Articles

The transcription factor reservoir and chromatin landscape in activated plasmacytoid dendritic cells

Transcription factors (TFs) control gene expression by direct binding to regulatory regions of target genes but also by impacting chromatin landscapes and modulating DNA accessibility for other TFs. In recent ...

Authors: Ritu Mann-Nüttel, Shafaqat Ali, Patrick Petzsch, Karl Köhrer, Judith Alferink and Stefanie Scheu

Correction to: Transcriptome signature of miRNA-26b KO mouse model suggests novel targets

Authors: Emiel P. C. van der Vorst, Mario A. A. Pepe, Linsey J. F. Peters, Markus Haberbosch, Yvonne Jansen, Ronald Naumann, Georgios T. Stathopoulos, Christian Weber and Kiril Bidzhekov

Development and validation of a 1 K sika deer (Cervus nippon) SNP Chip

China is the birthplace of the deer family and the country with the most abundant deer resources. However, at present, China’s deer industry faces the problem that pure sika deer and hybrid deer cannot be easi...

Authors: Huanhuan Fan, Tianjiao Wang, Yang Li, Huitao Liu, Yimeng Dong, Ranran Zhang, Hongliang Wang, Liyuan Shang and Xiumei Xing

Transcriptomic analysis of salt tolerance-associated genes and diversity analysis using indel markers in yardlong bean (Vigna unguiculata ssp. sesquipedialis)

High salinity is a devastating abiotic stresses for crops. To understand the molecular basis of salinity stress in yardlong bean (Vigna unguiculata ssp. sesquipedalis), and to develop robust markers for improving...

Authors: Hongmei Zhang, Wenjing Xu, Huatao Chen, Jingbin Chen, Xiaoqing Liu, Xin Chen and Shouping Yang

The choice of negative control antisense oligonucleotides dramatically impacts downstream analysis depending on the cellular background

The lymphatic and the blood vasculature are closely related systems that collaborate to ensure the organism’s physiological function. Despite their common developmental origin, they present distinct functional...

Authors: Luca Ducoli, Saumya Agrawal, Chung-Chau Hon, Jordan A. Ramilowski, Eliane Sibler, Michihira Tagami, Masayoshi Itoh, Naoto Kondo, Imad Abugessaisa, Akira Hasegawa, Takeya Kasukawa, Harukazu Suzuki, Piero Carninci, Jay W. Shin, Michiel J. L. de Hoon and Michael Detmar

Dynamic transcriptome profiles of postnatal porcine skeletal muscle growth and development

Skeletal muscle growth and development are closely associated with the quantity and quality of pork production. We performed a transcriptomic analysis of 12 Longissimus dorsi muscle samples from Tibetan piglets a...

Authors: Yanping Wang, Jiying Wang, Hongmei Hu, Huaizhong Wang, Cheng Wang, Haichao Lin and Xueyan Zhao

Genome-wide association study identifies new loci associated with noise-induced tinnitus in Chinese populations

Tinnitus is an auditory phantom sensation in the absence of an acoustic stimulus, which affects nearly 15% of the population. Excessive noise exposure is one of the main causes of tinnitus. To now, the knowled...

Authors: Chengyong Xie, Yuguang Niu, Jie Ping, Yahui Wang, Chenning Yang, Yuanfeng Li and Gangqiao Zhou

DNA methylation changes in African American women with a history of preterm birth from the InterGEN study

Preterm birth (< 37 weeks’ gestation) is a common outcome of pregnancy that has been associated with increased risk of cardiovascular disease for women later in life. Little is known about the physiologic mech...

Authors: Veronica Barcelona, Janitza L. Montalvo-Ortiz, Michelle L. Wright, Sheila T. Nagamatsu, Caitlin Dreisbach, Cindy A. Crusto, Yan V. Sun and Jacquelyn Y. Taylor

Insights into 6S RNA in lactic acid bacteria (LAB)

6S RNA is a regulator of cellular transcription that tunes the metabolism of cells. This small non-coding RNA is found in nearly all bacteria and among the most abundant transcripts. Lactic acid bacteria (LAB)...

Authors: Pablo Gabriel Cataldo, Paul Klemm, Marietta Thüring, Lucila Saavedra, Elvira Maria Hebert, Roland K. Hartmann and Marcus Lechner

Transcriptome profiling provides insights into the molecular mechanisms of maize kernel and silk development

Maize kernel filling, which is closely related to the process of double fertilization and is sensitive to a variety of environmental conditions, is an important component of maize yield determination. Silk is ...

