Articles

The effects of habitat fragmentation on the genetic structure of wild boar (Sus scrofa) population in Lithuania

Wild boar (Sus scrofa) is a widely distributed ungulate whose success can be attributed to a variety of ecological features. The genetic variation and population structure of Lithuania’s wild boar population have...

Authors: Loreta Griciuvienė, Žygimantas Janeliūnas, Vaclovas Jurgelevičius and Algimantas Paulauskas

The mtDNA mutation spectrum in the PolG mutator mouse reveals germline and somatic selection

Mitochondrial DNA (mtDNA) codes for products necessary for electron transport and mitochondrial gene translation. mtDNA mutations can lead to human disease and influence organismal fitness. The PolG mutator mo...

Authors: Kendra D. Maclaine, Kevin A. Stebbings, Daniel A. Llano and Justin C. Havird

Genetic analysis of pharmacogenomic VIP variants in the Wa population from Yunnan Province of China

The variation of drug responses and target does among individuals is mostly determined by genes. With the development of pharmacogenetics and pharmacogenomics, the differences in drug response between differen...

Authors: Dandan Li, Linna Peng, Shishi Xing, Chunjuan He and Tianbo Jin

The global carrier frequency and genetic prevalence of Upshaw-Schulman syndrome

Upshaw–Schulman syndrome (USS) is an autosomal recessive disease characterized by thrombotic microangiopathies caused by pathogenic variants in ADAMTS13. We aimed to (1) curate the ADAMTS13 gene pathogenic var...

Authors: Ting Zhao, Shanghua Fan and Liu Sun

Analysis of transcriptomic data sets supports the role of IL-6 in NETosis and immunothrombosis in severe COVID-19

There is an urgent need to understand the key events driving pathogenesis of severe COVID-19 disease, so that precise treatment can be instituted. In this respect NETosis is gaining increased attention in the ...

Authors: Samanwoy Mukhopadhyay, Subrata Sinha and Saroj Kant Mohapatra

In depth analysis of Cyprus-specific mutations of SARS-CoV-2 strains using computational approaches

This study aims to characterize SARS-CoV-2 mutations which are primarily prevalent in the Cypriot population. Moreover, using computational approaches, we assess whether these mutations are associated with cha...

Authors: Anastasis Oulas, Jan Richter, Maria Zanti, Marios Tomazou, Kyriaki Michailidou, Kyproula Christodoulou, Christina Christodoulou and George M. Spyrou

Associations between polymorphisms of SLC22A7, NGFR, ARNTL and PPP2R2B genes and Milk production traits in Chinese Holstein

Our preliminary work confirmed that, SLC22A7 (solute carrier family 22 member 7), NGFR (nerve growth factor receptor), ARNTL (aryl hydrocarbon receptor nuclear translocator like) and PPP2R2B (protein phosphatase ...

Authors: Ruike Jia, Yihan Fu, Lingna Xu, Houcheng Li, Yanhua Li, Lin Liu, Zhu Ma, Dongxiao Sun and Bo Han

Genomic resources of broomcorn millet: demonstration and application of a high-throughput BAC mapping pipeline

With high-efficient water-use and drought tolerance, broomcorn millet has emerged as a candidate for food security. To promote its research process for molecular breeding and functional research, a comprehensi...

Authors: Wei Xu, Mengjie Liang, Xue Yang, Hao Wang and Meizhong Luo

Brain areas involved with obsessive-compulsive disorder present different DNA methylation modulation

Obsessive-compulsive disorder (OCD) is characterized by intrusive thoughts and repetitive actions, that presents the involvement of the cortico-striatal areas. The contribution of environmental risk factors to...

Authors: Kátia Cristina de Oliveira, Caroline Camilo, Vinícius Daguano Gastaldi, Arthur Sant’Anna Feltrin, Bianca Cristina Garcia Lisboa, Vanessa de Jesus Rodrigues de Paula, Ariane Cristine Moretto, Beny Lafer, Marcelo Queiroz Hoexter, Euripedes Constantino Miguel, Mariana Maschietto and Helena Brentani

RNA-Seq analysis in giant pandas reveals the differential expression of multiple genes involved in cataract formation

The giant panda (Ailuropoda melanoleuca) is an endangered mammalian species native to China. Fewer than 2500 giant pandas are known to exist, many of which are bred in captivity as a means to preserve and repopul...

Authors: Yuyan You, Chao Bai, Xuefeng Liu, Yan Lu, Ting Jia, Maohua Xia, Yanqiang Yin, Wei Wang, Yucun Chen, Chenglin Zhang, Yan Liu, Liqin Wang, Tianchun Pu, Tao Ma, Yanhui Liu, Jun Zhou…

The performance of common SNP arrays in assigning African mitochondrial haplogroups

Mitochondrial haplogroup assignment is an important tool for forensics and evolutionary genetics. African populations are known to display a high diversity of mitochondrial haplogroups. In this research we exp...

Authors: Imke Lankheet, Mário Vicente, Chiara Barbieri and Carina Schlebusch

Whole genome sequence of a non-toxigenic Corynebacterium diphtheriae strain from a hospital in southeastern China

Sporadic cases of infection with non-toxigenic Corynebacterium diphtheriae (C. diphtheriae) isolates have been reported in regions covered by the Diphtheria-Tetanus-Pertussis vaccine, but no information describin...

Authors: Guogang Li, Sipei Wang, Sheng Zhao, Yangxiao Zhou and Xinling Pan

Identification of common microRNA between COPD and non-small cell lung cancer through pathway enrichment analysis

Different factors have been introduced which influence the pathogenesis of chronic obstructive pulmonary disease (COPD) and non-small cell lung cancer (NSCLC). COPD as an independent factor is involved in the ...

Authors: Amirhossein Fathinavid, Mohadeseh Zarei Ghobadi, Ali Najafi and Ali Masoudi-Nejad

Hsa-mir-548 family expression in human reproductive tissues

Hsa-miR-548ba expressed in ovarian granulosa cells targets PTEN and LIFR, which are essential for ovarian follicle activation and growth. The expression pattern of hsa-miR-548ba correlates with its host gene f...

Authors: Ilmatar Rooda, Birgitta Kaselt, Maria Liivrand, Olli-Pekka Smolander, Andres Salumets and Agne Velthut-Meikas

Genome-wide association studies of yield-related traits in high-latitude japonica rice

Heilongjiang Province is a high-quality japonica rice cultivation area in China. One in ten bowls of Chinese rice is produced here. Increasing yield is one of the main aims of rice production in this area. How...

Authors: Guomin Zhang, Rongsheng Wang, Juntao Ma, Hongru Gao, Lingwei Deng, Nanbo Wang, Yongli Wang, Jun Zhang, Kun Li, Wei Zhang, Fengchen Mu, Hui Liu and Ying Wang

Genomic stability among O3:K6 V. parahaemolyticus pandemic strains isolated between 1996 to 2012 in American countries

The V. parahaemolyticus pandemic clone, results in the development of gastrointestinal illness in humans. Toxigenic strains of this species are frequently isolated from aquatic habitats and organisms such as moll...

Authors: Abraham Guerrero, Bruno Gomez-Gil and Marcial Leonardo Lizarraga-Partida

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

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