Articles

Gene regulation network analyses of pistil development in papaya

The pistil is an essential part of flowers that functions in the differentiation of the sexes and reproduction in plants. The stigma on the pistil can accept pollen to allow fertilization and seed development....

Authors: Zhenyang Liao, Fei Dong, Juan Liu, Lele Xu, Amy Marshall-Colon and Ray Ming

Regulation of fatty acid desaturase- and immunity gene-expression by mbk-1/DYRK1A in Caenorhabditis elegans

In the nematode Caenorhabditis elegans, longevity in response to germline ablation, but not in response to reduced insulin/IGF1-like signaling, is strongly dependent on the conserved protein kinase minibrain-rela...

Authors: Hildegard I. D. Mack, Jennifer Kremer, Eva Albertini, Elisabeth K. M. Mack and Pidder Jansen-Dürr

Correction to: Genome-wide and comparative phylogenetic analysis of senescence-associated NAC transcription factors in sunfower (Helianthus annuus)

Authors: Sofa A. Bengoa Luoni, Alberto Cenci, Sebastian Moschen, Salvador Nicosia, Laura M. Radonic, Julia V. Sabio y García, Nicolas B. Langlade, Denis Vile, Cecilia Vazquez Rovere and Paula Fernandez

The genomic structure of isolation across breed, country and strain for important South African and Australian sheep populations

South Africa and Australia shares multiple important sheep breeds. For some of these breeds, genomic breeding values are provided to breeders in Australia, but not yet in South Africa. Combining genomic resour...

Authors: Cornelius Nel, Phillip Gurman, Andrew Swan, Julius van der Werf, Margaretha Snyman, Kennedy Dzama, Klint Gore, Anna Scholtz and Schalk Cloete

Genome-wide identification and functional analysis of circRNAs in Trichophyton rubrum conidial and mycelial stages

Circular RNAs (circRNAs) are a group of noncoding RNAs that participate in gene expression regulation in various pathways. The essential roles of circRNAs have been revealed in many species. However, knowledge...

Authors: Xingwei Cao, Xingye Xu, Jie Dong, Ying Xue, Lilian Sun, Yafang Zhu, Tao Liu and Qi Jin

Nearby transposable elements impact plant stress gene regulatory networks: a meta-analysis in A. thaliana and S. lycopersicum

Transposable elements (TE) make up a large portion of many plant genomes and are playing innovative roles in genome evolution. Several TEs can contribute to gene regulation by influencing expression of nearby ...

Authors: Jan Deneweth, Yves Van de Peer and Vanessa Vermeirssen

Gene expression profiling of trout muscle during flesh quality recovery following spawning

Sexual maturation causes loss of fish muscle mass and deterioration of fillet quality attributes that prevent market success. We recently showed that fillet yield and flesh quality recover in female trout afte...

Authors: Yéléhi-Diane Ahongo, Aurélie Le Cam, Jérôme Montfort, Jérôme Bugeon, Florence Lefèvre and Pierre-Yves Rescan

Comparative pangenomics: analysis of 12 microbial pathogen pangenomes reveals conserved global structures of genetic and functional diversity

With the exponential growth of publicly available genome sequences, pangenome analyses have provided increasingly complete pictures of genetic diversity for many microbial species. However, relatively few stud...

Authors: Jason C. Hyun, Jonathan M. Monk and Bernhard O. Palsson

Identification of an integrated stress and growth response signaling switch that directs vertebrate intestinal regeneration

Snakes exhibit extreme intestinal regeneration following months-long fasts that involves unparalleled increases in metabolism, function, and tissue growth, but the specific molecular control of this process is...

Authors: Aundrea K. Westfall, Blair W. Perry, Abu H. M. Kamal, Nicole R. Hales, Jarren C. Kay, Madhab Sapkota, Drew R. Schield, Mark W. Pellegrino, Stephen M. Secor, Saiful M. Chowdhury and Todd A. Castoe

Transcriptomic analysis of the maize inbred line Chang7-2 and a large-grain mutant tc19

Grain size is a key factor in crop yield that gradually develops after pollination. However, few studies have reported gene expression patterns in maize grain development using large-grain mutants. To investig...

Authors: Yanrong Zhang, Fuchao Jiao, Jun Li, Yuhe Pei, Meiai Zhao, Xiyun Song and Xinmei Guo

Inferring the genetic responses to acute drought stress across an ecological gradient

How do xerophytic species thrive in environments that experience extreme annual drought? Although critical to the survival of many species, the genetic responses to drought stress in many non-model organisms h...