Authors: Ting Li, Yapeng Wang, Yaqin Shi, Xiaonan Gou, Bingpeng Yang, Jianzhou Qu, Xinghua Zhang, Jiquan Xue and Shutu Xu

Complete genome sequence of an extensively drug resistant (XDR) M. morganii SMM01 isolated from a patient with urinary and fecal incontinence

M. morganii is a gram-negative, non-lactose fermenting and an opportunistic pathogen frequently associated with nosocomial infections. Although first isolated in 1906 from a pediatric fecal sample, not many M. mo...

Authors: Pachi Pulusu Chanakya, Balaram Khamari, Manmath Lama, Arun Sai Kumar Peketi, Prakash Kumar, Valakunja Nagaraja and Eswarappa Pradeep Bulagonda

Dissection of the impact of prioritized QTL-linked and -unlinked SNP markers on the accuracy of genomic selection¹

Use of genomic information has resulted in an undeniable improvement in prediction accuracies and an increase in genetic gain in animal and plant genetic selection programs in spite of oversimplified assumptio...

Authors: Ashley S. Ling, El Hamidi Hay, Samuel E. Aggrey and Romdhane Rekaya

Characterization and comparative analysis of transcriptional profiles of porcine colostrum and mature milk at different parities

Porcine milk is a complex fluid, containing a myriad of immunological, biochemical, and cellular components, made to satisfy the nutritional requirements of the neonate. Whole milk contains many different cell...

Authors: Brittney N. Keel, Amanda K. Lindholm-Perry, William T. Oliver, James E. Wells, Shuna A. Jones and Lea A. Rempel

A statistical measure for the skewness of X chromosome inactivation for quantitative traits and its application to the MCTFR data

X chromosome inactivation (XCI) is that one of two chromosomes in mammalian females is silenced during early development of embryos. There has been a statistical measure for the degree of the skewness of XCI f...

Authors: Bao-Hui Li, Wen-Yi Yu and Ji-Yuan Zhou

Transcriptome signature of miRNA-26b KO mouse model suggests novel targets

MicroRNAs (miRNAs) are short (20–24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRN...

Authors: Emiel P. C. van der Vorst, Mario A. A. Pepe, Linsey J. F. Peters, Markus Haberbosch, Yvonne Jansen, Ronald Naumann, Georgios T. Stathopoulos, Christian Weber and Kiril Bidzhekov

How well do genetic markers inform about responses to intraspecific admixture? A comparative analysis of microsatellites and RADseq

Fitness consequences of intraspecific genetic admixture can vary from positive to negative depending on the genetic composition of the populations and environmental conditions. Because admixture has potential ...

Authors: Yeşerin Yıldırım, Anders Forsman and Johanna Sunde

Genome-wide DNA methylation analysis in Chinese Chenghua and Yorkshire pigs

The Chinese Chenghua pig (CHP) is a typical Chinese domestic fatty pig breed with superior meat quality characteristics, while the Yorkshire pig (YP) has the characteristics of fast growth and a high rate of l...

Authors: Kai Wang, Pingxian Wu, Shujie Wang, Xiang Ji, Dong Chen, Anan Jiang, Weihang Xiao, Yiren Gu, Yanzhi Jiang, Yangshuang Zeng, Xu Xu, Xuewei Li and Guoqing Tang

Mapping methylation quantitative trait loci in cardiac tissues nominates risk loci and biological pathways in congenital heart disease

Most congenital heart defects (CHDs) result from complex interactions among genetic susceptibilities, epigenetic modifications, and maternal environmental exposures. Characterizing the complex relationship bet...

Authors: Ming Li, Chen Lyu, Manyan Huang, Catherine Do, Benjamin Tycko, Philip J. Lupo, Stewart L. MacLeod, Christopher E. Randolph, Nianjun Liu, John S. Witte and Charlotte A. Hobbs

Comparative transcriptome analysis of Alpinia oxyphylla Miq. reveals tissue-specific expression of flavonoid biosynthesis genes

Alpinia oxyphylla Miq. is an important edible and medicinal herb, and its dried fruits are widely used in traditional herbal medicine. Flavonoids are one of the main chemical compounds in A. oxyphylla; however, t...

Authors: Lin Yuan, Kun Pan, Yonghui Li, Bo Yi and Bingmiao Gao

Analysis of selection signatures on the Z chromosome of bidirectional selection broiler lines for the assessment of abdominal fat content

The discovery of selection signatures has enabled the identification of genomics regions under selective pressure, enhancing knowledge of evolutionary genotype-phenotypes. Sex chromosomes play an important rol...

