Articles

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

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

Transcriptomal dissection of soybean circadian rhythmicity in two geographically, phenotypically and genetically distinct cultivars

In soybean, some circadian clock genes have been identified as loci for maturity traits. However, the effects of these genes on soybean circadian rhythmicity and their impacts on maturity are unclear.

Authors: Yanlei Yue, Ze Jiang, Enoch Sapey, Tingting Wu, Shi Sun, Mengxue Cao, Tianfu Han, Tao Li, Hai Nian and Bingjun Jiang

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

Transcriptome and metabolome analyses of cold and darkness-induced pellicle cysts of Scrippsiella trochoidea

Dinoflagellates are a group of unicellular organisms that are a major component of aquatic eukaryotes and important contributors to marine primary production. Nevertheless, many dinoflagellates are considered ...

Authors: Xin Guo, Zhaohui Wang, Lei Liu and Yang Li

A machine learning approach for accurate and real-time DNA sequence identification

The all-electronic Single Molecule Break Junction (SMBJ) method is an emerging alternative to traditional polymerase chain reaction (PCR) techniques for genetic sequencing and identification. Existing work ind...

Authors: Yiren Wang, Mashari Alangari, Joshua Hihath, Arindam K. Das and M. P. Anantram

Trehalose in pine wood nematode participates in DJ3 formation and confers resistance to low-temperature stress

Recently, pine wood nematode (PWN, Bursaphelenchus xylophilus) has been found in the extreme cold area of northeast China. The third-stage dispersal juvenile (DJ3) of PWN, which is a long-lived stress-resistant s...

Authors: Qiaoli Chen, Ruizhi Zhang, Danlei Li, Feng Wang, Shengwei Jiang and Jianan Wang

Dual species dynamic transcripts reveal the interaction mechanisms between Chrysanthemum morifolium and Alternaria alternata

Chrysanthemum (Chrysanthemum morifolium) black spot disease caused by Alternaria alternata is one of the plant’s most destructive diseases. Dual RNA-seq was performed to simultaneously assess their transcriptomes...

Authors: Lina Liu, Fadi Chen, Sumei Chen, Weimin Fang, Ye Liu and Zhiyong Guan

Pangenome analysis and virulence profiling of Streptococcus intermedius

Streptococcus intermedius, a member of the S. anginosus group, is a commensal bacterium present in the normal microbiota of human mucosal surfaces of the oral, gastrointestinal, and urogenital tracts. However, it...

Authors: Dhiraj Sinha, Xifeng Sun, Mudra Khare, Michel Drancourt, Didier Raoult and Pierre-Edouard Fournier

Whole transcriptome analysis resulted in the identification of Chinese sprangletop (Leptochloa chinensis) genes involved in cyhalofop-butyl tolerance

Chinese sprangletop [Leptochloa chinensis (L.) Nees] is an annual malignant weed, which can often be found in paddy fields. Cyhalofop-butyl is a specialized herbicide which is utilized to control L. chinensis. Ho...

Authors: Ke Chen, Yajun Peng, Liang Zhang, Long Wang, Donghai Mao, Zhenghong Zhao, Lianyang Bai and Lifeng Wang

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

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