Articles

Correction to: Characterization of the gut microbiome in a porcine model of thoracic spinal cord injury

Authors: Adam Doelman, Seth Tigchelaar, Brian McConeghy, Sunita Sinha, Martin S. Keung, Neda Manouchehri, Megan Webster, Shera Fisk, Charlotte Morrison, Femke Streijger, Corey Nislow and Brian K. Kwon

Whole-genome resequencing of three Coilia nasus population reveals genetic variations in genes related to immune, vision, migration, and osmoregulation

Coilia nasus is an important anadromous fish, widely distributed in China, Japan, and Korea. Based on morphological and ecological researches of C. nasus, two ecotypes were identified. One is the anadromous popul...

Authors: Jun Gao, Gangchun Xu and Pao Xu

The theory on and software simulating large-scale genomic data for genotype-by-environment interactions

With the emphasis on analysing genotype-by-environment interactions within the framework of genomic selection and genome-wide association analysis, there is an increasing demand for reliable tools that can be ...

Authors: Xiujin Li, Hailiang Song, Zhe Zhang, Yunmao Huang, Qin Zhang and Xiangdong Ding

Nuclear transport genes recurrently duplicate by means of RNA intermediates in Drosophila but not in other insects

The nuclear transport machinery is involved in a well-known male meiotic drive system in Drosophila. Fast gene evolution and gene duplications have been major underlying mechanisms in the evolution of meiotic dri...

Authors: Ayda Mirsalehi, Dragomira N. Markova, Mohammadmehdi Eslamieh and Esther Betrán

Genetic architecture of protein expression and its regulation in the mouse brain

Natural variation in protein expression is common in all organisms and contributes to phenotypic differences among individuals. While variation in gene expression at the transcript level has been extensively i...

Authors: Alyssa Erickson, Suiping Zhou, Jie Luo, Ling Li, Xin Huang, Zachary Even, He Huang, Hai-Ming Xu, Junmin Peng, Lu Lu and Xusheng Wang

Comparative transcriptomic analysis of gonadal development and renewal in the ovoviviparous black rockfish (Sebastes schlegelii)

The black rockfish (Sebastes schlegelii) has an ovoviviparous reproductive pattern and long-term sperm storage, resulting in asynchronous gonadal development between the sexes. However, the comprehensive understa...

Authors: Jianshuang Li, Likang Lyu, Haishen Wen, Yun Li, Xiaojie Wang, Ying Zhang, Yijia Yao and Xin Qi

Genetic association tests in family samples for multi-category phenotypes

Advancements in statistical methods and sequencing technology have led to numerous novel discoveries in human genetics in the past two decades. Among phenotypes of interest, most attention has been given to st...

Authors: Shuai Wang, James B. Meigs and Josée Dupuis

Discovery of clinically relevant fusions in pediatric cancer

Pediatric cancers typically have a distinct genomic landscape when compared to adult cancers and frequently carry somatic gene fusion events that alter gene expression and drive tumorigenesis. Sensitive and sp...

Authors: Stephanie LaHaye, James R. Fitch, Kyle J. Voytovich, Adam C. Herman, Benjamin J. Kelly, Grant E. Lammi, Jeremy A. Arbesfeld, Saranga Wijeratne, Samuel J. Franklin, Kathleen M. Schieffer, Natalie Bir, Sean D. McGrath, Anthony R. Miller, Amy Wetzel, Katherine E. Miller, Tracy A. Bedrosian…

Histone acetylation regulates the expression of genes involved in worker reproduction in the ant Temnothorax rugatulus

In insect societies, queens monopolize reproduction while workers perform tasks such as brood care or foraging. Queen loss leads to ovary development and lifespan extension in workers of many ant species. Howe...

Authors: Marina Choppin, Barbara Feldmeyer and Susanne Foitzik

Integrated omics analysis reveals sirtuin signaling is central to hepatic response to a high fructose diet

Dietary high fructose (HFr) is a known metabolic disruptor contributing to development of obesity and diabetes in Western societies. Initial molecular changes from exposure to HFr on liver metabolism may be es...

Authors: Laura A. Cox, Jeannie Chan, Prahlad Rao, Zeeshan Hamid, Jeremy P. Glenn, Avinash Jadhav, Vivek Das, Genesio M. Karere, Ellen Quillen, Kylie Kavanagh and Michael Olivier

Gene regulatory network analysis defines transcriptome landscape with alternative splicing of human umbilical vein endothelial cells during replicative senescence

Endothelial cell senescence is the state of permanent cell cycle arrest and plays a critical role in the pathogenesis of age-related diseases. However, a comprehensive understanding of the gene regulatory netw...