Authors: Tao Wang, Meng Zhou, Jing Guo, Yuan-Yuan Guo, Kun Ding, Peng Wang and Zhi-Peng Wang

Chromosomal characteristics of salt stress heritable gene expression in the rice genome

Gene expression is potentially an important heritable quantitative trait that mediates between genetic variation and higher-level complex phenotypes through time and condition-dependent regulatory interactions...

Authors: Matthew T. McGowan, Zhiwu Zhang and Stephen P. Ficklin

Genome-wide (ChIP-seq) identification of target genes regulated by WRKY33 during submergence stress in Arabidopsis

Hypoxia induced by flooding causes significant losses to crop production almost every year. However, the molecular network of submergence signaling pathway is still poorly understood. According to previous stu...

Authors: Junlin Zhang, Bao Liu, Yan Song, Yang Chen, Jiao Fu, Jianquan Liu, Tao Ma, Zhenxiang Xi and Huanhuan Liu

De novo genome assembly and analysis unveil biosynthetic and metabolic potentials of Pseudomonas fragi A13BB

The role of rhizosphere microbiome in supporting plant growth under biotic stress is well documented. Rhizobacteria ward off phytopathogens through various mechanisms including antibiosis. We sought to recover...

Authors: Opeyemi K. Awolope, Noelle H. O’Driscoll, Alberto Di Salvo and Andrew J. Lamb

Association between apolipoprotein gene polymorphisms and hyperlipidemia: a meta-analysis

Hyperlipidemia plays an important role in the etiology of cardio-cerebrovascular disease. Over recent years, a number of studies have explored the impact of apolipoprotein genetic polymorphisms in hyperlipidem...

Authors: Xiao-Ning Zhao, Quan Sun, You-Qin Cao, Xiao Ran and Yu Cao

Long-term dynamic compression enhancement TGF-β3-induced chondrogenesis in bovine stem cells: a gene expression analysis

Bioengineering has demonstrated the potential of utilising mesenchymal stem cells (MSCs), growth factors, and mechanical stimuli to treat cartilage defects. However, the underlying genes and pathways are large...

Authors: Jishizhan Chen, Lidan Chen, Jia Hua and Wenhui Song

Cloning and expression analysis of GATA1 gene in Carassius auratus red var

GATA1 is a key transcription factor in the GATA family, and promotes the differentiation and maturation of red blood cell, which is essential for normal hematopoiesis.

Authors: Yusu Tian, Yuandong Sun, Mi Ou, Xiaojuan Cui, Dinggang Zhou and Wen’an Che

Enhanced tolerance to drought stress resulting from Caragana korshinskii CkWRKY33 in transgenic Arabidopsis thaliana

It is well known that WRKY transcription factors play important roles in plant growth and development, defense regulation and stress responses.

Authors: Zhen Li, Fengping Liang, Tianbao Zhang, Na Fu, Xinwu Pei and Yan Long

Genome-wide association studies of plant architecture-related traits and 100-seed weight in soybean landraces

Plant architecture-related traits (e.g., plant height (PH), number of nodes on main stem (NN), branch number (BN) and stem diameter (DI)) and 100-seed weight (100-SW) are important agronomic traits and are clo...

Authors: Xiaoli Zhang, Wentao Ding, Dong Xue, Xiangnan Li, Yang Zhou, Jiacheng Shen, Jianying Feng, Na Guo, Lijuan Qiu, Han Xing and Jinming Zhao

Pineal gland transcriptomic profiling reveals the differential regulation of lncRNA and mRNA related to prolificacy in STH sheep with two FecB genotypes

Long noncoding RNA (lncRNA) has been identified as important regulator in hypothalamic-pituitary-ovarian axis associated with sheep prolificacy. However, little is known of their expression pattern and potenti...

Authors: Chunyan Li, Xiaoyun He, Zijun Zhang, Chunhuan Ren and Mingxing Chu

A simple method to estimate the in-house limit of detection for genetic mutations with low allele frequencies in whole-exome sequencing analysis by next-generation sequencing

Next-generation sequencing (NGS) has profoundly changed the approach to genetic/genomic research. Particularly, the clinical utility of NGS in detecting mutations associated with disease risk has contributed t...

Authors: Takumi Miura, Satoshi Yasuda and Yoji Sato

Genetic diversity analysis of brown marmorated stink bug, Halyomorpha halys based on mitochondrial COI and COII haplotypes

In the past decade, the brown marmorated stink bug (BMSB), Halyomorpha halys (Hemiptera: Pentatomidae) has caused extensive damage to global agriculture. As a high-risk pest for many countries, including New Zeal...

