Articles

Multi-locus genome-wide association mapping for spike-related traits in bread wheat (Triticum aestivum L.)

Bread wheat (Triticum aestivum L.) is one of the most important cereal food crops for the global population. Spike-layer uniformity (the consistency of the spike distribution in the vertical space)-related traits...

Authors: Parveen Malik, Jitendra Kumar, Shiveta Sharma, Rajiv Sharma and Shailendra Sharma

QTL mapping for starch paste viscosity of rice (Oryza sativa L.) using chromosome segment substitution lines derived from two sequenced cultivars with the same Wx allele

The eating and cooking qualities (ECQs) of rice (Oryza sativa L.) are key characteristics affecting variety adoption and market value. Starch viscosity profiles tested by a rapid visco analyzer (RVA) offer a dire...

Authors: Ling Zhao, Chunfang Zhao, Lihui Zhou, Qingyong Zhao, Zhen Zhu, Tao Chen, Shu Yao, Yadong Zhang and Cailin Wang

Genome-wide development of insertion-deletion (InDel) markers for Cannabis and its uses in genetic structure analysis of Chinese germplasm and sex-linked marker identification

Cannabis sativa L., a dioecious plant derived from China, demonstrates important medicinal properties and economic value worldwide. Cannabis properties have been usually harnessed depending on the sex of the plan...

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

The transcriptomic blueprint of molt in rooster using various tissues from Ginkkoridak (Korean long-tailed chicken)

Annual molt is a critical stage in the life cycle of birds. Although the most extensively documented aspects of molt are the renewing of plumage and the remodeling of the reproductive tract in laying hens, in ...

Authors: Clémentine Charton, Dong-Jae Youm, Byung June Ko, Donghyeok Seol, Bongsang Kim, Han-Ha Chai, Dajeong Lim and Heebal Kim

Comprehensive analysis of lncRNAs involved in skeletal muscle development in ZBED6-knockout Bama pigs

The mutation of insulin-like growth factor 2 (IGF2 mutation) that a single-nucleotide substitution (G→A) in the third intron of IGF2 abrogates the interaction with zinc finger BED-type containing 6 (ZBED6) and le...

Authors: Dandan Wang, Yabin Pu, Yefang Li, Dengke Pan, Shengnan Wang, Wenjie Tian, Yuehui Ma and Lin Jiang

Multi-omics data integration reveals novel drug targets in hepatocellular carcinoma

Genetic aberrations in hepatocellular carcinoma (HCC) are well known, but the functional consequences of such aberrations remain poorly understood.

Authors: Christos Dimitrakopoulos, Sravanth Kumar Hindupur, Marco Colombi, Dritan Liko, Charlotte K. Y. Ng, Salvatore Piscuoglio, Jonas Behr, Ariane L. Moore, Jochen Singer, Hans-Joachim Ruscheweyh, Matthias S. Matter, Dirk Mossmann, Luigi M. Terracciano, Michael N. Hall and Niko Beerenwinkel

Apicidin biosynthesis is linked to accessory chromosomes in Fusarium poae isolates

Fusarium head blight is a disease of global concern that reduces crop yields and renders grains unfit for consumption due to mycotoxin contamination. Fusarium poae is frequently associated with cereal crops showi...

Authors: Thomas E. Witte, Linda J. Harris, Hai D. T. Nguyen, Anne Hermans, Anne Johnston, Amanda Sproule, Jeremy R. Dettman, Christopher N. Boddy and David P. Overy

Genome-wide CNV investigation suggests a role for cadherin, Wnt, and p53 pathways in primary open-angle glaucoma

To investigate whether copy number variations (CNVs) are implicated in molecular mechanisms underlying primary open-angle glaucoma (POAG), we used genotype data of POAG individuals and healthy controls from tw...

Authors: Valeria Lo Faro, Jacoline B. ten Brink, Harold Snieder, Nomdo M. Jansonius and Arthur A. Bergen

Increased abundance of secreted hydrolytic enzymes and secondary metabolite gene clusters define the genomes of latent plant pathogens in the Botryosphaeriaceae

The Botryosphaeriaceae are important plant pathogens, but also have the ability to establish asymptomatic infections that persist for extended periods in a latent state. In this study, we used comparative genome ...

