new High quality reviews or mini-reviews from leading experts are particularly welcome and they will be processed in high priority.
The Y chromosomes of Drosophila melanogaster and D. simulans contain only a handful of protein-coding genes, which are related to sperm mobility and reproductive fitness. Despite low or absent protein coding polymorphism, the Drosophila Y chromosome has been associated with natural phenotypic variation, including variation in the expression of hundreds to thousands of genes located on autosomes and on the X chromosome. Polymorphisms present in the large blocks of heterochromatin and consisting of differences in the amounts and kinds of sequences for satellite DNA and transposable elements may be the source of this modulation. ...more
It has long been recognized that men and women exhibit different risks for diverse disorders ranging from metabolic to autoimmune diseases. However, the underlying causes of these disparities remain obscure. Analysis of patients with chromosomal abnormalities, including Turner syndrome (45X) and Klinefelter syndrome (47XXY), has highlighted the importance of X-linked gene dosage as a contributing factor for disease susceptibility. Escape from X-inactivation and X-linked imprinting can result in transcriptional differences between normal men and women as well as in patients with sex chromosome abnormalities. ...more
Frog sex chromosomes offer an ideal system for advancing our understanding of genome evolution and function because of the variety of sex determination systems in the group, the diversity of sex chromosome maturation states, the ease of experimental manipulation during early development. After briefly reviewing sex chromosome biology generally, we focus on what is known about frog sex determination, sex chromosome evolution, and recent, genomics-facilitated advances in the field. ...more
Genetic variation in the genome of a given species is the basis for natural selection and genetic improvement through selective breeding. We applied 29 microsatellites located on 11 linkage groups to study genetic variation in 276 accessions of J. curcas collected from nine locations in five countries in South America, Asia and Africa to initiate a breeding program. To our surprise, we did not detect any genetic diversity at all 29 microsatellites loci. All the 276 accessions were homozygous at all loci and shared the same genotype at each locus, suggesting no microsatellite variation in the genome of Jatropha curcas. This result is quite unusual, and may have profound influence of the breeding strategies and genome study of this species. ...more
The Asian citrus psyllid, Diaphorina citri Kuwayama (Hemiptera: Psyllidae) is a vector for the causative agents of Huanglongbing, which threatens citrus production worldwide. This study reports and discusses the first D. citri transcriptomes, encompassing the three main life stages of D. citri, egg, nymph and adult. The transcriptomes were annotated using Gene Ontology (GO) and insecticide-related genes within each life stage were identified to aid the development of future D. citri insecticides. Transcriptome assemblies and other sequence data are available for download at the International Asian Citrus Psyllid Genome Consortium website and at NCBI. ...more
Candidate gene (CG) approaches provide a strategy for identification and characterization of major genes underlying complex phenotypes such as production traits and susceptibility to diseases, but the conclusions tend to be inconsistent across individual studies. Meta-analysis approaches can deal with these situations, e.g., by pooling effect-size estimates or combining P values from multiple studies. In this paper, we evaluated the performance of two types of statistical models, parametric and non-parametric, for meta-analysis of CG effects using simulated data. Both models estimated a “central” effect size while taking into account heterogeneity over individual studies. The empirical distribution of study-specific CG effects was multi-modal. ...more
A collection of investigations indicate the importance of adipose tissue stromal/stem cells to vasculogenesis and angiogenesis during adipogenesis. Early in development the stromal-vascular (S-V) elements control and dictate the extent of adipogenesis. For instance, the vasculature and connective tissue collagen matrix develops before overt adipocyte differentiation. Definitive studies of human adipose tissue stem cells (ADSC) provided an understanding of stem cell identity and function. In this regard, a novel vascular stem cell theory proposes that ADSC are a mixed population of vascular stem cells (VSC) with differential potential proportional to the angiogenic potential of the vasculature....more

Journal of Genomics cover

Journal of Genomics is a peer-reviewed journal publishing papers of high quality in all areas of gene, genetics, genomics, proteomics, metabolomics, DNA/RNA, computational biology, bioinformatics, and other relevant areas of research and application. Types of articles include:

  • Research paper
  • Short research communication
  • Review or mini-review
  • Commentary
  • Database or software paper

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Short Research Paper
Mitochondrial genomes of the South American frogs Eupsophus vertebralis and E. emiliopugini (Neobatrachia: Alsodidae) and their phylogenetic relationships
Elkin Y. Suárez-Villota, Camila A. Quercia, José J. Nuñez
J. Genomics 2018; 6: 98-102. doi:10.7150/jgen.26122
[Abstract] [Full text] [PDF]


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Research Paper
Genetic Diversity of Bovine Major Histocompatibility Complex Class II DRB3 locus in cattle breeds from Asia compared to those from Africa and America
Sunday O. Peters, Tanveer Hussain, Adeyemi S. Adenaike, Matthew A Adeleke, Marcos De Donato, Jordan Hazzard, Masroor E Babar, Ikhide G. Imumorin
J. Genomics 2018; 6: 88-97. doi:10.7150/jgen.26491
[Abstract] [Full text] [PDF]


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Research Paper
Genome Wide Analysis Reveals the Extrinsic Cellulolytic and Biohydrogen Generating Abilities of Neocallimastigomycota Fungi
Ayyappa Kumar Sista Kameshwar, Wensheng Qin
J. Genomics 2018; 6: 74-87. doi:10.7150/jgen.25648
[Abstract] [Full text] [PDF]


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Research Paper
Isolation and Identification of an Anthracimycin Analogue from Nocardiopsis kunsanensis, a Halophile from a Saltern, by Genomic Mining Strategy
Fernanda L. Sirota, Falicia Goh, Kia-Ngee Low, Lay-Kien Yang, Sharon C. Crasta, Birgit Eisenhaber, Frank Eisenhaber, Yoganathan Kanagasundaram, Siew Bee Ng
J. Genomics 2018; 6: 63-73. doi:10.7150/jgen.24368
[Abstract] [Full text] [PDF] [PubMed] [PMC]


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Research Paper
Identification of Sex-associated SNPs of Greater Amberjack (Seriola dumerili)
Junya Kawase, Jun-ya Aoki, Kazuhisa Hamada, Akiyuki Ozaki, Kazuo Araki
J. Genomics 2018; 6: 53-62. doi:10.7150/jgen.24788
[Abstract] [Full text] [PDF] [PubMed] [PMC]


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Research Paper
De novo Assembly of the Burying Beetle Nicrophorus orbicollis (Coleoptera: Silphidae) Transcriptome Across Developmental Stages with Identification of Key Immune Transcripts
Harim I. Won, Thomas T. Schulze, Emalie J. Clement, Gabrielle F. Watson, Sean M. Watson, Rosalie C. Warner, Elizabeth A. M. Ramler, Elias J. Witte, Mark A. Schoenbeck, Claudia M. Rauter, Paul H. Davis
J. Genomics 2018; 6: 41-52. doi:10.7150/jgen.24228
[Abstract] [Full text] [PDF] [PubMed] [PMC]


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Research Paper
In-silico Designing and Testing of Primers for Sanger Genome Sequencing of Dengue Virus Types of Asian Origin
Ajay Prakash Joshi, Annette Angel, Bennet Angel, Rajendra Kumar Baharia, Suman Rathore, Neha Sharma, Karuna Yadav, Sharad Thanvi, Indu Thanvi, Vinod Joshi
J. Genomics 2018; 6: 34-40. doi:10.7150/jgen.22460
[Abstract] [Full text] [PDF] [PubMed] [PMC]


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Short Research Paper
Complete Genome Sequence of Microcystis aeruginosa NIES-2481 and Common Genomic Features of group G M. aeruginosa
Haruyo Yamaguchi, Shigekatsu Suzuki, Yasunori Osana, Masanobu Kawachi
J. Genomics 2018; 6: 30-33. doi:10.7150/jgen.24935
[Abstract] [Full text] [PDF] [PubMed] [PMC]