Authors: Juncong Yan, Chandan Pal, Diane Anderson, Gábor Vétek, Péter Farkas, Allan Burne, Qing-Hai Fan, Jinping Zhang, Disna N. Gunawardana, Rebijith Kayattukandy Balan, Sherly George and Dongmei Li

Comparative transcriptome analysis reveals novel insights into transcriptional responses to phosphorus starvation in oil palm (Elaeis guineensis) root

Phosphorus (P), in its orthophosphate form (Pi) is an essential macronutrient for oil palm early growth development in which Pi deficiency could later on be reflected in lower biomass production. Application o...

Authors: Sze-Ling Kong, Siti Nor Akmar Abdullah, Chai-Ling Ho, Mohamed Hanafi bin Musa and Wan-Chin Yeap

Correction to: Analyzing a putative enhancer of optic disc morphology

An amendment to this paper has been published and can be accessed via the original article.

Authors: Vladimir N. Babenko, Roman O. Babenko and Yuriy N. Orlov

The influence of QTL allelic diversity on QTL detection in multi-parent populations: a simulation study in sugar beet

Multi-parent populations (MPPs) are important resources for studying plant genetic architecture and detecting quantitative trait loci (QTLs). In MPPs, the QTL effects can show various levels of allelic diversi...

Authors: Vincent Garin, Valentin Wimmer, Dietrich Borchardt, Marcos Malosetti and Fred van Eeuwijk

Morphological characterization and genetic diversity analysis of Tunisian durum wheat (Triticum turgidum var. durum) accessions

Tunisia is considered a secondary center of diversification of durum wheat and has a large number of abandoned old local landraces. An accurate investigation and characterization of the morphological and genet...

Authors: Maroua Ouaja, Bochra A. Bahri, Lamia Aouini, Sahbi Ferjaoui, Maher Medini, Thierry C. Marcel and Sonia Hamza

Whole-transcriptome analysis of differentially expressed genes in the mutant and normal capitula of Chrysanthemum morifolium

Chrysanthemum morifolium is one of the most economically important and popular floricultural crops in the family Asteraceae. Chrysanthemum flowers vary considerably in terms of colors and shapes. However, the mol...

Authors: Hua Liu, Chang Luo, Dongliang Chen, Yaqin Wang, Shuang Guo, Xiaoxi Chen, Jingyi Bai, Mingyuan Li, Xinlei Huang, Xi Cheng and Conglin Huang

Molecular mapping of a novel lesion mimic gene (lm4) associated with enhanced resistance to stripe rust in bread wheat

Lesion mimics (LMs) are disease-like symptoms that occur randomly on plant green leaves in the absence of pathogens. A previous study showed that LMs are related to enhanced resistance to a broad spectrum of d...

Authors: Rong Liu, Jing Lu, Shigang Zheng, Mei Du, Chihong Zhang, Minxiu Wang, Yunfang Li, Jiayi Xing, Yu Wu and Lei Zhang

Joint FAO/IAEA coordinated research project on “comparing rearing efficiency and competitiveness of sterile male strains produced by genetic, transgenic or symbiont-based technologies”

Authors: Kostas Bourtzis, Carlos Cáceres and Marc F. Schetelig

An early female lethal system of the New World screwworm, Cochliomyia hominivorax, for biotechnology-enhanced SIT

The New World Screwworm fly (NWS), Cochliomyia hominivorax, is an ectoparasite of warm-blooded animals and a major pest of livestock in parts of South America and the Caribbean where it remains endemic. In North ...

Authors: Carolina Concha, Ying Yan, Alex Arp, Evelin Quilarque, Agustin Sagel, Adalberto Pérez de León, W. Owen McMillan, Steven Skoda and Maxwell J. Scott

Building a transgenic sexing strain for genetic control of the Australian sheep blow fly Lucilia cuprina using two lethal effectors

The sterile insect technique (SIT) has been successfully used in many pest management programs worldwide. Some SIT programs release both ...

Authors: Ying Yan and Maxwell J. Scott

Improvement on the genetic engineering of an invasive agricultural pest insect, the cherry vinegar fly, Drosophila suzukii

The invasive fly Drosophila suzukii has become an established fruit pest in Europe, the USA, and South America with no effective and safe pest management. Genetic engineering enables the development of transgene-...

