Articles

Whole-genome sequencing of two Streptomyces strains isolated from the sand dunes of Sahara

Sahara is one of the largest deserts in the world. The harsh climatic conditions, especially high temperature and aridity lead to unique adaptation of organisms, which could be a potential source of new metabo...

Authors: Chahira Zerouki, Farid Bensalah, Suvi Kuittinen, Ari Pappinen and Ossi Turunen

Dynamic changes of miRNAs in skeletal muscle development at New Zealand rabbits

miRNA is one of the crucial roles in the complex and dynamic network that regulates the development of skeletal muscle. The landscape of skeletal muscle miRNAs from fetus to adult in New Zealand rabbits has no...

Authors: Jing Jing, Xichun Jiang, Cuiyun Zhu, Qi Zheng, Qianyun Ji, Huiqun Yin, Jingtong Huang, Yixiao Zhu, Jiao Wang, Shuaiqi Qin and Yinghui Ling

Identification of ferroptosis genes in immune infiltration and prognosis in thyroid papillary carcinoma using network analysis

Papillary thyroid carcinoma (PTC) is the most common thyroid cancer. While many patients survive, a portion of PTC cases display high aggressiveness and even develop into refractory differentiated thyroid carc...

Authors: Ruoting Lin, Conor E. Fogarty, Bowei Ma, Hejie Li, Guoying Ni, Xiaosong Liu, Jianwei Yuan and Tianfang Wang

Determination of genetic effects and functional SNPs of bovine HTR1B gene on milk fatty acid traits

Our previous genome-wide association study (GWAS) on milk fatty acid traits in Chinese Holstein cows revealed, the SNP, BTB-01556197, was significantly associated with C10:0 at genome-wide level (P = 0.0239). It ...

Authors: Mingyue Cao, Lijun Shi, Peng Peng, Bo Han, Lin Liu, Xiaoqing Lv, Zhu Ma, Shengli Zhang and Dongxiao Sun

LncGSEA: a versatile tool to infer lncRNA associated pathways from large-scale cancer transcriptome sequencing data

Long non-coding RNAs (lncRNAs) are a growing focus in cancer research. Deciphering pathways influenced by lncRNAs is important to understand their role in cancer. Although knock-down or overexpression of lncRN...

Authors: Yanan Ren, Ting-You Wang, Leah C. Anderton, Qi Cao and Rendong Yang

Exploring the genomic resources and analysing the genetic diversity and population structure of Chinese indigenous rabbit breeds by RAD-seq

Chinese indigenous rabbits have distinct characteristics, such as roughage resistance, stress resistance and environmental adaptability, which are of great significance to the sustainable development of the ra...

Authors: Chenmiao Liu, Shuhui Wang, Xianggui Dong, Jiping Zhao, Xiangyang Ye, Ruiguang Gong and Zhanjun Ren

Biofilm associated genotypes of multiple antibiotic resistant Pseudomonas aeruginosa

Pseudomonas aeruginosa is a ubiquitous environmental microorganism and also a common cause of infection. Its ability to survive in many different environments and persistently colonize humans is linked to its pre...

Authors: James Redfern, Janine Wallace, Alex van Belkum, Magali Jaillard, Elliot Whittard, Roobinidevi Ragupathy, Joanna Verran, Peter Kelly and Mark Charles Enright

Comparative chloroplast genome analysis of Impatiens species (Balsaminaceae) in the karst area of China: insights into genome evolution and phylogenomic implications

Impatiens L. is a genus of complex taxonomy that belongs to the family Balsaminaceae (Ericales) and contains approximately 1000 species. The genus is well known for its economic, medicinal, ornamental, and hortic...

Authors: Chao Luo, Wulue Huang, Huayu Sun, Huseyin Yer, Xinyi Li, Yang Li, Bo Yan, Qiong Wang, Yonghui Wen, Meijuan Huang and Haiquan Huang

Comprehensive analysis of formin gene family highlights candidate genes related to pollen cytoskeleton and male fertility in wheat (Triticum aestivum L.)

Formin, a highly conserved multi-domain protein, interacts with microfilaments and microtubules. Although specifically expressed formin genes in anthers are potentially significant in research on male sterility a...

Authors: Wen-jing Duan, Zi-han Liu, Jian-fang Bai, Shao-hua Yuan, Yan-mei Li, Feng-kun Lu, Tian-bao Zhang, Jia-hui Sun, Feng-ting Zhang, Chang-ping Zhao and Li-ping Zhang

Comparative genome and transcriptome analyses reveal innate differences in response to host plants by two color forms of the two-spotted spider mite Tetranychus urticae

The two-spotted spider mite, Tetranychus urticae, is a major agricultural pest with a cosmopolitan distribution, and its polyphagous habits provide a model for investigating herbivore-plant interactions. There ar...