Authors: Momoko Ohori, Yusuke Nakayama, Mari Ogasawara-Shimizu, Hiroyoshi Toyoshiba, Atsushi Nakanishi, Samuel Aparicio and Shinsuke Araki

Identification and functional deciphering suggested the regulatory roles of long intergenic ncRNAs (lincRNAs) in increasing grafting pepper resistance to Phytophthora capsici

As a popular and valuable technique, grafting is widely used to protect against soil-borne diseases and nematodes in vegetable production. Growing evidences have revealed that long intergenic ncRNAs (lincRNAs)...

Authors: Junliang Yin, Jiahui Yan, Lu Hou, Liling Jiang, Wenrong Xian and Qingyun Guo

Identification and expression analysis of the glycosyltransferase GT43 family members in bamboo reveal their potential function in xylan biosynthesis during rapid growth

Xylan is one of the most abundant hemicelluloses and can crosslink cellulose and lignin to increase the stability of cell walls. A number of genes encoding glycosyltransferases play vital roles in xylan biosyn...

Authors: Zhen Li, Xinyue Wang, Kebin Yang, Chenglei Zhu, Tingting Yuan, Jiongliang Wang, Ying Li and Zhimin Gao

Expression of transport proteins in the rete mirabile of european silver and yellow eel

In physoclist fishes filling of the swimbladder requires acid secretion of gas gland cells to switch on the Root effect and subsequent countercurrent concentration of the initial gas partial pressure increase ...

Authors: Gabriel Schneebauer, Victoria Drechsel, Ron Dirks, Klaus Faserl, Bettina Sarg and Bernd Pelster

Identification of proteins associated with bast fiber growth of ramie by differential proteomic analysis

Ramie is an important fiber-producing crop in China, and its fibers are widely used as textile materials. Fibers contain specialized secondary cellular walls that are mainly composed of cellulose, hemicellulos...

Authors: Fu Li, Zheng Zeng, Renyan Huang, Yanzhou Wang and Touming Liu

Genome-wide identification, characteristics and expression of the prolamin genes in Thinopyrum elongatum

Prolamins, unique to Gramineae (grasses), play a key role in the human diet. Thinopyrum elongatum (syn. Agropyron elongatum or Lophopyrum elongatum), a grass of the Triticeae family with a diploid E genome (2n = ...

Authors: Wenyang Ge, Yu Gao, Shoushen Xu, Xin Ma, Hongwei Wang, Lingrang Kong and Silong Sun

Gene regulatory networks analysis of muscle-invasive bladder cancer subtypes using differential graphical model

Recently, erdafitinib (Balversa), the first targeted therapy drug for genetic alteration, was approved to metastatic urothelial carcinoma. Cancer genomics research has been greatly encouraged. Currently, a lar...

Authors: Yongqing Zhang, Qingyuan Chen, Meiqin Gong, Yuanqi Zeng and Dongrui Gao

An evolutionary genomics view on neuropeptide genes in Hydrozoa and Endocnidozoa (Myxozoa)

The animal phylum Cnidaria consists of six classes or subphyla: Hydrozoa, Scyphozoa, Cubozoa, Staurozoa, Anthozoa, and Endocnidozoa. Cnidarians have an early evolutionary origin, diverging before the emergence...

Authors: Thomas L. Koch, Frank Hauser and Cornelis J. P. Grimmelikhuijzen

Transcriptome analysis of lncRNA expression patterns in human congenital lung malformations

To explore the long non-coding RNA (lncRNA) expression pattern of congenital lung malformations on a genome-wide scale and investigate their potential biological function in four subtypes of congenital lung ma...

Authors: Weili Yang, Pu Zhao, Yun Liu, Ping Cao, Xiang Ji, Ya Gao, Peng Li and Jiwen Cheng

ScLRTC: imputation for single-cell RNA-seq data via low-rank tensor completion

With single-cell RNA sequencing (scRNA-seq) methods, gene expression patterns at the single-cell resolution can be revealed. But as impacted by current technical defects, dropout events in scRNA-seq lead to mi...

