Second generation sequencing and analysis of complex genomes
Trabajo presentado en la 3rd Next Generation Sequencing Conference, celebrada en Palmerston North (Nueva Zelanda) el 23 y 24 de agosto de 2011.
Saved in:
| Main Authors: | , , , , , , , , , , , , , , , , , , |
|---|---|
| Format: | comunicación de congreso biblioteca |
| Published: |
2011-08
|
| Online Access: | http://hdl.handle.net/10261/98314 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| id |
dig-ias-es-10261-98314 |
|---|---|
| record_format |
koha |
| spelling |
dig-ias-es-10261-983142019-08-12T11:44:24Z Second generation sequencing and analysis of complex genomes Lai, Kaitao Lorenc, Michal Berkman, Paul J. Chan, Kenneth Imelfort, Mike Manoli, Sahana Duran, Chris Lee, Hong Ling, Edmund Šimková, Hana Kubaláková, Marie Rosic, Nela Kaniewska, Paulina Campbell, Emma Hernández Molina, Pilar Batley, Jacqueline Stiller, Jiri Doležel, Jaroslav Edwards, David Trabajo presentado en la 3rd Next Generation Sequencing Conference, celebrada en Palmerston North (Nueva Zelanda) el 23 y 24 de agosto de 2011. The genome sequence of an organism provides the basis for gene discovery, the analysis of genetic variation and the association of genomic variation with heritable traits. Second generation sequencing technologies and applied bioinformatics tools can provide an unprecedented insight into genome structure and variation. This technology is still in its infancy, yet is already making a huge impact in our understanding of biological processes. We have developed and applied novel bioinformatics tools and approaches for Illumina second generation sequence data analysis with the aim of understanding complex genomes. These range from large genome polyploid crops such as wheat and Brassica species, to complex environmental metagenomic samples. For crop genomes, we aim to identify genes, novel and mapped genetic markers and develop methods for the association of agronomic traits with underlying genomic variation. In canola (Brassica napus) we have identified more than 1 million SNPs across the polyploid genome, with a validation accuracy of 96%. This information has been integrated with mapped genetic marker and trait information within searchable databases. The resulting tools enable the association of candidate genes with trait associated genetic markers and the study of Brassica genome evolution under selection. The genome of bread wheat (Triticum aestivum) is greater than 16 Gbp in size and consists predominantly of repetitive elements. There has been some debate over whether second generation sequencing can be applied for such a large and complex genome. We have reduced genome sequence complexity by sequencing isolated chromosome arms, with the aim to assemble low copy and genic regions. Our approach enabled the assembly of all genes, as well as a substantial portion of the repetitive fraction. The syntenic relationship between wheat and a sequenced close relative, Brachypodium distachyon, has been used to produce annotated syntenic builds whereby the majority of genes have been placed in an approximate order and orientation. Our results suggest that the sequencing of isolated chromosome arms can provide valuable information on the gene content of wheat, and that these assemblies can be applied for genome wide SNP discovery, the identification of candidate genes associated with genetically mapped traits and investigation of genome evolution in this important crop. Finally, as an example of second generation metagenome bioinformatics, I will describe approaches to understand the complex coral holobiont and its response to environmental change, a study which is challenged by a lack of reference genomes or even knowledge of which species are present in the sample. Peer Reviewed 2014-06-13T07:37:50Z 2014-06-13T07:37:50Z 2011-08 2014-06-13T07:37:50Z comunicación de congreso http://purl.org/coar/resource_type/c_5794 3rd Next Generation Sequencing Conference (2011) http://hdl.handle.net/10261/98314 none |
| institution |
IAS ES |
| collection |
DSpace |
| country |
España |
| countrycode |
ES |
| component |
Bibliográfico |
| access |
En linea |
| databasecode |
dig-ias-es |
| tag |
biblioteca |
| region |
Europa del Sur |
| libraryname |
Biblioteca del IAS España |
| description |
Trabajo presentado en la 3rd Next Generation Sequencing Conference, celebrada en Palmerston North (Nueva Zelanda) el 23 y 24 de agosto de 2011. |
| format |
comunicación de congreso |
| author |
Lai, Kaitao Lorenc, Michal Berkman, Paul J. Chan, Kenneth Imelfort, Mike Manoli, Sahana Duran, Chris Lee, Hong Ling, Edmund Šimková, Hana Kubaláková, Marie Rosic, Nela Kaniewska, Paulina Campbell, Emma Hernández Molina, Pilar Batley, Jacqueline Stiller, Jiri Doležel, Jaroslav Edwards, David |
| spellingShingle |
Lai, Kaitao Lorenc, Michal Berkman, Paul J. Chan, Kenneth Imelfort, Mike Manoli, Sahana Duran, Chris Lee, Hong Ling, Edmund Šimková, Hana Kubaláková, Marie Rosic, Nela Kaniewska, Paulina Campbell, Emma Hernández Molina, Pilar Batley, Jacqueline Stiller, Jiri Doležel, Jaroslav Edwards, David Second generation sequencing and analysis of complex genomes |
| author_facet |
Lai, Kaitao Lorenc, Michal Berkman, Paul J. Chan, Kenneth Imelfort, Mike Manoli, Sahana Duran, Chris Lee, Hong Ling, Edmund Šimková, Hana Kubaláková, Marie Rosic, Nela Kaniewska, Paulina Campbell, Emma Hernández Molina, Pilar Batley, Jacqueline Stiller, Jiri Doležel, Jaroslav Edwards, David |
| author_sort |
Lai, Kaitao |
| title |
Second generation sequencing and analysis of complex genomes |
| title_short |
Second generation sequencing and analysis of complex genomes |
| title_full |
Second generation sequencing and analysis of complex genomes |
| title_fullStr |
Second generation sequencing and analysis of complex genomes |
| title_full_unstemmed |
Second generation sequencing and analysis of complex genomes |
| title_sort |
second generation sequencing and analysis of complex genomes |
| publishDate |
2011-08 |
| url |
http://hdl.handle.net/10261/98314 |
| work_keys_str_mv |
AT laikaitao secondgenerationsequencingandanalysisofcomplexgenomes AT lorencmichal secondgenerationsequencingandanalysisofcomplexgenomes AT berkmanpaulj secondgenerationsequencingandanalysisofcomplexgenomes AT chankenneth secondgenerationsequencingandanalysisofcomplexgenomes AT imelfortmike secondgenerationsequencingandanalysisofcomplexgenomes AT manolisahana secondgenerationsequencingandanalysisofcomplexgenomes AT duranchris secondgenerationsequencingandanalysisofcomplexgenomes AT leehong secondgenerationsequencingandanalysisofcomplexgenomes AT lingedmund secondgenerationsequencingandanalysisofcomplexgenomes AT simkovahana secondgenerationsequencingandanalysisofcomplexgenomes AT kubalakovamarie secondgenerationsequencingandanalysisofcomplexgenomes AT rosicnela secondgenerationsequencingandanalysisofcomplexgenomes AT kaniewskapaulina secondgenerationsequencingandanalysisofcomplexgenomes AT campbellemma secondgenerationsequencingandanalysisofcomplexgenomes AT hernandezmolinapilar secondgenerationsequencingandanalysisofcomplexgenomes AT batleyjacqueline secondgenerationsequencingandanalysisofcomplexgenomes AT stillerjiri secondgenerationsequencingandanalysisofcomplexgenomes AT dolezeljaroslav secondgenerationsequencingandanalysisofcomplexgenomes AT edwardsdavid secondgenerationsequencingandanalysisofcomplexgenomes |
| _version_ |
1777663064450007040 |