Authors: Shi-Mei Huo, Zhi-Chao Yan, Feng Zhang, Lei Chen, Jing-Tao Sun, Ary A. Hoffmann and Xiao-Yue Hong

Research on the drought tolerance mechanism of Pennisetum glaucum (L.) in the root during the seedling stage

Drought is one of the major environmental stresses resulting in a huge reduction in crop growth and biomass production. Pearl millet (Pennisetum glaucum L.) has excellent drought tolerance, and it could be used a...

Authors: Ailing Zhang, Yang Ji, Min Sun, Chuang Lin, Puding Zhou, Juncai Ren, Dan Luo, Xiaoshan Wang, Congyu Ma, Xinquan Zhang, Guangyan Feng, Gang Nie and Linkai Huang

Fine dissection of limber pine resistance to Cronartium ribicola using targeted sequencing of the NLR family

Proteins with nucleotide binding site (NBS) and leucine-rich repeat (LRR) domains (NLR) make up one of most important resistance (R) families for plants to resist attacks from various pathogens and pests. The ...

Authors: Jun-Jun Liu, Anna W. Schoettle, Richard A. Sniezko, Holly Williams, Arezoo Zamany and Benjamin Rancourt

Genetic mapping of novel modifiers for Apc^Min induced intestinal polyps’ development using the genetic architecture power of the collaborative cross mice

Familial adenomatous polyposis is an inherited genetic disease, characterized by colorectal polyps. It is caused by inactivating mutations in the Adenomatous polyposis coli (Apc) gene. Mice carrying a nonsense mu...

Authors: Alexandra Dorman, Ilona Binenbaum, Hanifa J. Abu-Toamih Atamni, Aristotelis Chatziioannou, Ian Tomlinson, Richard Mott and Fuad A. Iraqi

Genome-wide analysis of MYB transcription factors of Vaccinium corymbosum and their positive responses to drought stress

Blueberry (Vaccinium corymbosum L.) is an important species with a high content of flavonoids in fruits. As a perennial shrub, blueberry is characterized by shallow-rooted property and susceptible to drought stre...

Authors: Aibin Wang, Kehao Liang, Shiwen Yang, Yibo Cao, Lei Wang, Ming Zhang, Jing Zhou and Lingyun Zhang

Identification and characterization of amphibian SLC26A5 using RNA-Seq

Prestin (SLC26A5) is responsible for acute sensitivity and frequency selectivity in the vertebrate auditory system. Limited knowledge of prestin is from experiments using site-directed mutagenesis or domain-sw...

Authors: Zhongying Wang, Qixuan Wang, Hao Wu and Zhiwu Huang

Single nucleotide replacement in the Atlantic salmon genome using CRISPR/Cas9 and asymmetrical oligonucleotide donors

New breeding technologies (NBT) using CRISPR/Cas9-induced homology directed repair (HDR) has the potential to expedite genetic improvement in aquaculture. The long generation time in Atlantic salmon makes bree...

Authors: Anne Hege Straume, Erik Kjærner-Semb, Kai Ove Skaftnesmo, Hilal Güralp, Simon Lillico, Anna Wargelius and Rolf Brudvik Edvardsen

Evolution of Toll, Spatzle and MyD88 in insects: the problem of the Diptera bias

Arthropoda, the most numerous and diverse metazoan phylum, has species in many habitats where they encounter various microorganisms and, as a result, mechanisms for pathogen recognition and elimination have ev...

Authors: Letícia Ferreira Lima, André Quintanilha Torres, Rodrigo Jardim, Rafael Dias Mesquita and Renata Schama

Genome-wide characterization and expression profiling of B3 superfamily during ethylene-induced flowering in pineapple (Ananas comosus L.)

The B3 superfamily (B3s) represents a class of large plant-specific transcription factors, which play diverse roles in plant growth and development process including flowering induction. However, identificatio...

Authors: Cheng Cheng Ruan, Zhe Chen, Fu Chu Hu, Wei Fan, Xiang He Wang, Li Jun Guo, Hong Yan Fan, Zhi Wen Luo and Zhi Li Zhang

Non-coding RNAs in the interaction between rice and Meloidogyne graminicola

Root knot nematodes (RKN) are plant parasitic nematodes causing major yield losses of widely consumed food crops such as rice (Oryza sativa). Because non-coding RNAs, including small interfering RNAs (siRNA), mic...