Authors: Xiutao Pan, Zhong Li, Shengwei Qin, Minzhe Yu and Hang Hu

Correction to: Characterization of the chicken T cell receptor γ repertoire by high-throughput sequencing

Authors: Tongtong Zhang, Qian Li, Xiaoqing Li, Li Kang, Yunliang Jiang and Yi Sun

Characterisation of novel endogenous geminiviral elements in macadamia

The presence of geminivirus sequences in a preliminary analysis of sRNA sequences from the leaves of macadamia trees with abnormal vertical growth (AVG) syndrome was investigated.

Authors: Mohamed C. M. Zakeel, Andrew D. W. Geering, John E. Thomas and Olufemi A. Akinsanmi

Baiting out a full length sequence from unmapped RNA-seq data

As a powerful tool, RNA-Seq has been widely used in various studies. Usually, unmapped RNA-seq reads have been considered as useless and been trashed or ignored.

Authors: Dongwei Li, Qitong Huang, Lei Huang, Jikai Wen, Jing Luo, Qing Li, Yanling Peng and Yubo Zhang

Holstein Friesian dairy cattle edited for diluted coat color as a potential adaptation to climate change

High-producing Holstein Friesian dairy cattle have a characteristic black and white coat, often with large proportions of black. Compared to a light coat color, black absorbs more solar radiation which is a co...

Authors: G. Laible, S.-A. Cole, B. Brophy, J. Wei, S. Leath, S. Jivanji, M. D. Littlejohn and D. N. Wells

Prediction of functional microexons by transfer learning

Microexons are a particular kind of exon of less than 30 nucleotides in length. More than 60% of annotated human microexons were found to have high levels of sequence conservation, suggesting their potential f...

Authors: Qi Cheng, Bo He, Chengkui Zhao, Hongyuan Bi, Duojiao Chen, Shuangze Han, Haikuan Gao and Weixing Feng

RNAseq analysis of treatment-dependent signaling changes during inflammation in a mouse cutaneous wound healing model

Despite proven therapeutic effects in inflammatory conditions, the specific mechanisms of phytochemical therapies are not well understood. The transcriptome effects of Traumeel (Tr14), a multicomponent natural...

Authors: Georges St. Laurent III, Ian Toma, Bernd Seilheimer, Konstantin Cesnulevicius, Myron Schultz, Michael Tackett, Jianhua Zhou, Maxim Ri, Dmitry Shtokalo, Denis Antonets, Tisha Jepson and Timothy A. McCaffrey

Alternative splicing level related to intron size and organism complexity

Alternative splicing is the process of selecting different combinations of splice sites to produce variably spliced mRNAs. However, the relationships between alternative splicing prevalence and level (ASP/L) a...

Authors: Pengcheng Yang, Depin Wang and Le Kang

Urinary peptidomics reveals proteases involved in idiopathic membranous nephropathy

Idiopathic membranous nephropathy (IMN) is a cause of nephrotic syndrome that is increasing in incidence but has unclear pathogenesis. Urinary peptidomics is a promising technology for elucidating molecular me...

Authors: Baoxu Lin, Jianhua Liu, Yue Zhang, Yabin Wu, Shixiao Chen, Yibo Bai, Qiuying Liu and Xiaosong Qin

Profile of gene expression changes during estrodiol-17β-induced feminization in the Takifugu rubripes brain

As the critical tissue of the central nervous system, the brain has been found to be involved in gonad development. Previous studies have suggested that gonadal fate may be affected by the brain. Identifying b...

Authors: Xufang Shen, Hongwei Yan, Jieming Jiang, Weiyuan Li, Yuyu Xiong, Qi Liu and Ying Liu

Universal probe-based intermediate primer-triggered qPCR (UPIP-qPCR) for SNP genotyping

The detection and identification of single nucleotide polymorphism (SNP) is essential for determining patient disease susceptibility and the delivery of medicines targeted to the individual. At present, SNP ge...

Authors: Baowei Li, Yanran Liu, Xiaodan Hao, Jinhua Dong, Limei Chen, Haimei Li, Wei Wu, Ying Liu, Jianxun Wang, Yin Wang and Peifeng Li

Benchmarking different approaches for Norovirus genome assembly in metagenome samples

Genome assembly of viruses with high mutation rates, such as Norovirus and other RNA viruses, or from metagenome samples, poses a challenge for the scientific community due to the coexistence of several viral ...