Authors: Jessica K. Devitt, Albert Chung and John J. Schenk

Developmental and Injury-induced Changes in DNA Methylation in Regenerative versus Non-regenerative Regions of the Vertebrate Central Nervous System

Because some of its CNS neurons (e.g., retinal ganglion cells after optic nerve crush (ONC)) regenerate axons throughout life, whereas others (e.g., hindbrain neurons after spinal cord injury (SCI)) lose this cap...

Authors: Sergei Reverdatto, Aparna Prasad, Jamie L. Belrose, Xiang Zhang, Morgan A. Sammons, Kurt M. Gibbs and Ben G. Szaro

Comprehensive analysis of the long noncoding RNA-associated competitive endogenous RNA network in the osteogenic differentiation of periodontal ligament stem cells

The mechanism implicated in the osteogenesis of human periodontal ligament stem cells (PDLSCs) has been investigated for years. Previous genomics data analyses showed that long noncoding RNA (lncRNA), microRNA...

Authors: Lingzhi Lai, Zhaodan Wang, Yihong Ge, Wei Qiu, Buling Wu, Fuchun Fang, Huiyong Xu and Zhao Chen

New insights into the evolution of SPX gene family from algae to legumes; a focus on soybean

SPX-containing proteins have been known as key players in phosphate signaling and homeostasis. In Arabidopsis and rice, functions of some SPXs have been characterized, but little is known about their function ...

Authors: Mahnaz Nezamivand-Chegini, Esmaeil Ebrahimie, Ahmad Tahmasebi, Ali Moghadam, Saeid Eshghi, Manijeh Mohammadi-Dehchesmeh, Stanislav Kopriva and Ali Niazi

Epigenetic features improve TALE target prediction

The yield of many crop plants can be substantially reduced by plant-pathogenic Xanthomonas bacteria. The infection strategy of many Xanthomonas strains is based on transcription activator-like effectors (TALEs), ...

Authors: Annett Erkes, Stefanie Mücke, Maik Reschke, Jens Boch and Jan Grau

Correction to: Methylome and transcriptome analyses of soybean response to bean pyralid larvae

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

A systematic review and meta-analysis of host genetic factors associated with influenza severity

The severity of influenza disease can range from mild symptoms to severe respiratory failure and can partly be explained by host genetic factors that predisposes the host to severe influenza. Here, we aimed to...

Authors: Nina Van Goethem, Célestin Danwang, Nathalie Bossuyt, Herman Van Oyen, Nancy H. C. Roosens and Annie Robert

Comparative transcriptome and DNA methylation analysis in temperature-sensitive genic male sterile wheat BS366

Known as the prerequisite component for the heterosis breeding system, the male sterile line determines the hybrid yield and seed purity. Therefore, a deep understanding of the mechanism and gene network that ...

Authors: Yong-jie Liu, Dan Li, Jie Gong, Yong-bo Wang, Zhao-bo Chen, Bin-shuang Pang, Xian-chao Chen, Jian-gang Gao, Wei-bing Yang, Feng-ting Zhang, Yi-miao Tang, Chang-ping Zhao and Shi-qing Gao

GEP-EpiSeeker: a gene expression programming-based method for epistatic interaction detection in genome-wide association studies

Identification of epistatic interactions provides a systematic way for exploring associations among different single nucleotide polymorphism (SNP) and complex diseases. Although considerable progress has been ...

Authors: Yu Zhong Peng, Yanmei Lin, Yiran Huang, Ying Li, Guangsheng Luo and Jianping Liao

Intellectual disability genomics: current state, pitfalls and future challenges

Intellectual disability (ID) can be caused by non-genetic and genetic factors, the latter being responsible for more than 1700 ID-related disorders. The broad ID phenotypic and genetic heterogeneity, as well a...

Authors: Nuno Maia, Maria João Nabais Sá, Manuel Melo-Pires, Arjan P. M. de Brouwer and Paula Jorge

InMut-finder: a software tool for insertion identification in mutagenesis using Nanopore long reads

Biological mutagens (such as transposon) with sequences inserted, play a crucial role to link observed phenotype and genotype in reverse genetic studies. For this reason, accurate and efficient software tools ...