Authors: Hassan M. M. Ahmed, Fabienne Heese and Ernst A. Wimmer

Comparative genomics of Klebsiella michiganensis BD177 and related members of Klebsiella sp. reveal the symbiotic relationship with Bactrocera dorsalis

Bactrocera dorsalis is a destructive polyphagous and highly invasive insect pest of tropical and subtropical species of fruit and vegetable crops. The sterile insect technique (SIT) has been used for decades to c...

Authors: Zhaohui Cai, Qiongyu Guo, Zhichao Yao, Wenping Zheng, Junfei Xie, Shuai Bai and Hongyu Zhang

The hAT-family transposable element, hopper, from Bactrocera dorsalis is a functional vector for insect germline transformation

The hopper hAT-family transposable element isolated from the Oriental fruit fly, Bactrocera dorsalis, is distantly related to both the Drosophila hobo element and the Activator element from maize. The original 31...

Authors: Alfred M. Handler and Marc F. Schetelig

Transcriptome analysis of Anastrepha fraterculus sp. 1 males, females, and embryos: insights into development, courtship, and reproduction

Anastrepha fraterculus sp. 1 is considered a quarantine pest in several American countries. Since chemical control applied in an integrated pest management program is the only strategy utilized against this pest,...

Authors: Alejandra Carla Scannapieco, Claudia Alejandra Conte, Máximo Rivarola, Juan Pedro Wulff, Irina Muntaabski, Andrés Ribone, Fabián Milla, Jorge Luis Cladera and Silvia Beatriz Lanzavecchia

Climate stress resistance in male Queensland fruit fly varies among populations of diverse geographic origins and changes during domestication

The highly polyphagous Queensland fruit fly (Bactrocera tryoni Froggatt) expanded its range substantially during the twentieth century and is now the most economically important insect pest of Australian horticul...

Authors: Ángel-David Popa-Báez, Siu Fai Lee, Heng Lin Yeap, Shirleen S. Prasad, Michele Schiffer, Roslyn G. Mourant, Cynthia Castro-Vargas, Owain R. Edwards, Phillip W. Taylor and John G. Oakeshott

Development and characterization of a pupal-colour based genetic sexing strain of Anastrepha fraterculus sp. 1 (Diptera: Tephritidae)

Area-wide integrated pest management programs (AW-IPM) incorporating sterile insect technique (SIT) have been successful in suppressing populations of different fruit fly species during the last six decades. I...

Authors: José S. Meza, Kostas Bourtzis, Antigone Zacharopoulou, Angeliki Gariou-Papalexiou and Carlos Cáceres

Separating two tightly linked species-defining phenotypes in Bactrocera with hybrid recombinant analysis

Bactrocera tryoni and Bactrocera neohumeralis mate asynchronously; the former mates exclusively around dusk while the latter mates during the day. The two species also differ in the colour of the post-pronotal lo...

Authors: Heng Lin Yeap, Siu Fai Lee, Freya Robinson, Roslyn G. Mourant, John A. Sved, Marianne Frommer, Alexie Papanicolaou, Owain R. Edwards and John G. Oakeshott

Genetic stability, genetic variation, and fitness performance of the genetic sexing Salaya1 strain for Bactrocera dorsalis, under long-term mass rearing conditions

A genetic sexing strain (GSS) is an essential component for pest control using the sterile insect technique (SIT). A GSS is developed using a combination of Y-autosome translocation and a selectable marker suc...

Authors: Nidchaya Aketarawong, Siriwan Isasawin, Kamoltip Laohakieat and Sujinda Thanaphum

Precise single base substitution in the shibire gene by CRISPR/Cas9-mediated homology directed repair in Bactrocera tryoni

Pest eradication using the Sterile Insect Technique (SIT) involves high-density releases of sterilized males that mate with wild females and ultimately suppress the population. Sterilized females are not requi...

Authors: Amanda Choo, Elisabeth Fung, Isabel Y. Chen, Robert Saint, Peter Crisp and Simon W. Baxter

Transcribed sex-specific markers on the Y chromosome of the oriental fruit fly, Bactrocera dorsalis

The Oriental fruit fly, Bactrocera dorsalis, is a highly polyphagous invasive species with a high reproductive potential. In many tropical and subtropical parts of the world it ranks as one of the major pests of ...

Authors: Davide Carraretto, Nidchaya Aketarawong, Alessandro Di Cosimo, Mosè Manni, Francesca Scolari, Federica Valerio, Anna R. Malacrida, Ludvik M. Gomulski and Giuliano Gasperi