Authors: Azahara Fuentes-Trillo, Carolina Monzó, Iris Manzano, Cristina Santiso-Bellón, Juliana da Silva Ribeiro de Andrade, Roberto Gozalbo-Rovira, Ana-Bárbara García-García, Jesús Rodríguez-Díaz and Felipe Javier Chaves

Machine learning approaches to predict the Plant-associated phenotype of Xanthomonas strains

The genus Xanthomonas has long been considered to consist predominantly of plant pathogens, but over the last decade there has been an increasing number of reports on non-pathogenic and endophytic members. As Xan...

Authors: Dennie te Molder, Wasin Poncheewin, Peter J. Schaap and Jasper J. Koehorst

Transcriptome dynamics in developing testes of domestic cats and impact of age on tissue resilience to cryopreservation

Fundamental knowledge of cellular and molecular mechanisms in developing testicular tissues is critical to better understand gonadal biology and responses to non-physiological conditions. The objective of our ...

Authors: Olga Amelkina, Andreia M. da Silva, Alexandre R. Silva and Pierre Comizzoli

Rapidly evolving genetic features for desert adaptations in Stipagrostis pennata

Stipagrostis pennata is distributed in the mobile and semi-mobile sand dunes which can adapt well to extreme environments such as drought and high temperature. It is a pioneer plant species with potential for sta...

Authors: Xixu Ding, Tingting Zhang and Lei Ma

Chromatin enrichment for proteomics in plants (ChEP-P) implicates the histone reader ALFIN-LIKE 6 in jasmonate signalling

Covalent modifications of core histones govern downstream DNA-templated processes such as transcription by altering chromatin structure and function. Previously, we reported that the plant homeodomain protein ...

Authors: Isabel Cristina Vélez-Bermúdez and Wolfgang Schmidt

The whole-genome sequencing in predicting Mycobacterium tuberculosis drug susceptibility and resistance in Papua, Indonesia

Tuberculosis is one of the deadliest disease caused by Mycobacterium tuberculosis. Its treatment still becomes a burden for many countries including Indonesia. Drug resistance is one of the problems in TB treatme...

Authors: Yustinus Maladan, Hana Krismawati, Tri Wahyuni, Ratna Tanjung, Kamla Awaludin, Kholis Abdurachim Audah and Arli Aditya Parikesit

Successful intergeneric transfer of a major apple scab resistance gene (Rvi6) from apple to pear and precise comparison of the downstream molecular mechanisms of this resistance in both species

Scab is the most important fungal disease of apple and pear. Apple (Malus x domestica Borkh.) and European pear (Pyrus communis L.) are genetically related but they are hosts of two different fungal species: Vent...

Authors: L. Perchepied, E. Chevreau, E. Ravon, S. Gaillard, S. Pelletier, M. Bahut, P. Berthelot, R. Cournol, H. J. Schouten and E. Vergne

Comparative analysis of transposable elements provides insights into genome evolution in the genus Camelus

Transposable elements (TEs) are common features in eukaryotic genomes that are known to affect genome evolution critically and to play roles in gene regulation. Vertebrate genomes are dominated by TEs, which c...

Authors: Mohanad A. Ibrahim, Badr M. Al-Shomrani, Mathew Simenc, Sultan N. Alharbi, Fahad H. Alqahtani, Mohamed B. Al-Fageeh and Manee M. Manee

Comparison of carbohydrate ABC importers from Mycobacterium tuberculosis

Mycobacterium tuberculosis, the etiological agent of tuberculosis, has at least four ATP-Binding Cassette (ABC) transporters dedicated to carbohydrate uptake: LpqY/SugABC, UspABC, Rv2038c-41c, and UgpAEBC. LpqY/S...

Authors: Lilia I. De la Torre, José G. Vergara Meza, Sindy Cabarca, André G. Costa-Martins and Andrea Balan

Systematic analysis of the lysine malonylome in Sanghuangporus sanghuang

Sanghuangporus sanghuang is a well-known traditional medicinal mushroom associated with mulberry. Despite the properties of this mushroom being known for many years, the regulatory mechanisms of bioactive compoun...

Authors: Tong Wang, Guangyuan Wang, Guoli Zhang, Ranran Hou, Liwei Zhou and Xuemei Tian

Transcriptome and metabolome analysis to reveal major genes of saikosaponin biosynthesis in Bupleurum chinense

Bupleurum chinense DC. is a widely used traditional Chinese medicinal plant. Saikosaponins are the major bioactive constituents of B. chinense, but relatively little is known about saikosaponin biosynthesis. In t...

