Harnessing the bovine genome sequence for the Australian cattle and sheep industries

2005 ◽  
Vol 45 (8) ◽  
pp. 1011 ◽  
Author(s):  
B. P. Dalrymple
Keyword(s):  
Genome Sequence ◽  
Bovine Genome ◽  
Expression Data ◽  
Protein Coding ◽  
Bovine Genome Sequence ◽  
Number Of Genes ◽  
Mammalian Genomes ◽  
Non Coding Rnas ◽  
Human And Mouse ◽  
Cattle And Sheep

Genomics is an emerging science and the release of the human and mouse genomes has significantly altered our picture of the information content of mammalian genomes. A smaller number of protein coding genes, and a larger number of genes that do not appear to encode protein products, the so-called non-coding RNAs (ncRNAs), have been identified. The first 2 drafts of the bovine genome sequence have been released, and work to utilise the framework of the bovine genome to facilitate ovine genomics is underway. In anticipation of the requirement for a detailed analysis of the ruminant genomes, their transcriptomes, interactomes, regulomes and similar, we have been developing the informatics platform for the analysis and integration of genome sequences and expression data for cattle and sheep. This resource will enable us to utilise the ruminant datasets and integrate them with equivalent data from other mammals for the advancement of animal scientific research for applications in the cattle and sheep industries in Australia.

scholarly journals Complete Genome Sequence of Bacillus vallismortis NBIF-001, a Novel Strain from Shangri-La, China, That Has High Activity against Fusarium oxysporum

2017 ◽  
Vol 5 (48) ◽  
Author(s):  
Xiaoyan Liu ◽  
Yong Min ◽  
Daye Huang ◽  
Ronghua Zhou ◽  
Wei Fang ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Positive Bacterium ◽  
Protein Coding ◽  
Content Type ◽  
Number Of Genes ◽  
Genes Encoding ◽  
Bacillus Vallismortis ◽  
Rna Genes

ABSTRACT Bacillus vallismortis NBIF-001, a Gram-positive bacterium, was isolated from soil in Shangri-La, China. Here, we provide the complete genome sequence of this bacterium, which has a 3,929,787-bp-long genome, including 4,030 protein-coding genes and 195 RNA genes. This strain possesses a number of genes encoding virulence factors of pathogens.

scholarly journals Deciphering the Role of the Non-Coding Genome in Regulating Gene-Diet Interactions

Nutrients ◽  
2018 ◽  
Vol 10 (12) ◽  
pp. 1831
Author(s):  
Pui-Pik Law ◽  
Michelle Holland
Keyword(s):  
Protein Translation ◽  
Nutritional Intervention ◽  
Transcriptional Level ◽  
Nutritional Regulation ◽  
Protein Coding ◽  
Protein Encoding ◽  
Mammalian Genomes ◽  
Non Coding Rnas ◽  
Number Of Classes

Protein encoding genes constitute a small fraction of mammalian genomes. In addition to the protein coding genes, there are other functional units within the genome that are transcribed, but not translated into protein, the so called non-coding RNAs. There are many types of non-coding RNAs that have been identified and shown to have important roles in regulating gene expression either at the transcriptional or post-transcriptional level. A number of recent studies have highlighted that dietary manipulation in mammals can influence the expression or function of a number of classes of non-coding RNAs that contribute to the protein translation machinery. The identification of protein translation as a common target for nutritional regulation underscores the need to investigate how this may mechanistically contribute to phenotypes and diseases that are modified by nutritional intervention. Finally, we describe the state of the art and the application of emerging ‘-omics’ technologies to address the regulation of protein translation in response to diet.

Construction of a dense SNP map for bovine chromosome 6 to assist the assembly of the bovine genome sequence

2008 ◽  
Vol 39 (2) ◽  
pp. 97-104 ◽  
Author(s):  
H. Nilsen ◽  
B. Hayes ◽  
P. R. Berg ◽  
A. Roseth ◽  
K. K. Sundsaasen ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Bovine Genome ◽  
Bovine Chromosome ◽  
Chromosome 6 ◽  
Bovine Genome Sequence ◽  
Snp Map

Capturing benefits from the bovine genome sequence

2007 ◽  
Vol 47 (9) ◽  
pp. 1039 ◽  
Author(s):  
Ross L. Tellam
Keyword(s):  
Genome Sequence ◽  
Production Systems ◽  
Bovine Genome ◽  
Value Added ◽  
Nucleotide Polymorphisms ◽  
Pedigree Data ◽  
Breeding Programs ◽  
Efficient Management ◽  
Bovine Genome Sequence ◽  
Large Numbers

The bovine genome sequence in ‘draft’ form will be complete in 2007. The availability of the sequence and very large numbers of single nucleotide polymorphisms will have profound effects on livestock production. The dairy industry is well positioned to capture the benefits of this enormous and enabling resource because of its comprehensive databases containing phenotypic and pedigree data for large numbers of animals, intense utilisation of genetics in breeding programs and efficient management of reproductive performance. The bovine genome sequence will assist in the development of novel products, especially value-added products, and markedly enhance the rate of genetic gain in the Australian dairy population. The immediate challenge facing the industry is the integration of new technological capabilities into existing breeding programs and production systems.