Authors: Rui Song, Ziyao Wang, Hui Wang, Han Zhang, Xuemeng Wang, Hanh Nguyen, David Holding, Bin Yu, Tom Clemente, Shangang Jia and Chi Zhang

Bioinformatic comparison of Kunitz protease inhibitors in Echinococcus granulosus sensu stricto and E. multilocularis and the genes expressed in different developmental stages of E. granulosus s.s.

Cystic and alveolar echinococcosis caused by the tapeworms Echinococcus granulosus sensu stricto (s.s.) and E. multilocularis, respectively, are important zoonotic diseases. Protease inhibitors are crucial for...

Authors: Hui Zhang, Mengxiao Tian, Wenjing Qi, Juan Wu, Huajun Zheng, Gang Guo, Liang Zhang, Shiwanthi L. Ranasinghe, Donald P. McManus, Jun Li and Wenbao Zhang

Comprehensive epigenomic profiling of human alveolar epithelial differentiation identifies key epigenetic states and transcription factor co-regulatory networks for maintenance of distal lung identity

Disruption of alveolar epithelial cell (AEC) differentiation is implicated in distal lung diseases such as chronic obstructive pulmonary disease, idiopathic pulmonary fibrosis, and lung adenocarcinoma that imp...

Authors: B. Zhou, T. R. Stueve, E. A. Mihalakakos, L. Miao, D. Mullen, Y. Wang, Y. Liu, J. Luo, E. Tran, K. D. Siegmund, S. K. Lynch, A. L. Ryan, I. A. Offringa, Z. Borok and C. N. Marconett

Design and performance of a bovine 200 k SNP chip developed for endangered German Black Pied cattle (DSN)

German Black Pied cattle (DSN) are an endangered dual-purpose breed which was largely replaced by Holstein cattle due to their lower milk yield. DSN cattle are kept as a genetic reserve with a current herd siz...

Authors: Guilherme B. Neumann, Paula Korkuć, Danny Arends, Manuel J. Wolf, Katharina May, Monika Reißmann, Salma Elzaki, Sven König and Gudrun A. Brockmann

Multi-omics analyses of early liver injury reveals cell-type-specific transcriptional and epigenomic shift

Liver fibrosis is a wound-healing response to tissue injury and inflammation hallmarked by the extracellular matrix (ECM) protein deposition in the liver parenchyma and tissue remodelling. Different cell types...

Authors: Maciej Migdał, Eugeniusz Tralle, Karim Abu Nahia, Łukasz Bugajski, Katarzyna Zofia Kędzierska, Filip Garbicz, Katarzyna Piwocka, Cecilia Lanny Winata and Michał Pawlak

The Dawn of next generation DNA sequencing in myelodysplastic syndromes- experience from Pakistan

Myelodysplastic syndromes (MDS) are clonal disorders of hematopoietic stem cells exhibiting ineffective hematopoiesis and tendency for transformation into acute myeloid leukemia (AML). The available karyotypin...

Authors: Nida Anwar, Faheem Ahmed Memon, Saba Shahid, Muhammad Shakeel, Muhammad Irfan, Aisha Arshad, Arshi Naz, Ikram Din Ujjan and Tahir Shamsi

Using DNA testing for the precise, definite, and low-cost diagnosis of sickle cell disease and other Haemoglobinopathies: findings from Tanzania

Sickle cell disease (SCD) is an important cause of under-five mortality. Tanzania is the 5th country in the world with the highest births prevalence of SCD individuals. Significant advances in the neonatal dia...

Authors: Heavenlight Christopher, Adam Burns, Emmanuel Josephat, Julie Makani, Anna Schuh and Siana Nkya

Genome-wide identification of enhancers and transcription factors regulating the myogenic differentiation of bovine satellite cells

Satellite cells are the myogenic precursor cells in adult skeletal muscle. The objective of this study was to identify enhancers and transcription factors that regulate gene expression during the differentiati...

Authors: Pengcheng Lyu, Robert E. Settlage and Honglin Jiang

Mapping pre-harvest sprouting resistance loci in AAC Innova × AAC Tenacious spring wheat population

Pre-harvest sprouting (PHS) is a major problem for wheat production due to its direct detrimental effects on wheat yield, end-use quality and seed viability. Annually, PHS is estimated to cause > 1.0 billion U...

