Xu Wang

Xu Wang
Auburn University | AU · Department of Pathobiology

Ph.D.

About

75
Publications
6,847
Reads
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1,651
Citations
Additional affiliations
August 2017 - present
Auburn University
Position
  • Professor (Assistant)
July 2017 - present
HudsonAlpha Institute for Biotechnology
Position
  • Professor (Associate)
August 2011 - August 2017
Cornell University
Position
  • Research Associate
Education
August 2005 - August 2011
Cornell University
Field of study
  • Genetics and Genomics
September 2000 - June 2004
Fudan University
Field of study
  • Biological Sciences

Publications

Publications (75)
Article
Full-text available
Imprinted genes display differential allelic expression in a manner that depends on the sex of the transmitting parent. The degree of imprinting is often tissue-specific and/or developmental stage-specific, and may be altered in some diseases including cancer. Here we applied Illumina/Solexa sequencing of the transcriptomes of reciprocal F1 mouse n...
Article
The discovery of genomic imprinting through studies of manipulated mouse embryos indicated that the paternal genome has a major influence on placental development. However, previous research has not demonstrated paternal bias in imprinted genes. We applied RNA sequencing to trophoblast tissue from reciprocal hybrids of horse and donkey, where genot...
Article
Full-text available
Gene expression divergence between closely related species could be attributed to both cis- and trans- DNA sequence changes during evolution, but it is unclear how the evolutionary dynamics of epigenetic marks are regulated. In eutherian mammals, biparental DNA methylation marks are erased and reset during gametogenesis, resulting in paternal or ma...
Article
Background: Fecal specimens are critical for disease screening, diagnosis, and gut microbiome research. For domestic cats, lubricants are often necessary to obtain a sufficient quantity of sample. However, the effect of lubrication on feline microbiome analysis has not been assessed. Objectives: To evaluate if lubrication using mineral oil durin...
Article
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The hybrids of female channel catfish (Ictalurus punctatus) and male blue catfish (I. furca-tus) account for >50% of US catfish production due to superior growth, feed conversion, and disease resistance compared to both parental species. However, these hybrids can rarely be naturally spawned. Sperm collection is a lethal procedure, and sperm sample...
Article
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Background The blue catfish is of great value in aquaculture and recreational fisheries. The F1 hybrids of female channel catfish (Ictalurus punctatus) × male blue catfish (Ictalurusfurcatus) have been the primary driver of US catfish production in recent years because of superior growth, survival, and carcass yield. The channel–blue hybrid also pr...
Article
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Telomeres consist of highly conserved simple tandem telomeric repeat motif (TRM): (TTAGG)n in arthropods, (TTAGGG)n in vertebrates, and (TTTAGGG)n in most plants. TRM can be detected from chromosome-level assembly, which typically requires long-read sequencing data. To take advantage of short-read data, we developed an ultra-fast Telomeric Repeats...
Article
Despite significant advances in cancer diagnosis and treatment, osteosarcoma (OSA), an aggressive primary bone tumor, has eluded attempts at improving patient survival for many decades. Spontaneously occurring OSA in the dog shares remarkably similar clinical, histological, and molecular characteristics and therefore serves as an excellent model fo...
Article
Constructs bearing the cecropin B gene from the moth Hyalophora cecropia, driven by the cytomegalovirus (CMV) promoter, or the common carp beta-actin (ꞵ-actin) promoter were transferred to channel catfish, Ictalurus punctatus via electroporation. One F3 channel catfish family transgenic for cecropin transgene driven by the CMV promoter, and one F1 c...
Article
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Overweight and obesity are growing health problems in domestic cats, increasing the risks of insulin resistance, lipid dyscrasias, neoplasia, cardiovascular disease, and decreasing longevity. The signature of obesity in the feline gut microbiota has not been studied at the whole-genome metagenomic level. We performed whole-genome shotgun metagenomi...
Article
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Despite significant advances in cancer diagnosis and treatment, osteosarcoma (OSA), an aggressive primary bone tumor, has eluded attempts at improving patient survival for many decades. The difficulty in managing OSA lies in its extreme genetic complexity, drug resistance, and heterogeneity, making it improbable that a single-target treatment would...
Article
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The hybrid between female channel catfish (Ictalurus punctatus) and male blue catfish (Ictalurus furcatus) is superior in feed conversion, disease resistance, carcass yield, and harvestability compared to both parental species. However, heterosis and heterobeltiosis only occur in pond culture, and channel catfish grow much faster than the other gen...
