Bovine Genome Database: integrated tools for genome annotation and discovery

Abstract The Bovine Genome Database (BGD) (http://bovinegenome.org) has been the key community bovine genomics database for more than a decade. To accommodate the increasing amount and complexity of bovine genomics data, BGD continues to advance its practices in data acquisition, curation, integration and efficient data retrieval. BGD provides tools for genome browsing (JBrowse), genome annotation (Apollo), data mining (BovineMine) and sequence database searching (BLAST). To augment the BGD genome annotation capabilities, we have developed a new Apollo plug-in, called the Locus-Specific Alternate Assembly (LSAA) tool, which enables users to identify and report potential genome assembly errors and structural variants. BGD now hosts both the newest bovine reference genome assembly, ARS-UCD1.2, as well as the previous reference genome, UMD3.1.1, with cross-genome navigation and queries supported in JBrowse and BovineMine, respectively. Other notable enhancements to BovineMine include the incorporation of genomes and gene annotation datasets for non-bovine ruminant species (goat and sheep), support for multiple assemblies per organism in the Regions Search tool, integration of additional ontologies and development of many new template queries. To better serve the research community, we continue to focus on improving existing tools, developing new tools, adding new datasets and encouraging researchers to use these resources.

Download Full-text

Pseudomonas aeruginosa Genome Database and PseudoCAP: facilitating community-based, continually updated, genome annotation

Nucleic Acids Research ◽

10.1093/nar/gki047 ◽

2004 ◽

Vol 33 (Database issue) ◽

pp. D338-D343 ◽

Cited By ~ 86

Author(s):

G. L. Winsor

Keyword(s):

Pseudomonas Aeruginosa ◽

Genome Annotation ◽

Community Based ◽

Genome Database

Download Full-text

Bovine Genome Database: Tools for Mining the Bos taurus Genome

Methods in Molecular Biology - Eukaryotic Genomic Databases ◽

10.1007/978-1-4939-7737-6_9 ◽

2018 ◽

pp. 211-249 ◽

Cited By ~ 2

Author(s):

Darren E. Hagen ◽

Deepak R. Unni ◽

Aditi Tayal ◽

Gregory W. Burns ◽

Christine G. Elsik

Keyword(s):

Bos Taurus ◽

Bovine Genome ◽

Genome Database

Download Full-text

Bovine Genome Database: new tools for gleaning function from theBos taurusgenome

Nucleic Acids Research ◽

10.1093/nar/gkv1077 ◽

2015 ◽

Vol 44 (D1) ◽

pp. D834-D839 ◽

Cited By ~ 55

Author(s):

Christine G. Elsik ◽

Deepak R. Unni ◽

Colin M. Diesh ◽

Aditi Tayal ◽

Marianne L. Emery ◽

...

Keyword(s):

Bovine Genome ◽

Genome Database

Download Full-text

Using online tools at the Bovine Genome Database to manually annotate genes in the new reference genome

Animal Genetics ◽

10.1111/age.12962 ◽

2020 ◽

Vol 51 (5) ◽

pp. 675-682

Author(s):

D. A. Triant ◽

J. J. Le Tourneau ◽

C. M. Diesh ◽

D. R. Unni ◽

M. Shamimuzzaman ◽

...

Keyword(s):

Reference Genome ◽

Bovine Genome ◽

Genome Database ◽

Online Tools

Download Full-text

Mikan Genome Database (MiGD): integrated database of genome annotation, genomic diversity, and CAPS marker information for mandarin molecular breeding

Breeding Science ◽

10.1270/jsbbs.19097 ◽

2020 ◽

Vol 70 (2) ◽

pp. 200-211 ◽

Cited By ~ 1

Author(s):

Yoshihiro Kawahara ◽

Tomoko Endo ◽

Mitsuo Omura ◽

Yumiko Teramoto ◽

Takeshi Itoh ◽

...

Keyword(s):

Genome Annotation ◽

Molecular Breeding ◽

Genomic Diversity ◽

Caps Marker ◽

Genome Database ◽

Marker Information

Download Full-text

5 CLONING AND CHARACTERIZATION OF NEWBORN OVARY HOMEOBOX GENE (NOBOX) IN CATTLE

Reproduction Fertility and Development ◽

10.1071/rdv22n1ab5 ◽

2010 ◽

Vol 22 (1) ◽

pp. 160

Author(s):

S. K. Tripurani ◽

K. B. Lee ◽

L. Wang ◽

G. W. Smith ◽

J. Yao

Keyword(s):

Bovine Genome ◽

Expression Patterns ◽

Homeobox Gene ◽

Early Embryogenesis ◽

Pcr Analysis ◽

Dna Encoding ◽

Coding Region ◽

Rt Pcr ◽

Cell Stage ◽

Genome Database

Newborn ovary homeobox (NOBOX) is a homeobox gene that is preferentially expressed in the oocytes and is essential for folliculogenesis in mice. NOBOX knockout mice are infertile, and lack of NOBOX perturbs the expression of many germ-cell-specific genes and microRNAs. Furthermore, mutations in the NOBOX gene associated with premature ovarian failure have been described in humans. However, the temporal and cell-specific expression of NOBOX in bovine oocytes and the potential function of NOBOX in early embryogenesis have not been described previously. The objectives of this study were to clone the complementary (c)DNA encoding for bovine NOBOX, analyze the expression of NOBOX mRNA in bovine tissues including fetal ovaries of different developmental stages, and characterize the temporal expression patterns of NOBOX mRNA during oocyte maturation and early embryogenesis. Based on the sequence of a predicted cDNA for bovine NOBOX, we successfully amplified, using RT-PCR, a cDNA fragment representing the coding region of bovine NOBOX from bovine fetal ovary cDNA. Additional 5′ and 3′ sequences were obtained using rapid amplification of cDNA ends (RACE) procedures. The assembled full-length NOBOX cDNA is 2275 bp with an open reading frame encoding a protein of 500 amino acids with a conserved homeodomain and typical nuclear localization signal. The predicted NOBOX protein shares 61% and 49% amino acid sequence identity with its human and mouse counterparts, respectively. A BLAST search of the bovine genome database at the National Center for Biotechnology Information (NCBI) revealed that the bovine NOBOX gene is located on chromosome 4, spans approximately 5.5 kb, and is encoded by 7 exons. Northern blot analysis revealed an approximately 2.3-kb bovine NOBOX RNA transcript. RT-PCR analysis of RNA samples from a panel of 14 different bovine tissues revealed that expression of NOBOX mRNA is restricted to ovarian samples and can be detected in fetal ovaries harvested as early as 105 days of gestation, when primary follicles start to form. Further RT-PCR analysis using RNA isolated from oocytes and granulosa and cumulus cells of antral follicles indicates that bovine NOBOX is expressed in oocytes but not in other follicular cells. Real-time PCR analysis demonstrated that NOBOX mRNA is abundant in germinal vesicle and metaphase II stage oocytes, as well as from pronuclear to 8-cell stage embryos, but barely detectable in embryos collected at the morula and blastocyst stages, suggesting that NOBOX might be a maternal effect gene. Collectively, our results demonstrate that bovine NOBOX is specifically expressed in oocytes and may play a role in early embryonic development in addition to its known function in folliculogenesis.

Download Full-text