Authors: Raman Dhariwal, Colin W. Hiebert, Mark E. Sorrells, Dean Spaner, Robert J. Graf, Jaswinder Singh and Harpinder S. Randhawa

Transcriptome comparative analysis of ovarian follicles reveals the key genes and signaling pathways implicated in hen egg production

Ovarian follicle development plays an important role in determination of poultry egg production. The follicles at the various developmental stages possess their own distinct molecular genetic characteristics a...

Authors: Xue Sun, Xiaoxia Chen, Jinghua Zhao, Chang Ma, Chunchi Yan, Simushi Liswaniso, Rifu Xu and Ning Qin

A high-continuity and annotated tomato reference genome

Genetic and functional genomics studies require a high-quality genome assembly. Tomato (Solanum lycopersicum), an important horticultural crop, is an ideal model species for the study of fruit development.

Authors: Xiao Su, Baoan Wang, Xiaolin Geng, Yuefan Du, Qinqin Yang, Bin Liang, Ge Meng, Qiang Gao, Wencai Yang, Yingfang Zhu and Tao Lin

The genetic scenario of Mercheros: an under-represented group within the Iberian Peninsula

The general picture of human genetic variation has been vastly depicted in the last years, yet many populations remain broadly understudied. In this work, we analyze for the first time the Merchero population,...

Authors: André Flores-Bello, Neus Font-Porterias, Julen Aizpurua-Iraola, Sara Duarri-Redondo and David Comas

Seminal fluid proteins induce transcriptome changes in the Aedes aegypti female lower reproductive tract

Mating induces behavioral and physiological changes in the arbovirus vector Aedes aegypti, including stimulation of egg development and oviposition, increased survival, and reluctance to re-mate with subsequent m...

Authors: I. Alexandra Amaro, Yasir H. Ahmed-Braimah, Garrett P. League, Sylvie A. Pitcher, Frank W. Avila, Priscilla C. Cruz, Laura C. Harrington and Mariana F. Wolfner

Correction to: Testing assembly strategies of Francisella tularensis genomes to infer an evolutionary conservation analysis of genomic structures

Authors: Kerstin Neubert, Eric Zuchantke, Robert Maximilian Leidenfrost, Röbbe Wünschiers, Josephine Grützke, Burkhard Malorny, Holger Brendebach, Sascha Al Dahouk, Timo Homeier, Helmut Hotzel, Knut Reinert, Herbert Tomaso and Anne Busch

Genetic stability of Aedes aegypti populations following invasion by wMel Wolbachia

Wolbachia wMel is the most commonly used strain in rear and release strategies for Aedes aegypti mosquitoes that aim to inhibit the transmission of arboviruses such as dengue, Zika, Chikungunya and yellow fever....

Authors: Meng-Jia Lau, Thomas L. Schmidt, Qiong Yang, Jessica Chung, Lucien Sankey, Perran A. Ross and Ary A. Hoffmann

Genome-wide and comparative phylogenetic analysis of senescence-associated NAC transcription factors in sunflower (Helianthus annuus)

Leaf senescence delay impacts positively in grain yield by maintaining the photosynthetic area during the reproductive stage and during grain filling. Therefore a comprehensive understanding of the gene famili...

Authors: Sofia A. Bengoa Luoni, Alberto Cenci, Sebastian Moschen, Salvador Nicosia, Laura M. Radonic, Julia V. Sabio y García, Nicolas B. Langlade, Denis Vile, Cecilia Vazquez Rovere and Paula Fernandez

The effect of lipocalin-2 (LCN2) on apoptosis: a proteomics analysis study in an LCN2 deficient mouse model

Recent studies have shown that lipocalin-2 (LCN2) has multiple functions involved in various biological and pathological processes including energy homeostasis, cancer, inflammation, and apoptosis. We aimed to...

Authors: Dongming Wu, Xiaopeng Wang, Ye Han and Yayun Wang

Transcriptomic analysis of resistance and short-term induction response to pyrethroids, in Anopheles coluzzii legs

Insecticide-treated bed nets and indoor residual spraying comprise the major control measures against Anopheles gambiae sl, the dominant vector in sub-Saharan Africa. The primary site of contact with insecticide ...

Authors: M. Kefi, J. Charamis, V. Balabanidou, P. Ioannidis, H. Ranson, V. A. Ingham and J. Vontas

Putative antigenic proteins identified by comparative and subtractive reverse vaccinology in necrotic enteritis-causing Clostridium perfringens isolated from broiler chickens

Avian necrotic enteritis (NE) caused by Clostridium perfringens is a disease with a major economic impact, generating losses estimated to 6 billion of dollars annually for the poultry industry worldwide. The inci...