Article
Obesity is caused by a combination of hereditary and environmental factors. Despite extensive study, contemporary through diet, exercise, education, surgery, and pharmacological treatments, no effective long-term solution has been found to this epidemic. Over the last decade, there has been a tremendous advancement in understanding the science of e...
Article
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The parasitoid wasp Muscidifurax raptorellus (Hymenoptera: Pteromalidae) is a gregarious species that has received extensive attention for its potential in biological pest control against house fly, stable fly, and other filth flies. It has a high reproductive capacity and can be reared easily. However, genome assembly is not available for M. rapto...
Article
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The gray short-tailed opossum (Monodelphis domestica) is an established laboratory-bred marsupial model for biomedical research. It is a critical species for comparative genomics research, providing the pivotal phylogenetic outgroup for studies of derived vs. ancestral states of genomic/epigenomic characteristics for eutherian mammal lineages. To c...
Article
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Liberibacter pathogens are associated with several severe crop diseases, including citrus Huanglongbing, the most destructive disease to the citrus industry. Currently, no effective cure or treatments are available, and no resistant citrus variety has been found.
Preprint
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The gray short-tailed opossum is an established laboratory-bred marsupial model for biomedical research. It serves as a critical species for comparative genomics research, providing the pivotal phylogenetic outgroup for studies of derived vs. ancestral states of genomic/epigenomic characteristics for all eutherian mammal lineages. To characterize t...
Article
The precious rare edible fungus Morchella conica is popular worldwide for its rich nutrition, savory flavor, and varieties of bioactive components. Due to its high commercial, nutritional, and medicinal value, it has always been a hot spot. However, the molecular mechanism and endophytic bacterial communities in M. conica were poorly understood. In...
Preprint
Full-text available
Liberibacter pathogens are the causative agents of several severe crop diseases worldwide, including citrus Huanglongbing and potato Zebra Chip. These bacteria are endophytic and non-culturable, which makes experimental approaches challenging and highlights the need for bioinformatic analysis in advancing our understanding about Liberibacter pathog...
Article
Background: Antimicrobial resistance is a growing concern in canine Staphylococcus pseudintermedius dermatitis. Treatment with rifampicin (RFP) is considered only in meticillin-resistant and multidrug-resistant S. pseudintermedius (MDR-MRSP). Hypothesis/objectives: To determine an optimal RFP dosing for MDR-MRSP treatment without induction of RF...
Article
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The bighead catfish (Clarias macrocephalus) and channel catfish (Ictalurus punctatus) are freshwater species in the Siluriformes order. C. macrocephalus has both gills and modified gill structures serving as an air-breathing organ (ABO), while I. punctatus does not possess such an organ, and cannot breathe in air, providing an excellent model for s...
Article
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Animal taxa show remarkable variability in sexual reproduction, where separate sexes, or gonochorism, is thought to have evolved from hermaphroditism for most cases. Hermaphroditism accounts for 5% in animals, and sequential hermaphroditism has been found in teleost. In this study, we characterized a novel form of the transient hermaphroditic stage...
Article
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Tra catfish ( Pangasianodon hypophthalmus ), also known as striped catfish, is a facultative air-breather that uses its swim bladder as an air-breathing organ (ABO). A related species in the same order (Siluriformes), channel catfish ( Ictalurus punctatus ), does not possess an ABO and thus cannot breathe in the air. Tra and channel catfish serve a...
Article
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CRISPR/Cas9-based gene knockout in animal cells, particularly in teleosts, has proven to be very efficient with regards to mutation rates, but the precise insertion of exogenous DNA or gene knock-in via the homology-directed repair (HDR) pathway has seldom been achieved outside of the model organisms. Here, we succeeded in integrating with high eff...
Article
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Background Brain metastases explain the majority of mortality associated with lung cancer, which is the leading cause of cancer death. Cytology analysis of the cerebrospinal fluid (CSF) remains the diagnostic gold standard, however, the circulating tumor cells (CTCs) in CSF (CSF‐CTCs) are not well defined at the molecular and transcriptome levels....
Article
Insect mitochondrial DNA (mtDNA) ranges from 14 to 19 kbp, and the size difference is attributed to the AT-rich control region. Jewel wasps have a parasitoid lifestyle, which may affect mitochondria function and evolution. We sequenced, assembled, and annotated mitochondrial genomes in Nasonia and outgroup species. Gene composition and order are co...
Article
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Wolbachia are widespread intracellular bacteria that mediate many important biological processes in arthropod species. In this study, we identified 210 conserved single-copy genes in 33 genome-sequenced Wolbachia strains in the A, B, C, D, E and F supergroups. Phylogenomic analyses with these core genes indicate that all 33 Wolbachia strains mainta...