Authors: Bruno Verstraeten, Mohammad Reza Atighi, Virginia Ruiz-Ferrer, Carolina Escobar, Tim De Meyer and Tina Kyndt

Correction to: Fine-scale population structure and evidence for local adaptation in Australian giant black tiger shrimp (Penaeus monodon) using SNP analysis

Authors: Nga T. T. Vu, Kyall R. Zenger, Jarrod L. Guppy, Melony J. Sellars, Catarina N. S. Silva, Shannon R. Kjeldsen and Dean R. Jerry

Genome-wide association screening and verification of potential genes associated with root architectural traits in maize (Zea mays L.) at multiple seedling stages

Breeding for new maize varieties with propitious root systems has tremendous potential in improving water and nutrients use efficiency and plant adaptation under suboptimal conditions. To date, most of the pre...

Authors: Abdourazak Alio Moussa, Ajmal Mandozai, Yukun Jin, Jing Qu, Qi Zhang, He Zhao, Gulaqa Anwari, Mohamed Abdelsamiaa Sayed Khalifa, Abraham Lamboro, Muhammad Noman, Yacoubou Bakasso, Mo Zhang, Shuyan Guan and Piwu Wang

Multi-omics approach highlights differences between RLP classes in Arabidopsis thaliana

The Leucine rich-repeat (LRR) receptor-like protein (RLP) family is a complex gene family with 57 members in Arabidopsis thaliana. Some members of the RLP family are known to be involved in basal developmental pr...

Authors: C. E. Steidele and R. Stam

Identification of QTL related to anther color and hull color by RAD sequencing in a RIL population of Setaria italica

Foxtail millet (Setaria italica) is one of the oldest domesticated crops and has been considered as an ideal model plant for C₄ grasses. It has abundant type of anther and hull colors which is not only a most int...

Authors: Huifang Xie, Junliang Hou, Nan Fu, Menghan Wei, Yunfei Li, Kang Yu, Hui Song, Shiming Li and Jinrong Liu

Correction to: RNA_seq and quantitative proteomic analysis of Dictyostelium knock-out cells lacking the core autophagy proteins ATG9 and/or ATG16

Authors: Qiuhong Xiong, Ning Song, Ping Li, Sarah Fischer, Roman Konertz, Prerana Wagle, Gernot Glöckner, Changxin Wu and Ludwig Eichinger

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

Authors: Xinlei Wang, Lei Yu and Angela Ruohao Wu

Comparative and functional genomics of the ABC transporter superfamily across arthropods

The ATP-binding cassette (ABC) transporter superfamily is comprised predominantly of proteins which directly utilize energy from ATP to move molecules across the plasma membrane. Although they have been the su...

Authors: Shane Denecke, Ivan Rankić, Olympia Driva, Megha Kalsi, Ngoc Bao Hang Luong, Benjamin Buer, Ralf Nauen, Sven Geibel and John Vontas

Analyzing the gonadal transcriptome of the frog Hoplobatrachus rugulosus to identify genes involved in sex development

The tiger frog (Hoplobatrachus rugulosus) is listed as a national Class II protected species in China. In the context of global warming, the sex ratio of amphibians will be affected, and the development of the po...

Authors: Yun Tang, Jing-Yi Chen, Guo-Hua Ding and Zhi-Hua Lin

Transcriptomic analyses of cacao flavonoids produced in photobioreactors

Theobroma cacao is a major source of flavonoids such as catechins and their monomers proanthocyanidins (PAs), widely studied for their potential benefits in cardiovascular diseases. Light has been shown to promot...

Authors: Adriana M. Gallego, Luisa F. Rojas, Wilmar G. Valencia, Lucía Atehortúa, Aura I. Urrea, Andrew S. Fister, Mark J. Guiltinan, Siela N. Maximova and Natalia Pabón-Mora

Discovery of fibrillar adhesins across bacterial species

Fibrillar adhesins are long multidomain proteins that form filamentous structures at the cell surface of bacteria. They are an important yet understudied class of proteins composed of adhesive and stalk domain...

Authors: Vivian Monzon, Aleix Lafita and Alex Bateman

The CaCA superfamily genes in Saccharum: comparative analysis and their functional implications in response to biotic and abiotic stress

In plants, Calcium (Ca²⁺) acts as a universal messenger in various signal transduction pathways, including responses to biotic and abiotic stresses and regulation of cellular and developmental processes. The Ca²⁺

Authors: Weihua Su, Chang Zhang, Dongjiao Wang, Yongjuan Ren, Tingting Sun, Jingfang Feng, Yachun Su, Liping Xu, Mutian Shi and Youxiong Que

Genome-wide analysis and expression patterns of lipid phospholipid phospholipase gene family in Brassica napus L.

