Talk:Z3186093

http://www.fao.org/docrep/t1690E/t1690e06.htm#TopOfPage

Nucleotide sequencing: http://www.ncbi.nlm.nih.gov/nuccore/256946799

• Too many nucleotides to list (9986)
• 3 papers to look at
• 84024 rc by 31-AUG-2009
• Sequence has been completed twice by Initial Shotgun Sequence and assembly. Currently there are another 7 groups to recomplete this.

Embryological development is after all the opportunity for a specific Genome to be expressed, regulated and utilized as it will never be again in the adult animal.

Assessment Criteria:

Procedure

   * Project initial assessment by other groups after the Group Project submission date.
         o Written comments will be added to the discussion page. 
   * Group will have opportunity to work on the project in response to comments.
         o Individuals will provide an assessment of their contribution to the final project on their own student page. 
   * Final assessment by course co-ordinator. 20% of final course assessment mark 

Content

Does the group project include the following information?

   * Timeline of Development (how long and key events)
   * Staging (is there a species specific staging and what criteria are used)
   * History of Model Use (what embryological studies have used this model)
   * Genetics (chromosome number, genome sequencing)
   * Current Embryology Research (what embryological studies have used this model) 

Structure

   * Are there visual ways of representing information?
   * Is the content correctly referenced in a reference list?
   * Are there links to related resources/research laboratories? 

Contribution

   * Have all group members contributed?
   * Has the group responded to peer assessment feedback?

Genetics

Sequencing

The National Human Genome Research Institute selected the European rabbit (Oryctolagus cuniculus) for whole genome sequencing to enhance their understanding of the human genome and use it experimentally for an animal model for human disease. (1)

The European rabbit (Oryctolagus cuniculus) has been sequenced twice by The Broad Institute as part of the mammalian genome project. It is now currently undergoing 7 more sequencing projects. Its sequencing is made by the Whole Genome Shotgun (WGS) and assembly method. (2) This is when genomic DNA is sheared into small pieces of approximately 2000 base pairs which are then cloned into plasmids and sequenced on both strands. Once the contig fragments are read, realigned and reassembled by computer algorithms, it will give the overall sequence. (3) (4) [A contig is a set of overlapping DNA segments, derived from a single source of genetic material, from which the complete sequence may be deduced.]

"The whole genome shotgun (WGS) "unfinished Oryctolagus cuniculus database" has serious gaps, yet the information has already proven useful for immunological as well as in silico studies. Deeper 7x coverage started in September 2007. The NCBI Rabbit Genome Resources site has links to searches for genes in the assemblies of the 2x WGS sequence at Ensembl and UCSC useful for designing primers for PCR by predicting mRNA sequences and exon boundaries" (5)

Genome

The Rabbit genome was published by two groups.

1. Lindblad-Toh,K., Chang,J.L., Gnerre,S., Clamp,M. and Lander,E.S. published their admission of 84024 bases on May 5th 2005 to The Broad Institute (USA) by shotgun sequencing
2. Di Palma,F., Heiman,D., Young,S., Gnerre,S., Johnson,J., Lander,E.S. and Lindblad-Toh,K. published their admission of 84024 bases on August 3rd 2009 to The Broad Institute (USA) by shotgun sequencing.

Rabbit Genome from the Nucleotide Data Bank

The rabbit genome was sequenced in 2005 by Ensembl and managed to produce: (6)

• 2,076,044,328 supercontigs (ordered Contigs with gaps)
• 495 Known protein-coding genes
• 11,357 Projected protein-coding genes
• 2,343 RNA genes
• 212,581 Gene exons
• 20,311 Gene transcripts

Mitochondrial Genome

The mitochondiral genome (mtDNA) of the rabbit was sequenced on November 14th 20066 with 17245 base pairs/nucleotides in circular form. Apparently the "length is not absolute due to the presence of different numbers of repeated motifs in the control region". "PMID 9653643"

Taxonomy

The taxonomy ID number for the Rabbit is: 9986 Taxonomy Data

Chromosomes

There are 22 different chromosome pairs existing in each cell of the rabbit except the sex cells and red blood cells (9) Rabbit chromosomes 12, 19 and X were found to be completely homologous to human chromosomes 6, 17 and X, respectively. All other human chromosomes were homologous to two or sometimes three rabbit chromosomes. (7) Chromosome 12 was shorter than chromosomes 13 and 14. (8)

References

1. National Center for Biotechnology Information. (June 16, 2009). Rabbit Genome Resources, Retrieved August 20, 2009, from NCBI Rabbit Genome Site
2. The Broad Institute. (2008). Rabbit Genome Sequencing Project. Retrieved only August 29, 2009, from Rabbit Genome Sequencing Project
3. Campbell, M. A. (2002). Sequencing Whole Genomes: Hierarchical Shotgun Sequencing v. Shotgun Sequencing Retrieved August 31, 2009, from Shotgun Sequencing - 1
4. Trivedi, B. (2000). Sequencing the Genome. Retrieved September 4, 2009, from Shotgun Sequencing - 2
5. Mage, R. (2008). Rabbit genome sequencing update: genes of immunological interest found in the 2x genome assemblies, ENCODE, and the 7x trace archive. Journal of FASEB 22(Retrieved September 5, 2009, from Rabbit Genome & its Immunological Interest
6. Ensembl (2009). Rabbit (Oryctolagus cuniculus). Retrieved September 5, 2009, from Ensembl Genome Project
7. Korstanje, R. et al. (1999) Complete homology maps of the rabbit (Oryctolagus cuniculus) and human by reciprocal chromosome painting. Cytogenetics and cell genetics 86(3-4), 317-322. Retrieved September 6, 2009, from Complete homology maps of the rabbit Article "PMID 10575232"
8. Brunner, R., Knopp, A., Rudolph, W. (n.d). Rabbit chromosome analysis by image processing. Journal of Applied Rabbit Research.
9. DebMark Rabbit Education Resource (2006). Rabbit Genetics. Retrieved September 6, 2009, from Rabbit Genetics