Species-Specific Functions For Long Noncoding RNAs During Erythropoeisis

Blood ◽  
2013 ◽  
Vol 122 (21) ◽  
pp. 2441-2441 ◽  
Author(s):  
Vikram R Paralkar ◽  
Tejaswini Mishra ◽  
Jing Luan ◽  
Yu Yao ◽  
Andrew Kossenkov ◽  
...  
Keyword(s):  
Cell Line ◽  
Chromatin Immunoprecipitation ◽  
Conflicts Of Interest ◽  
Rna Seq ◽  
Protein Coding ◽  
Mammalian Genomes ◽  
Erythroid Maturation ◽  
Low Levels ◽  
Species Specific ◽  
Human And Mouse

Abstract Mammalian genomes encode thousands of long noncoding (lnc) RNAs, although the extent to which lncRNAs regulate biological functions is not known. Indeed, most lncRNAs show low levels of conservation among mammals, which could suggest limited or species-restricted functions. We used RNA-seq to identify 683 and 1189 lncRNAs expressed during mouse and human erythropoiesis respectively, of which ∼25% are erythroid-specific. Primary cell chromatin immunoprecipitation (ChIP) studies indicate that most mouse erythroid lncRNAs arise from classical promoters, and their genomic loci are bound by the hematopoietic transcription factors GATA1 and SCL/TAL1. Using the G1E-ER4 cell line, which has an inducible form of GATA1, we found that lncRNAs whose genomic loci are bound by GATA1 in primary cells are upregulated on GATA1 induction in the cell line, similar to coding genes. We compared RNA-Seq transcriptomes of erythroblasts from 8 different mice strains and showed that lncRNA expression is highly conserved within strains of the same species. A comparison of the human and mouse lncRNA transcriptomes showed that only 15% of mouse erythroblast lncRNAs have detectable syntenic transcripts in human erythroblasts, and that most lncRNAs are not detectable in humans. To identify functional lncRNAs, we used RNA interference in primary erythroblasts to analyze the functions of 21 abundantly expressed murine erythroid lncRNAs, 15 of which are mouse specific and 6 of which have orthologous transcripts in humans. Suppression of seven different lncRNAs inhibited various aspects of erythroid maturation including loss of cell volume, down-regulation of the surface marker CD44, and enucleation. The suppression of enucleation ranged from 25% reduction to 75% reduction of enucleation demonstrated with at least 2 separate shRNAs for each of the 7 lncRNAs (p<0.0005) (Figure 1). Of the seven lncRNAs that have a demonstrable function in murine erythropoiesis, none are expressed in human erythroblasts, indicating that lack of conservation between different species does not necessarily predict a lack of function. These results reflect marked evolutionary differences between protein-coding genes and lncRNAs, and indicate that the latter exert tissue- and species-specific roles in mammalian development.Figure 1Figure 1. Disclosures: No relevant conflicts of interest to declare.

scholarly journals High resolution radiation hybrid maps of bovine chromosomes 19 and 29: comparison with the bovine genome sequence assembly

BMC Genomics ◽  
2007 ◽  
Vol 8 (1) ◽  
pp. 310 ◽  
Author(s):  
Aparna Prasad ◽  
Thomas Schiex ◽  
Stephanie McKay ◽  
Brenda Murdoch ◽  
Zhiquan Wang ◽  
...  
Keyword(s):  
High Resolution ◽  
Genome Sequence ◽  
Radiation Hybrid ◽  
Bovine Genome ◽  
Sequence Assembly ◽  
Genome Sequence Assembly ◽  
Bovine Genome Sequence

Insights and applications from sequencing the bovine genome

2008 ◽  
Vol 20 (1) ◽  
pp. 54 ◽  
Author(s):  
David L. Adelson
Keyword(s):  
Genome Sequence ◽  
Association Studies ◽  
Bovine Genome ◽  
Genetic Selection ◽  
Genetic Association Studies ◽  
Physiological Data ◽  
Economic Traits ◽  
Bovine Genome Sequence ◽  
Breeding Schemes ◽  
And Function

Humans have sought to improve/tailor cattle since their domestication a few thousand years ago. Up until the last 40–50 years, consistent genetic improvement of cattle was a hit or miss proposition. Recent progress has been more rapid, thanks to applications of quantitative genetics to breeding schemes. With the availability of the bovine genome sequence, genetic selection and on-farm management are likely to be revolutionised yet again. Genetic association studies that were previously impossible to carry out due to a lack of markers are now possible. In addition to improved genetic mapping of economic traits, the bovine genome sequence allows us to create a common context for genetic and physiological data, which will provide novel insights into gene regulation and function.

scholarly journals A second generation radiation hybrid map to aid the assembly of the bovine genome sequence

BMC Genomics ◽  
2006 ◽  
Vol 7 (1) ◽  
Author(s):  
Oliver C Jann ◽  
Jan Aerts ◽  
Michelle Jones ◽  
Nicola Hastings ◽  
Andy Law ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Radiation Hybrid ◽  
Second Generation ◽  
Bovine Genome ◽  
Bovine Genome Sequence ◽  
Radiation Hybrid Map

scholarly journals Draft Genome Sequence of Urease-Producing Pseudorhodobacter sp. Strain E13, Isolated from the Yellow Sea in Gunsan, South Korea

2019 ◽  
Vol 8 (23) ◽  
Author(s):  
Si Chul Kim ◽  
Hyo Jung Lee
Keyword(s):  
South Korea ◽  
Genome Sequence ◽  
Yellow Sea ◽  
Draft Genome ◽  
The Yellow Sea ◽  
Draft Genome Sequence ◽  
Protein Coding ◽  
Coding Sequences ◽  
Gram Negative ◽  
Content Type

Here, we report the draft genome sequence of Pseudorhodobacter sp. strain E13, a Gram-negative, aerobic, nonflagellated, and rod-shaped bacterium which was isolated from the Yellow Sea in South Korea. The assembled genome sequence is 3,878,578 bp long with 3,646 protein-coding sequences in 159 contigs.

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