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A draft physical map of a D-genome cotton species (Gossypium raimondii)
BACKGROUND: Genetically anchored physical maps of large eukaryotic genomes have proven useful both for their intrinsic merit and as an adjunct to genome sequencing. Cultivated tetraploid cottons, Gossypium hirsutum and G. barbadense, share a common ancestor formed by a merger of the A and D genomes...
Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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Formato: | Texto |
Lenguaje: | English |
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BioMed Central
2010
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2996926/ https://www.ncbi.nlm.nih.gov/pubmed/20569427 http://dx.doi.org/10.1186/1471-2164-11-395 |
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author | Lin, Lifeng Pierce, Gary J Bowers, John E Estill, James C Compton, Rosana O Rainville, Lisa K Kim, Changsoo Lemke, Cornelia Rong, Junkang Tang, Haibao Wang, Xiyin Braidotti, Michele Chen, Amy H Chicola, Kristen Collura, Kristi Epps, Ethan Golser, Wolfgang Grover, Corrinne Ingles, Jennifer Karunakaran, Santhosh Kudrna, Dave Olive, Jaime Tabassum, Nabila Um, Eareana Wissotski, Marina Yu, Yeisoo Zuccolo, Andrea ur Rahman, Mehboob Peterson, Daniel G Wing, Rod A Wendel, Jonathan F Paterson, Andrew H |
author_facet | Lin, Lifeng Pierce, Gary J Bowers, John E Estill, James C Compton, Rosana O Rainville, Lisa K Kim, Changsoo Lemke, Cornelia Rong, Junkang Tang, Haibao Wang, Xiyin Braidotti, Michele Chen, Amy H Chicola, Kristen Collura, Kristi Epps, Ethan Golser, Wolfgang Grover, Corrinne Ingles, Jennifer Karunakaran, Santhosh Kudrna, Dave Olive, Jaime Tabassum, Nabila Um, Eareana Wissotski, Marina Yu, Yeisoo Zuccolo, Andrea ur Rahman, Mehboob Peterson, Daniel G Wing, Rod A Wendel, Jonathan F Paterson, Andrew H |
author_sort | Lin, Lifeng |
collection | PubMed |
description | BACKGROUND: Genetically anchored physical maps of large eukaryotic genomes have proven useful both for their intrinsic merit and as an adjunct to genome sequencing. Cultivated tetraploid cottons, Gossypium hirsutum and G. barbadense, share a common ancestor formed by a merger of the A and D genomes about 1-2 million years ago. Toward the long-term goal of characterizing the spectrum of diversity among cotton genomes, the worldwide cotton community has prioritized the D genome progenitor Gossypium raimondii for complete sequencing. RESULTS: A whole genome physical map of G. raimondii, the putative D genome ancestral species of tetraploid cottons was assembled, integrating genetically-anchored overgo hybridization probes, agarose based fingerprints and 'high information content fingerprinting' (HICF). A total of 13,662 BAC-end sequences and 2,828 DNA probes were used in genetically anchoring 1585 contigs to a cotton consensus genetic map, and 370 and 438 contigs, respectively to Arabidopsis thaliana (AT) and Vitis vinifera (VV) whole genome sequences. CONCLUSION: Several lines of evidence suggest that the G. raimondii genome is comprised of two qualitatively different components. Much of the gene rich component is aligned to the Arabidopsis and Vitis vinifera genomes and shows promise for utilizing translational genomic approaches in understanding this important genome and its resident genes. The integrated genetic-physical map is of value both in assembling and validating a planned reference sequence. |
format | Text |
id | pubmed-2996926 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2010 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-29969262010-12-07 A draft physical map of a D-genome cotton species (Gossypium raimondii) Lin, Lifeng Pierce, Gary J Bowers, John E Estill, James C Compton, Rosana O Rainville, Lisa K Kim, Changsoo Lemke, Cornelia Rong, Junkang Tang, Haibao Wang, Xiyin Braidotti, Michele Chen, Amy H Chicola, Kristen Collura, Kristi Epps, Ethan Golser, Wolfgang Grover, Corrinne Ingles, Jennifer Karunakaran, Santhosh Kudrna, Dave Olive, Jaime Tabassum, Nabila Um, Eareana Wissotski, Marina Yu, Yeisoo Zuccolo, Andrea ur Rahman, Mehboob Peterson, Daniel G Wing, Rod A Wendel, Jonathan F Paterson, Andrew H BMC Genomics Research Article BACKGROUND: Genetically anchored physical maps of large eukaryotic genomes have proven useful both for their intrinsic merit and as an adjunct to genome sequencing. Cultivated tetraploid cottons, Gossypium hirsutum and G. barbadense, share a common ancestor formed by a merger of the A and D genomes about 1-2 million years ago. Toward the long-term goal of characterizing the spectrum of diversity among cotton genomes, the worldwide cotton community has prioritized the D genome progenitor Gossypium raimondii for complete sequencing. RESULTS: A whole genome physical map of G. raimondii, the putative D genome ancestral species of tetraploid cottons was assembled, integrating genetically-anchored overgo hybridization probes, agarose based fingerprints and 'high information content fingerprinting' (HICF). A total of 13,662 BAC-end sequences and 2,828 DNA probes were used in genetically anchoring 1585 contigs to a cotton consensus genetic map, and 370 and 438 contigs, respectively to Arabidopsis thaliana (AT) and Vitis vinifera (VV) whole genome sequences. CONCLUSION: Several lines of evidence suggest that the G. raimondii genome is comprised of two qualitatively different components. Much of the gene rich component is aligned to the Arabidopsis and Vitis vinifera genomes and shows promise for utilizing translational genomic approaches in understanding this important genome and its resident genes. The integrated genetic-physical map is of value both in assembling and validating a planned reference sequence. BioMed Central 2010-06-22 /pmc/articles/PMC2996926/ /pubmed/20569427 http://dx.doi.org/10.1186/1471-2164-11-395 Text en Copyright ©2010 Lin et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Lin, Lifeng Pierce, Gary J Bowers, John E Estill, James C Compton, Rosana O Rainville, Lisa K Kim, Changsoo Lemke, Cornelia Rong, Junkang Tang, Haibao Wang, Xiyin Braidotti, Michele Chen, Amy H Chicola, Kristen Collura, Kristi Epps, Ethan Golser, Wolfgang Grover, Corrinne Ingles, Jennifer Karunakaran, Santhosh Kudrna, Dave Olive, Jaime Tabassum, Nabila Um, Eareana Wissotski, Marina Yu, Yeisoo Zuccolo, Andrea ur Rahman, Mehboob Peterson, Daniel G Wing, Rod A Wendel, Jonathan F Paterson, Andrew H A draft physical map of a D-genome cotton species (Gossypium raimondii) |
title | A draft physical map of a D-genome cotton species (Gossypium raimondii) |
title_full | A draft physical map of a D-genome cotton species (Gossypium raimondii) |
title_fullStr | A draft physical map of a D-genome cotton species (Gossypium raimondii) |
title_full_unstemmed | A draft physical map of a D-genome cotton species (Gossypium raimondii) |
title_short | A draft physical map of a D-genome cotton species (Gossypium raimondii) |
title_sort | draft physical map of a d-genome cotton species (gossypium raimondii) |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2996926/ https://www.ncbi.nlm.nih.gov/pubmed/20569427 http://dx.doi.org/10.1186/1471-2164-11-395 |
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