seq of grapes_anoop

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SEQUENCING OF GRAPES. Anoop Inder Kaur L-2010-A-123-M:

SEQUENCING OF GRAPES. Anoop Inder Kaur L-2010-A-123-M

About grapes:

About grapes Perennial plant. Highly heterozygous. Long reproductive cycle. Belongs to family Vitaceae. 17 genera Genus vitis produces edible berries.

Vitis vinifera:

Vitis vinifera First species to be sequenced. Diploid genome. Haploid chromosome number 19. Estimated genome size 500 Mbase.

Why sequence the genome of grape?:

Why sequence the genome of grape? To better understand the biological features. To facilitate the exploration of genetic resources. To develop tools for a more precise viticulture. To increase its economic competitivity. To adapt its cultivation to new production objectives .

IGGP:

IGGP Stands for International Grape Genome Program . White paper(2002)-explaining detailed research objectives and the advantages. Goal-to understand the genetic and the molecular basis of all biological processes. Completed in 2007.

Genome Sequencing and Gene Prediction :

Genome Sequencing and Gene Prediction Strategy used- WHOLE GENOME SHOTGUN APPROACH. Performed on nearly homozygous genotype PN 40024. Initially 8X version was released( Aug,2007). Later on 12X version was also released (Feb,2008).

According to 12X version: :

According to 12X version: 2059 scaffolds total length-485 Mb. assembled into 33 chromosomes and chromosomal fragments of total length 486 Mb. Predicted number of genes- 30,434.

Shotgun Approach:

Shotgun Approach Several plasmid libraries of insert sizes( 3 and 10 Kb) were constructed and sequenced. Hind III BAC library of 70,656 clones was cloned and end sequenced. Fosmid library(35 kb) was constructed to obtain long distance clones links. Obtained sequences were assembled using ARACHNE assembler.

Whole genome :

Whole genome

Summary :

Summary Assembly: IGGP_12x Database version: 62.2 Base Pairs: 485,185,630 Golden Path Length: 486,198,630 Genebuild by: IGGP

Gene counts :

Gene counts Known protein-coding genes: 26,112 Novel protein-coding genes: 234 Gene exons : 0 Gene transcripts: 0

Other:

Other Short Variants (SNPs, indels , somatic mutations): 457,404

Current projects:

Current projects Presently there are more than 50 different grape genome sequencing projects in progress.

PowerPoint Presentation:

Species Genotype Research Group Country Coverage Status Objective V. aestivalis Norton Missouri State University USA 10x Done SNP discovery V. amurensis PI 483145.01 USDA/ Cornell University USA Done SNP discovery V. labrusca 3 genotypes Consortium FR;IT;SP;D 14x In progress SNP discovery V. riparia NA South Dakota State University USA 40x proposed SNP discovery, de novo assembly V. sylvestris Dirmstein mâle Consortium FR;IT;SP;D 14x In progress SNP discovery V. vinifera Grenache University of Udine Italy >10x In progress Annotation,SNP discovery,Genome comparisons

THANKS.:

THANKS .

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