions on the plateau. However, the mechanisms used by these...

Authors: Qianyun Ge, Yongbo Guo, Wangshan Zheng, Yuan Cai, Xuebin Qi and Shengguo Zhao

Comprehensive genome-wide analysis of calmodulin-binding transcription activator (CAMTA) in Durio zibethinus and identification of fruit ripening-associated DzCAMTAs

Fruit ripening is an intricate developmental process driven by a highly coordinated action of complex hormonal networks. Ethylene is considered as the main phytohormone that regulates the ripening of climacter...

Authors: Zahra Iqbal, Mohammed Shariq Iqbal, Lalida Sangpong, Gholamreza Khaksar, Supaart Sirikantaramas and Teerapong Buaboocha

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

Identification of long noncoding RNAs in injury-resilient and injury-susceptible mouse retinal ganglion cells

Emerging evidence indicates that long noncoding RNAs (lncRNAs) are important regulators of various biological processes, and their expression can be altered following certain pathological conditions, including...

Authors: Ana C. Ayupe, Felipe Beckedorff, Konstantin Levay, Benito Yon, Yadira Salgueiro, Ramin Shiekhattar and Kevin K. Park

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

Data integration and evolutionary analysis of long non-coding RNAs in 25 flowering plants

Long non-coding RNAs (lncRNAs) play vital roles in many important biological processes in plants. Currently, a large fraction of plant lncRNA studies center at lncRNA identification and functional analysis. On...

Authors: Shiye Sang, Wen Chen, Di Zhang, Xuan Zhang, Wenjing Yang and Changning Liu

Genome-wide identification and expression profile analysis of trihelix transcription factor family genes in response to abiotic stress in sorghum [Sorghum bicolor (L.) Moench]

Transcription factors, including trihelix transcription factors, play vital roles in various growth and developmental processes and in abiotic stress responses in plants. The trihelix gene has been systematically...

Authors: Kuiyin Li, Lili Duan, Yubo Zhang, Miaoxiao Shi, Songshu Chen, Mingfang Yang, Yanqing Ding, Yashu Peng, Yabing Dong, Hao Yang, Zhenhua Li, Liyi Zhang, Yu Fan and Mingjian Ren

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