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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...

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Autores principales: 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
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2010
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.
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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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