Lipid phosphate phosphatases (LPP) are critical for regulating the production and degradation of phosphatidic acid (PA), an essential signaling molecule under stress conditions. Thus far, the LPP family genes hav...

Authors: Wei Su, Ali Raza, Liu Zeng, Ang Gao, Yan Lv, Xiaoyu Ding, Yong Cheng and Xiling Zou

ARPEGGIO: Automated Reproducible Polyploid EpiGenetic GuIdance workflOw

Whole genome duplication (WGD) events are common in the evolutionary history of many living organisms. For decades, researchers have been trying to understand the genetic and epigenetic impact of WGD and its u...

Authors: Stefan Milosavljevic, Tony Kuo, Samuele Decarli, Lucas Mohn, Jun Sese, Kentaro K. Shimizu, Rie Shimizu-Inatsugi and Mark D. Robinson

Post-genotyping optimization of dataset formation could affect genetic diversity parameters: an example of analyses with alpine goat breeds

Local breeds retained unique genetic variability important for adaptive potential especially in light of challenges related to climate change. Our first objective was to perform, for the first time, a genome-w...

Authors: Neža Pogorevc, Mojca Simčič, Negar Khayatzadeh, Johann Sölkner, Beate Berger, Danijela Bojkovski, Minja Zorc, Peter Dovč, Ivica Medugorac and Simon Horvat

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

The flesh pigmentation of farmed Atlantic salmon is formed by accumulation of carotenoids derived from commercial diets. In the salmon gastrointestinal system, the hindgut is considered critical in the process...

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

Third-generation sequencing and metabolome analysis reveal candidate genes and metabolites with altered levels in albino jackfruit seedlings

Most plants rely on photosynthesis; therefore, albinism in plants with leaves that are white instead of green causes slow growth, dwarfing, and even death. Although albinism has been characterized in annual mo...

Authors: Xiangxu Meng, Jiahong Xu, Maoning Zhang, Ruyue Du, Wenxiu Zhao, Qing Zeng, Zhihua Tu, Jinhui Chen and Beibei Chen

Global analysis of protein lysine 2-hydroxyisobutyrylation (K_hib) profiles in Chinese herb rhubarb (Dahuang)

Lysine 2-hydroxyisobutyrylation (K_hib) is a newly discovered protein posttranslational modification (PTM) and is involved in the broad-spectrum regulation of cellular processes that are found in both prokaryotic ...

Authors: Tong Qi, Jinping Li, Huifang Wang, Xiaofan Han, Junrong Li and Jinzhe Du

The DUB family in Populus: identification, characterization, evolution and expression patterns

The deubiquitinase (DUB) family constitutes a group of proteases that regulate the stability or reverse the ubiquitination of many proteins in the cell. These enzymes participate in cell-cycle regulation, cell...

Authors: Wenqing Zheng and Liang Du

Whole genome sequencing and phylogenetic analysis of six SARS-CoV-2 strains isolated during COVID-19 pandemic in Tunisia, North Africa

In Tunisia a first SARS-CoV-2 confirmed case was reported in March 03, 2020. Since then, an increase of cases number was observed from either imported or local cases. The aim of this preliminary study was to b...

Authors: Wasfi Fares, Anissa Chouikha, Kais Ghedira, Meriam Gdoura, Dorra Rezig, Sondes Haddad Boubaker, Imen Ben Dhifallah, Henda Touzi, Walid Hammami, Zina Meddeb, Amel Sadraoui, Nahed Hogga, Imen Abouda, Aurélia Kwasiborski, Véronique Hourdel, Guillain Mikaty…

Validation of a novel associative transcriptomics pipeline in Brassica oleracea: identifying candidates for vernalisation response

Associative transcriptomics has been used extensively in Brassica napus to enable the rapid identification of markers correlated with traits of interest. However, within the important vegetable crop species, Bras...

Authors: Shannon Woodhouse, Zhesi He, Hugh Woolfenden, Burkhard Steuernagel, Wilfried Haerty, Ian Bancroft, Judith A. Irwin, Richard J. Morris and Rachel Wells

Grid search approach to discriminate between old and recent inbreeding using phenotypic, pedigree and genomic information

Although inbreeding caused by the mating of animals related through a recent common ancestor is expected to have more harmful effects on phenotypes than ancient inbreeding (old inbreeding), estimating these ef...

Authors: Pattarapol Sumreddee, El Hamidi Hay, Sajjad Toghiani, Andrew Roberts, Samuel E. Aggrey and Romdhane Rekaya

Linking genotype to phenotype in multi-omics data of small sample

Genome-wide association studies (GWAS) that link genotype to phenotype represent an effective means to associate an individual genetic background with a disease or trait. However, single-omics data only provid...

