vervet pic

Vervet Monkey Genomics:
Genome Canada and Genome Quebec Physical Map Project

McGill University and Genome Quebec Innovation Centre

What's new ?

- February 2010: custom track of vervet genome sequencing reads (Genome Centre at Washington University)

Now available on the UCSC genome browser for the human hg19 assembly is the mapping information of the vervet reads (4X coverage) from the Vervet Genome Sequencing Project (NIH).

Vervet reads

- January 2010: vervet BAC clone sequencing (Genome Centre at Washington University)

Summary (Excel file)

- September 2009: direct access to the FISH experiments results

A new page has been added to this site, providing an easier and faster way than through the UCSC genome browser, to get to the results of the FISH experiments for vervet centromere localization. A table lists the experiments by Human or Vervet chromosome.
FISH experiments

- April 2009: some custom tracks of clone size

Now available on the UCSC genome browser for the human hg18 assembly are 2 wiggle tracks:
- in blue "average clone size": each bar shows the observed average size of all concordant clones covering that position
- in green "filtered percentile clone size": after creating the percentile distribution of observed clone sizes for the whole population of concordant clones, the percentiles of clones belonging to <=25th percentile or >=75th percentile are plotted.

clone sz

- December 2008: vervet cytogenomics

FISH experiments are being achieved in order to locate vervet centromeres (blood samples provided by Professor Roberta Palmour, McGill University). The clones predicted to flank vervet centromeres and used to hybridize the vervet karyotype slides are visible in a track on the UCSC genome browser called "FISH: localizing vervet chrN centromere", and colored according to their fluorescent label in the experiment. Clicking on the clones in this track will display the FISH image resulting from the hybridization.

Fish

- August 2008

15820 extra BAC end sequences have been sent to GSS: these clones are concordant clones on human hg18, one of the ends is longer than 400bp, the other end is longer than 100bp but both ends map on human hg18 (FI169229-FI185048).

- In the week of June 02 2008

The goal of the project of sequencing the vervet BAC library with a success rate of 81% has been achieved.
The 328.458th BAC end sequence was generated with a minimum length of 400bp at a minimum quality of 20.

- April 2008: Integration of new data in the browser

REMOVED June 09: go to http://vervet.bmap.ucla.edu:8080/vervet-1.0/index.html for an updated dataset.
Some Affymetrix vervet brain gene expression data (source UCLA) is now available on the UCSC genome browser with the vervet BAC end sequences. The data has been integrated at the bottom of the custom tracks window.

Vervet brain gene expression

- March 2008: 7X Genome Coverage attained

As of March 2008, more than 40% of the genome is covered by 8 or more concordant vervet BAC clones.
More information

- March 2008: Human/Rhesus parallel browser view

This tool was developped to visualize a specific region of interest in human and rhesus in parallel, in order to compare the colinearity to vervet for both genomes.
Human/Rhesus parallel browser

Parallel browser

- August 2007: Gap closure

This new feature in 'Progress reports' has been implemented to keep track of the progress in closing gaps. Each month the update of the vervet assembly compared to human hg18 allows to calculate the count of the remaining gaps.
Gap closure

- August 2007: GSS submissions

On August 2nd 2007, the 200.000th BAC end sequence was submitted to GSS.
The species Cercopithecus aethiops then ranks 23rd in the GSS database summary in number of public entries by organism.

- June 2007: a custom track for gaps on human hg18

The human genome browser now shows the regions of the chromosomes non covered by quality/concordant clones in a new category of custom tracks (in light green). They are updated monthly.

Gaps custom tracks

- April 2007: Vervet vs species - new software feature

The browser to retrieve the sequences aligning on a portion of the genome of Human, Chimp or Rhesus now provides the fasta file of BAC ends sequences for that region.

Fasta sequences link

- March 2007: Search by clone

A new searching tool has been developed, allowing the user to look for the mapping data of any vervet BAC clone by its name or its GSS accession number. It also provides an access to the genome browser directly from the results.
Search by clone

- March 2007: Chimp comparative genomics

As of March 2007, the mapping information of all vervet BAC clones is available on chimp build panTro1 via the page Vervet vs. Chimp

Please note that as of this date the comparative data between human and the new vervet sequences will only be available on build hg18 (the data for human hg17 will still be available for sequences generated between Sept 26, 2005 and March 09, 2007).

- January 2007: 2X Genome Coverage attained

As of January 2007, more than 60% of the genome is covered by 2 or more concordant vervet BAC clones.
More information

- January 2007: Mapping on human build hg18 (released March 2006)

As of January 2007, the mapping information is also available for human on build hg18.
Vervet vs Human Hg18

- December 2006: GSS submissions

On December 5 2006, the 100.000th BAC end sequence was submitted to GSS.
On January 5 2007, the species Cercopithecus aethiops ranks 34th in the GSS database summary in number of public entries by organism.