Authors: Yilian He, Hua Chen, Jun Zhao, Yuxia Yang, Bin Yang, Liang Feng, Yiguan Zhang, Ping Wei, Dabin Hou, Junning Zhao and Ma Yu

Small RNA sequencing reveals various microRNAs involved in piperine biosynthesis in black pepper (Piper nigrum L.)

Black pepper (Piper nigrum L.), an important and long-cultivated spice crop, is native to South India and grown in the tropics. Piperine is the main pungent and bioactive alkaloid in the berries of black pepper, ...

Authors: Yuanhao Ding, Yuyuan Mao, Yi Cen, Lisong Hu, Yuefeng Su, Xuemin Ma, Lu Long, Haiyan Hu, Chaoyun Hao and Jie Luo

Land use and life history constrain adaptive genetic variation and reduce the capacity for climate change adaptation in turtles

Rapid anthropogenic climate change will require species to adapt to shifting environmental conditions, with successful adaptation dependent upon current patterns of genetic variation. While landscape genomic a...

Authors: Nathan W. Byer, Emily D. Fountain, Brendan N. Reid, Kristen Miller, Paige J. Kulzer and M. Zachariah Peery

Methylome and transcriptome analyses of soybean response to bean pyralid larvae

Bean pyralid is one of the major leaf-feeding insects that affect soybean crops. DNA methylation can control the networks of gene expressions, and it plays an important role in responses to biotic stress. Howe...

Authors: Wei-Ying Zeng, Yu-Rong Tan, Sheng-Feng Long, Zu-Dong Sun, Zhen-Guang Lai, Shou-Zhen Yang, Huai-Zhu Chen and Xia-Yan Qing

The web-based multiplex PCR primer design software Ultiplex and the associated experimental workflow: up to 100- plex multiplicity

A large number of variants have been employed in various medical applications, such as providing medication instructions, disease susceptibility testing, paternity testing, and tumour diagnosis. A high multipl...

Authors: Jie Yuan, Ji Yi, Meixiao Zhan, Qingqing Xie, Ting Ting Zhen, Jian Zhou, Zeqing Li and Zhou Li

Genome-wide characterization and analysis of WRKY transcription factors in Panax ginseng

Panax ginseng is a well-known medicinal plant worldwide. As an herbal medicine, ginseng is also known for its long lifecycle, which can reach several decades. WRKY proteins play regulatory roles in many aspects o...

Authors: Peng Di, Ping Wang, Min Yan, Peng Han, Xinyi Huang, Le Yin, Yan Yan, Yonghua Xu and Yingping Wang

Identification and functional analysis of novel oncogene DDX60L in pancreatic ductal adenocarcinoma

Pancreatic ductal adenocarcinoma (PDAC) is a lethal cancer. Approximately 80% of patients initially diagnosed with locally advanced or metastatic disease survive only 4–11 months after diagnosis. Tremendous ef...

Authors: Hongjin Wu, Weiwei Tian, Xiang Tai, Xuanpeng Li, Ziwei Li, Jing Shui, Juehua Yu, Zhihua Wang and Xiaosong Zhu

A novel approach to co-expression network analysis identifies modules and genes relevant for moulting and development in the Atlantic salmon louse (Lepeophtheirus salmonis)

The salmon louse (Lepeophtheirus salmonis) is an obligate ectoparasitic copepod living on Atlantic salmon and other salmonids in the marine environment. Salmon lice cause a number of environmental problems and le...

Authors: Zhaoran Zhou, Christiane Eichner, Frank Nilsen, Inge Jonassen and Michael Dondrup

Telomere-to-telomere genome assembly of asparaginase-producing Trichoderma simmonsii

Trichoderma is a genus of fungi in the family Hypocreaceae and includes species known to produce enzymes with commercial use. They are largely found in soil and terrestrial plants. Recently, Trichoderma simmonsii

Authors: Dawoon Chung, Yong Min Kwon and Youngik Yang

Comprehensive characterization of copy number variation (CNV) called from array, long- and short-read data

SNP arrays, short- and long-read genome sequencing are genome-wide high-throughput technologies that may be used to assay copy number variants (CNVs) in a personal genome. Each of these technologies comes with...

Authors: Ksenia Lavrichenko, Stefan Johansson and Inge Jonassen