Article
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The transition from fertilized egg to larva in fish is accompanied with various biological processes. We selected seven early developmental stages in channel catfish, Ictalurus punctatus, for transcriptome analysis, and covered 22,635 genes with 590 million high-quality RNA-sequencing (seq) reads. Differential expression analysis between neighborin...
Article
In recent years, obesity has reached epidemic proportions globally and has become a major public health concern. The development of obesity is likely caused by several behavioral, environmental, and genetic factors. Genomic variability among individuals is largely due to copy number variations (CNVs). Recent genome-wide association studies (GWAS) h...
Article
Objective: To examine the effectiveness of applying selective pressure to improve hip joint quality in purpose-bred detection dogs by use of PennHIP distraction index (DI) values along with Orthopedic Foundation for Animals (OFA) hip joint scores and to determine whether age, sex, coat color, breed, and body weight were associated with hip joint q...
Article
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Jewel wasps in the genus of Nasonia are parasitoids with haplodiploidy sex determination, rapid development and are easy to culture in the laboratory. They are excellent models for insect genetics, genomics, epigenetics, development, and evolution. Nasonia vitripennis ( Nv ) and N. giraulti ( Ng ) are closely-related species that can be intercrosse...
Article
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Staphylococcus pseudintermedius is a Gram-positive bacterial species highly relevant to animal and human health. In this study, we report the draft genome sequences of two clinical isolates of S. pseudintermedius from canine skin biopsy specimens at the Dermatology Service of the Auburn University Small Animal Teaching Hospital.
Article
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Dogs with spontaneous high-grade gliomas increasingly are being proposed as useful large animal pre-clinical models for the human disease. Hypoxia is a critical microenvironmental condition that is common in both canine and human high-grade gliomas and drives increased angiogenesis, chemo- and radioresistance, and acquisition of a stem-like phenoty...
Preprint
Full-text available
Metastatic lung cancer accounts for about half of the brain metastases (BM). Development of leptomeningeal metastases (LM) are becoming increasingly common, and its prognosis is still poor despite the advances in systemic and local approaches. Until now, the cytology analysis in the cerebrospinal fluid (CSF) remains the gold diagnostic standard. Al...
Article
Eimeria spp. are important intestinal pathogens of chickens (Gallus gallus domesticus). Anticoccidial feed additives, chemicals, and ionophores have traditionally been used to control Eimeria infections in broiler production. Thus, the trend toward antibiotic-free and organic production requires new approaches to coccidiosis prevention. Two not mut...
Article
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Wolbachia are obligate intracellular bacteria which commonly infect various nematode and arthropod species. Genome sequences have been generated from arthropod samples following enrichment for the intracellular bacteria, and genomes have also been assembled from arthropod whole-genome sequencing projects. However, these methods remain challenging f...
Article
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The underlying neurological events accompanying dog domestication remain elusive. To reconstruct the domestication process in an experimental setting, silver foxes (Vulpes vulpes) have been deliberately bred for tame vs aggressive behaviors for more than 50 generations at the Institute for Cytology and Genetics in Novosibirsk, Russia. The hypothala...
Preprint
Full-text available
Wolbachia are obligate intracellular bacteria which commonly infect various nematode and arthropod species. Based on depth differences, we assembled the genome of Wolbachia in the parasitoid jewel wasp species Nasonia oneida ( w One), using 10X Genomics Chromium linked-read technology. The final draft assembly consists of 1,293,406 bp in 47 scaffol...
Article
Predicting genetic regulatory variants, most of which locate in noncoding genomic regions, still remains a challenge in genetic research. Among all non-coding regulatory variants, cis-eQTL single nucleotide variants (SNVs) are of particular interest for their crucial role in regulating gene expression. Since different gene expression patterns are b...
Article
Animal domestication efforts have led to a shared spectrum of striking behavioral and morphological changes. To recapitulate this process, silver foxes have been selectively bred for tame and aggressive behaviors for more than 50 generations at the Institute for Cytology and Genetics in Novosibirsk, Russia. To understand the genetic basis and molec...
Article
Full-text available
Strains of red fox (Vulpes vulpes) with markedly different behavioural phenotypes have been developed in the famous long-term selective breeding programme known as the Russian farm-fox experiment. Here we sequenced and assembled the red fox genome and re-sequenced a subset of foxes from the tame, aggressive and conventional farm-bred populations to...