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Research Paper
Genomic Analysis of Propane Metabolism in Methyl Tert-Butyl Ether-Degrading Mycobacterium Sp. Strain ENV421
Peter Robert Tupa, Hisako Masuda
J. Genomics 2018; 6: 24-29. doi:10.7150/jgen.24929
[Abstract] [Full text] [PDF] [PubMed] [PMC]


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Short Research Paper
High Quality Draft Genomes of the Type Strains Geobacillus thermocatenulatus DSM 730T, G. uzenensis DSM 23175T And Parageobacillus galactosidasius DSM 18751T
Winnie Thabisa Ramaloko, Nadine Koen, Shamara Polliack, Habibu Aliyu, Pedro Humberto Lebre, Teresa Mohr, Florian Oswald, Michaela Zwick, Daniel Ray Zeigler, Anke Neumann, Christoph Syldatk, Don Arthur Cowan, Pieter De Maayer
J. Genomics 2018; 6: 20-23. doi:10.7150/jgen.22986
[Abstract] [Full text] [PDF] [PubMed] [PMC]


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Research Paper
Constructing a 'Chromonome' of Yellowtail (Seriola quinqueradiata) for Comparative Analysis of Chromosomal Rearrangements
Junya Kawase, Jun-ya Aoki, Kazuo Araki
J. Genomics 2018; 6: 9-19. doi:10.7150/jgen.23222
[Abstract] [Full text] [PDF] [PubMed] [PMC]


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Research Paper
Genetic variation in N- and C-terminal regions of bovine DNAJA1 heat shock protein gene in African, Asian and American cattle
Oyeyemi O. Ajayi, Sunday O. Peters, Marcos De Donato, F. Denis Mujibi, Waqas A. Khan, Tanveer Hussain, Masroor E. Babar, Ikhide G. Imumorin, Bolaji N. Thomas
J. Genomics 2018; 6: 1-8. doi:10.7150/jgen.23248
[Abstract] [Full text] [PDF] [PubMed] [PMC]


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Short Research Paper
Exploring Effects of Sex and Diet on Drosophila melanogaster Head Gene Expression
Maria D. L. A. Jaime, Juan Hurtado, Mariana Ramirez Loustalot-Laclette, Brian Oliver, Therese Markow
J. Genomics 2017; 5: 128-131. doi:10.7150/jgen.22393
[Abstract] [Full text] [PDF] [PubMed] [PMC]


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Short Research Paper
Draft genome sequence of a biosurfactant producing, Bacillus aquimaris strain SAMM MCC 3014 isolated from Indian Arabian coastline sea water
Samadhan Waghmode, Laxmikant Dama, Tejashri Hingamire, Nidhi Bharti, Swapnil Doijad, Mangesh Suryavanshi
J. Genomics 2017; 5: 124-127. doi:10.7150/jgen.21724
[Abstract] [Full text] [PDF] [PubMed] [PMC]


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Short Research Paper
Permanent Draft Genome sequence for Frankia sp. strain CcI49, a Nitrogen-Fixing Bacterium Isolated from Casuarina cunninghamiana that Infects Elaeagnaceae
Samira Mansour, Erik Swanson, Zakkary McNutt, Céline Pesce, Kelsey Harrington, Feseha Abebe-Alele, Stephen Simpson, Krystalynne Morris, W. Kelley Thomas, Louis S. Tisa
J. Genomics 2017; 5: 119-123. doi:10.7150/jgen.22138
[Abstract] [Full text] [PDF] [PubMed] [PMC]


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Research Paper
Small Non-coding RNA Abundance in Adrenocortical Carcinoma: A Footprint of a Rare Cancer
Srinivas V. Koduru, Ashley N. Leberfinger, Dino J. Ravnic
J. Genomics 2017; 5: 99-118. doi:10.7150/jgen.22060
[Abstract] [Full text] [PDF] [PubMed] [PMC]