Authors: Xinpeng Guo, Yafei Song, Shuhui Liu, Meihong Gao, Yang Qi and Xuequn Shang

Genome sequence of Apostasia ramifera provides insights into the adaptive evolution in orchids

The Orchidaceae family is one of the most diverse among flowering plants and serves as an important research model for plant evolution, especially “evo-devo” study on floral organs. Recently, sequencing of sev...

Authors: Weixiong Zhang, Guoqiang Zhang, Peng Zeng, Yongqiang Zhang, Hao Hu, Zhongjian Liu and Jing Cai

Investigating the genetic architecture of disease resilience in pigs by genome-wide association studies of complete blood count traits collected from a natural disease challenge model

Genetic improvement for disease resilience is anticipated to be a practical method to improve efficiency and profitability of the pig industry, as resilient pigs maintain a relatively undepressed level of perf...

Authors: Xuechun Bai, Tianfu Yang, Austin M. Putz, Zhiquan Wang, Changxi Li, Frédéric Fortin, John C. S. Harding, Michael K. Dyck, Jack C. M. Dekkers, Catherine J. Field and Graham S. Plastow

Transcriptome analysis uncovers the key pathways and candidate genes related to the treatment of Echinococcus granulosus protoscoleces with the repurposed drug pyronaridine

Cystic echinococcosis (CE) is a life-threatening zoonosis caused by the larval form of Echinococcus granulosus tapeworm. Our previous study showed that an approved drug pyronaridine (PND) is highly effective agai...

Authors: Yingfang Yu, Jun Li, Weisi Wang, Tian Wang, Wenjing Qi, Xueting Zheng, Lei Duan, Jiaxu Chen, Shizhu Li, Xiumin Han, Wenbao Zhang and Liping Duan

The BBX gene family in Moso bamboo (Phyllostachys edulis): identification, characterization and expression profiles

The BBX (B-box) family are zinc finger protein (ZFP) transcription factors that play an essential role in plant growth, development and response to abiotic stresses. Although BBX genes have been characterized ...

Authors: Ruifang Ma, Jialu Chen, Bin Huang, Zhinuo Huang and Zhijun Zhang

Genome-wide identification of cyclin-dependent kinase (CDK) genes affecting adipocyte differentiation in cattle

Cyclin-dependent kinases (CDKs) are protein kinases regulating important cellular processes such as cell cycle and transcription. Many CDK genes also play a critical role during adipogenic differentiation, but...

Authors: Cuili Pan, Zhaoxiong Lei, Shuzhe Wang, Xingping Wang, Dawei Wei, Xiaoyan Cai, Zhuoma Luoreng, Lei Wang and Yun Ma

Population differentiated copy number variation of Bos taurus, Bos indicus and their African hybrids

CNV comprises a large proportion in cattle genome and is associated with various traits. However, there were few population-scale comparison studies on cattle CNV.

Authors: Jisung Jang, Kwondo Kim, Young Ho Lee and Heebal Kim

Epidemiological and genomic characteristics of Acinetobacter baumannii from different infection sites using comparative genomics

Acinetobacter baumannii is a common nosocomial pathogen that poses a huge threat to global health. Owing to the severity of A. baumannii infections, it became necessary to investigate the epidemiological characte...

Authors: Xingchen Bian, Xiaofen Liu, Xuefei Zhang, Xin Li, Jing Zhang, Huajun Zheng, Sichao Song, Xiang Li and Meiqing Feng

Elevated methylation of the vault RNA2-1 promoter in maternal blood is associated with preterm birth

Preterm birth, defined as parturition before 37 completed weeks of gestation, is associated with an increased risk of neonatal complications and death, as well as poor health and disease later in life. Epigene...

Authors: Young-Ah You, Eun Jin Kwon, Han-Sung Hwang, Suk-Joo Choi, Sae Kyung Choi and Young Ju Kim

Benchmark of 16S rRNA gene amplicon sequencing using Japanese gut microbiome data from the V1–V2 and V3–V4 primer sets

16S rRNA gene amplicon sequencing (16S analysis) is widely used to analyze microbiota with next-generation sequencing technologies. Here, we compared fecal 16S analysis data from 192 Japanese volunteers using ...

Authors: Shoichiro Kameoka, Daisuke Motooka, Satoshi Watanabe, Ryuichi Kubo, Nicolas Jung, Yuki Midorikawa, Natsuko O. Shinozaki, Yu Sawai, Aya K. Takeda and Shota Nakamura