Authors: Jan H. Nagel, Michael J. Wingfield and Bernard Slippers

Transcriptome-wide m⁶A profiling reveals mRNA post-transcriptional modification of boar sperm during cryopreservation

Cryopreservation induces transcriptomic and epigenetic modifications that strongly impairs sperm quality and function, and thus decrease reproductive performance. N⁶-methyladenosine (m⁶A) RNA methylation varies i...

Authors: Ziyue Qin, Wencan Wang, Malik Ahsan Ali, Yihan Wang, Yan Zhang, Ming Zhang, Guangbin Zhou, Jian-dong Yang and Changjun Zeng

Diet-derived transmission of MicroRNAs from host plant into honey bee Midgut

MicroRNA (miRNA) is a class of small noncoding RNAs, which targets on thousands of mRNA and thus plays important roles in many biological processes. It has been reported that miRNA has cross-species regulation...

Authors: Leila Gharehdaghi, Mohammad Reza Bakhtiarizadeh, Kang He, Taher Harkinezhad, Gholamhosein Tahmasbi and Fei Li

Reverse complementary matches simultaneously promote both back-splicing and exon-skipping

Circular RNAs (circRNAs) play diverse roles in different biological and physiological environments and are always expressed in a tissue-specific manner. Especially, circRNAs are enriched in the brain tissues o...

Authors: Dong Cao

Stage-specific transcriptomic changes in pancreatic α-cells after massive β-cell loss

Loss of pancreatic insulin-secreting β-cells due to metabolic or autoimmune damage leads to the development of diabetes. The discovery that α-cells can be efficiently reprogrammed into insulin-secreting cells ...

Authors: Daniel Oropeza, Valentina Cigliola, Agustín Romero, Simona Chera, Santiago A. Rodríguez-Seguí and Pedro L. Herrera

Stage- and sex-specific transcriptome analyses reveal distinctive sensory gene expression patterns in a butterfly

Animal behavior is largely driven by the information that animals are able to extract and process from their environment. However, the function and organization of sensory systems often change throughout ontog...

Authors: David A. Ernst and Erica L. Westerman

Genomic signatures of natural selection at phenology-related genes in a widely distributed tree species Fagus sylvatica L

Diversity among phenology-related genes is predicted to be a contributing factor in local adaptations seen in widely distributed plant species that grow in climatically variable geographic areas, such as fores...

Authors: Joanna Meger, Bartosz Ulaszewski and Jaroslaw Burczyk

InvertypeR: Bayesian inversion genotyping with Strand-seq data

Single cell Strand-seq is a unique tool for the discovery and phasing of genomic inversions. Conventional methods to discover inversions with Strand-seq data are blind to known inversion locations, limiting th...

Authors: Vincent C. T. Hanlon, Carl-Adam Mattsson, Diana C. J. Spierings, Victor Guryev and Peter M. Lansdorp

A chromosome-level genome assembly of Cairina moschata and comparative genomic analyses

The Muscovy duck (Cairina moschata) is an economically important duck species, with favourable growth and carcass composition parameters in comparison to other ducks. However, limited genomic resources for Muscov...

Authors: Fan Jiang, Yaoxin Jiang, Wenxuan Wang, Changyi Xiao, Ruiyi Lin, Tanghui Xie, Wing-Kin Sung, Shijun Li, Ivan Jakovlić, Jianhai Chen and Xiaoyong Du

Comparative transcriptome profiling of heat stress response of the mangrove crab Scylla serrata across sites of varying climate profiles

The fishery and aquaculture of the widely distributed mangrove crab Scylla serrata is a steadily growing, high-value, global industry. Climate change poses a risk to this industry as temperature elevations are ex...

Authors: Anish M.S. Shrestha, Crissa Ann I. Lilagan, Joyce Emlyn B. Guiao, Maria Rowena R. Romana-Eguia and Ma. Carmen Ablan Lagman

Putative genes in alkaloid biosynthesis identified in Dendrobium officinale by correlating the contents of major bioactive metabolites with genes expression between Protocorm-like bodies and leaves

Dendrobium officinale, an endangered Chinese herb, possesses extensive therapeutic effects and contains bioactive ingredients such as major polysaccharides, alkaloids, and minimal flavonoids. We first obtained th...

Authors: Zhaojian Wang, Weimin Jiang, Yingying Liu, Xiaoxi Meng, Xinglong Su, Mengyang Cao, Liping Wu, Nianjun Yu, Shihai Xing and Daiyin Peng

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