Article
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In the version of this Article originally published, there were some errors in the affiliations: Stephen J. O'Brien's affiliations were incorrectly listed as 8,9; they should have been 7,9. Affiliation 3 was incorrectly named the Institute of Cytology and Genetics of the Russian Academy of Sciences; it should have read Institute of Cytology and Gen...
Preprint
Full-text available
Animal domestications have led to a shared spectrum of striking behavioral and morphological changes. To recapitulate this process, silver foxes have been selectively bred for tame and aggressive behaviors for over 50 generations at the Institute for Cytology and Genetics in Novosibirsk, Russia. To understand the genetic basis and molecular mechani...
Article
Full-text available
Background The ubiquitin protein E3A ligase gene (UBE3A) gene is imprinted with maternal-specific expression in neurons and biallelically expressed in all other cell types. Both loss-of-function and gain-of-function mutations affecting the dosage of UBE3A are associated with several neurodevelopmental syndromes and psychological conditions, suggest...
Article
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Background Nasonia vitripennis is an emerging insect model system with haplodiploid genetics. It holds a key position within the insect phylogeny for comparative, evolutionary and behavioral genetic studies. The draft genomes for N. vitripennis and two sibling species were published in 2010, yet a considerable amount of transcriptiome data have sin...
Data
List of super cis- genes and their functional annotation. (PDF)
Data
A depiction of cis- versus trans-regulatory divergence from hybrid F1s of two closely related species. (A) Suppose two closely related species (species A and B) are evolved from a single ancestral species. After divergence, some orthologous genes are differentially expressed between the two species. The gene expression divergence could be attribute...
Data
Estimation and validation of allele-specific methylation and detection of cis-regulation of DNA methylation for Ank2 gene. (A) Plot of the exon model, translation start site and CpG methylation profile for Ank2 gene in Nv female, Nv male, Ng female, Ng male, F1VG, and F1GV (from top to bottom). A vertical bar is drawn for each covered CpG at its po...
Data
Validation of methylation percentages for nine differentially methylated genes between Nasonia vitripennis (Nv) and Nasonia giraulti (Ng) using the PyroMark assay in independent biological replicates. Plotted in each bar plot are CpG methylation percentages estimated from whole-genome bisulfite sequencing data (left six bars) and single gene PyroMa...
Data
Boxplot of parental Nv/Ng male expression difference for differentially methylated gene between Nasonia vitripennis (Nv) and Nasonia giraulti (Ng). Differentially expressed genes (FDR < 0.05) are shown in red. Among these genes, methylated species show significantly higher expression between species. Data presented in this figure can be found at ht...
Data
Methylation and allelic expression profile for 26 differentially genes with allelic expression bias. Plot of parental/F1 methylation and F1 differentially allelic expression profile for 26 differentially methylated genes with 60% or more allelic expression bias. For DNA methylation, the upper panel is the methylation percentage in Nv or the V allel...
Data
Total expression correlation between whole adult samples from reciprocal crosses F1VG and F1GV. Plotted on the x-axis is the total expression level for 8,622 genes in F1VG progeny RNA-seq data quantified by log2(FPKM). Plotted on the y-axis is the total expression level in the reciprocal F1GV progeny. Significant differentially expressed genes are...
Article
Full-text available
Genomic imprinting depends on the establishment and maintenance of DNA methylation at imprinting control regions. However, the mechanisms by which these heritable marks influence allele-specific expression are not fully understood. By analyzing maternal, zygotic, maternal-zygotic, and conditional Trim28 mutants, we found that the transcription fact...
Article
There is extraordinary diversity in sexual dimorphism (SD) among animals, but little is known about its epigenetic basis. To study the epigenetic architecture of SD in a haplodiploid system, we performed RNA-seq and whole-genome bisulfite sequencing of adult females and males from two closely related parasitoid wasps, Nasonia vitripennis and Nasoni...
Article
Full-text available
Endoplasmic reticulum (ER) stress occurs when misfolded proteins accumulate in the ER. The cellular response to ER stress involves complex transcriptional and translational changes, important to the survival of the cell. ER stress is a primary cause and a modifier of many human diseases. A first step to understanding how the ER stress response impa...
Article
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Genomic imprinting is manifested as differential allelic expression (DAE) depending on the parent-of-origin. The most direct way to identify imprinted genes is to directly score the DAE in a context where one can identify which parent transmitted each allele. Because many genes display DAE, simply scoring DAE in an individual is not sufficient to i...
Article
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Imprinted genes have been extensively documented in eutherian mammals and found to exhibit significant interspecific variation in the suites of genes that are imprinted and in their regulation between tissues and developmental stages. Much less is known about imprinted loci in metatherian (marsupial) mammals, wherein studies have been limited to a...