MGRC seminar Part II: Plant Genomics
This talk is presented by Dr. Jane Rogers. She was the Head of Sequencing in Wellcome Trust Sanger Institute before joining The Genome Analysis Centre, JIC. She started her presentation with a brief introduction on genome sequencing methods and the types of genome sequences based on sequence quality. The sequence quality measure based on human genome project is showed below:
The main problem in genome sequencing is closing the gaps between large contigs which is thought to be caused by large repeats. According to Dr. Rogers, there are about 340 gaps in the human genome project completed in 2003. Recent studies showed that these gaps are caused by copy number variations (CNV) and different clones that are used for sequencing. This is a fascinating discovery!
Out of nearly 50 plant genome sequencing projects, only complete Arabidopsis and rice genome are obtained. The rest produce draft genome sequences. So why do we need to sequence so many plant genome? The ultimate goal is crop breeding. Genomics assisted selection program is expected to take at least 9 years time before phenotypic selection can be carried out.
Polyploidy plants are the most difficult species to sequence due to huge genome size, repetitive regions and complexity. One example is hexaploid wheat. 80% of this genome is repetitive. Physical mapping of wheat genome using BAC clones has been initiated in 2005. Now Dr. Rogers and her team are interested in sequencing chromosome 3DL of wheat.
Most sequencing projects involve plants with small genome size. Besides Arabidopsis, poplar and Medicago trunculata is used as model plant for tree and legume. Medicago trunculata is a nitrogen fixing plant. The original size of this plant is thought to be 200 Mb but may reach up to 300 Mb. Almost 2600 BAC clones have been sequenced up until Oct 2008. Additional shotgun sequencing using 454 and Illumina platforms are used. The scientists are interested to study nodulation pathway of this plant using genomic approach.
Another important application of genomics is to understand plant resistance. She elaborated on the recent work of Prof. Jonathan Jones which is highly cited. His team sequenced two strains of Arabidopsis white rust using Illumina platform. The 36 bp short reads are assembled using Velvet. Comparison of these two genomes has successfully identified candidate effectors in host resistance mechanism.
The main problem in genome sequencing is closing the gaps between large contigs which is thought to be caused by large repeats. According to Dr. Rogers, there are about 340 gaps in the human genome project completed in 2003. Recent studies showed that these gaps are caused by copy number variations (CNV) and different clones that are used for sequencing. This is a fascinating discovery!
Out of nearly 50 plant genome sequencing projects, only complete Arabidopsis and rice genome are obtained. The rest produce draft genome sequences. So why do we need to sequence so many plant genome? The ultimate goal is crop breeding. Genomics assisted selection program is expected to take at least 9 years time before phenotypic selection can be carried out.
Polyploidy plants are the most difficult species to sequence due to huge genome size, repetitive regions and complexity. One example is hexaploid wheat. 80% of this genome is repetitive. Physical mapping of wheat genome using BAC clones has been initiated in 2005. Now Dr. Rogers and her team are interested in sequencing chromosome 3DL of wheat.
Most sequencing projects involve plants with small genome size. Besides Arabidopsis, poplar and Medicago trunculata is used as model plant for tree and legume. Medicago trunculata is a nitrogen fixing plant. The original size of this plant is thought to be 200 Mb but may reach up to 300 Mb. Almost 2600 BAC clones have been sequenced up until Oct 2008. Additional shotgun sequencing using 454 and Illumina platforms are used. The scientists are interested to study nodulation pathway of this plant using genomic approach.
Another important application of genomics is to understand plant resistance. She elaborated on the recent work of Prof. Jonathan Jones which is highly cited. His team sequenced two strains of Arabidopsis white rust using Illumina platform. The 36 bp short reads are assembled using Velvet. Comparison of these two genomes has successfully identified candidate effectors in host resistance mechanism.
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