Authors: Ilhem Meniaï, Alexandre Thibodeau, Sylvain Quessy, Valeria R. Parreira, Philippe Fravalo, Guy Beauchamp and Marie-Lou Gaucher

Genome-wide characterization, evolution, structure, and expression analysis of the F-box genes in Caenorhabditis

F-box proteins represent a diverse class of adaptor proteins of the ubiquitin-proteasome system (UPS) that play critical roles in the cell cycle, signal transduction, and immune response by removing or modifyi...

Authors: Ailan Wang, Wei Chen and Shiheng Tao

Biological factors in the synthetic construction of overlapping genes

Overlapping genes (OLGs) with long protein-coding overlapping sequences are disallowed by standard genome annotation programs, outside of viruses. Recently however they have been discovered in Archaea, diverse...

Authors: Stefan Wichmann, Siegfried Scherer and Zachary Ardern

Interaction between Rag genes results in a unique synergistic transcriptional response that enhances soybean resistance to soybean aphids

Pyramiding different resistance genes into one plant genotype confers enhanced resistance at the phenotypic level, but the molecular mechanisms underlying this effect are not well-understood. In soybean, aphid...

Authors: Martha I. Natukunda, Jessica D. Hohenstein, Chantal E. McCabe, Michelle A. Graham, Yunhui Qi, Asheesh K. Singh and Gustavo C. MacIntosh

Regulatory modules of human thermogenic adipocytes: functional genomics of large cohort and Meta-analysis derived marker-genes

Recently, ProFAT and BATLAS studies identified brown and white adipocytes marker genes based on analysis of large databases. They offered scores to determine the thermogenic status of adipocytes using the gene...

Authors: Beáta B. Tóth, Zoltán Barta, Ákos Barnabás Barta and László Fésüs

Transcriptomic and metabolomic changes triggered by Macrosiphum rosivorum in rose (Rosa longicuspis)

Rose is one of the most popular flowers in the wold. Its field growth and quality are negatively affected by aphids. However, the defence mechanisms used by rose plants against aphids are unclear. Therefore, t...

Authors: Penghua Gao, Hao Zhang, Huijun Yan, Ningning Zhou, Bo Yan, Yuanlan Fan, Kaixue Tang and Xianqin Qiu

Th17 cell differentiation induced by cytopathogenic biotype BVDV-2 in bovine PBLCs

Bovine viral diarrhea virus (BVDV) is a major pathogen that causes bovine viral diarrhea/mucosal disease (BVD-MD), which has become a global infectious disease due to its wide spread and the lack of effective ...

Authors: Yanping Li, Tingli Liu, Guoliang Chen, Liqun Wang, Aimin Guo, Zhi Li, Li Pan, Li Mao and Xuenong Luo

Genome-wide and expression analysis of B-box gene family in pepper

BBX transcription factors are a kind of zinc finger transcription factors with one or two B-box domains, which partilant in plant growth, development and response to abiotic or biotic stress. The BBX family ha...

Authors: Jing Ma, Jia-xi Dai, Xiao-wei Liu and Duo Lin

QTL and candidate gene identification of the node of the first fruiting branch (NFFB) by QTL-seq in upland cotton (Gossypium hirsutum L.)

The node of the first fruiting branch (NFFB) is an important precocious trait in cotton. Many studies have been conducted on the localization of quantitative trait loci (QTLs) and genes related to fiber qualit...

Authors: Jingjing Zhang, Xiaoyun Jia, Xiaohao Guo, Hengling Wei, Meng Zhang, Aimin Wu, Shuaishuai Cheng, Xiaoqian Cheng, Shuxun Yu and Hantao Wang

Complete chloroplast genome of Stephania tetrandra (Menispermaceae) from Zhejiang Province: insights into molecular structures, comparative genome analysis, mutational hotspots and phylogenetic relationships

The Stephania tetrandra S. Moore (S. tetrandra) is a medicinal plant belonging to the family Menispermaceae that has high medicinal value and is well worth doing further exploration. The wild resources of S. tetr...

Authors: Shujie Dong, Zhiqi Ying, Shuisheng Yu, Qirui Wang, Guanghui Liao, Yuqing Ge and Rubin Cheng

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