A draft physical map of a D-genome cotton species (Gossypium raimondii)

Persistent Link:
http://hdl.handle.net/10150/610009
Title:
A draft physical map of a D-genome cotton species (Gossypium raimondii)
Author:
Lin, Lifeng; Pierce, Gary; Bowers, John; Estill, James; Compton, Rosana; Rainville, Lisa; Kim, Changsoo; Lemke, Cornelia; Rong, Junkang; Tang, Haibao; Wang, Xiyin; Braidotti, Michele; Chen, Amy; 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; Wing, Rod; Wendel, Jonathan; Paterson, Andrew
Affiliation:
Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30605, USA; Department of Ecology, Evolution, & Organismal Biology, Iowa State University, Ames, IA 50011, USA; Arizona Genomics Institute, School of Plant Sciences and BIO5 Institute for Collaborative Research, University of Arizona, Tucson, AZ 85721, USA; National Institute for Biotechnology & Genetic Engineering (NIBGE), Faisalabad, Pakistan; Life Sciences & Biotechnology Institute, Mississippi State University, Mississippi State, MS 39762 USA; Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA; School of Agriculture and Food Sciences, Zhejiang Forestry University, Lin'an, Hangzhou, Zhejiang, 311300, China; Department of Plant and Microbiology, College of Natural Resources, University of California, Berkeley, CA, USA
Issue Date:
2010
Publisher:
BioMed Central
Citation:
Lin et al. BMC Genomics 2010, 11:395 http://www.biomedcentral.com/1471-2164/11/395
Journal:
BMC Genomics
Rights:
© 2010 Lin et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0)
Collection Information:
This item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at repository@u.library.arizona.edu.
Abstract:
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.
EISSN:
1471-2164
DOI:
10.1186/1471-2164-11-395
Version:
Final published version
Additional Links:
http://www.biomedcentral.com/1471-2164/11/395

Full metadata record

DC FieldValue Language
dc.contributor.authorLin, Lifengen
dc.contributor.authorPierce, Garyen
dc.contributor.authorBowers, Johnen
dc.contributor.authorEstill, Jamesen
dc.contributor.authorCompton, Rosanaen
dc.contributor.authorRainville, Lisaen
dc.contributor.authorKim, Changsooen
dc.contributor.authorLemke, Corneliaen
dc.contributor.authorRong, Junkangen
dc.contributor.authorTang, Haibaoen
dc.contributor.authorWang, Xiyinen
dc.contributor.authorBraidotti, Micheleen
dc.contributor.authorChen, Amyen
dc.contributor.authorChicola, Kristenen
dc.contributor.authorCollura, Kristien
dc.contributor.authorEpps, Ethanen
dc.contributor.authorGolser, Wolfgangen
dc.contributor.authorGrover, Corrinneen
dc.contributor.authorIngles, Jenniferen
dc.contributor.authorKarunakaran, Santhoshen
dc.contributor.authorKudrna, Daveen
dc.contributor.authorOlive, Jaimeen
dc.contributor.authorTabassum, Nabilaen
dc.contributor.authorUm, Eareanaen
dc.contributor.authorWissotski, Marinaen
dc.contributor.authorYu, Yeisooen
dc.contributor.authorZuccolo, Andreaen
dc.contributor.authorur Rahman, Mehbooben
dc.contributor.authorPeterson, Danielen
dc.contributor.authorWing, Roden
dc.contributor.authorWendel, Jonathanen
dc.contributor.authorPaterson, Andrewen
dc.date.accessioned2016-05-20T08:56:22Z-
dc.date.available2016-05-20T08:56:22Z-
dc.date.issued2010en
dc.identifier.citationLin et al. BMC Genomics 2010, 11:395 http://www.biomedcentral.com/1471-2164/11/395en
dc.identifier.doi10.1186/1471-2164-11-395en
dc.identifier.urihttp://hdl.handle.net/10150/610009-
dc.description.abstractBACKGROUND: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.en
dc.language.isoenen
dc.publisherBioMed Centralen
dc.relation.urlhttp://www.biomedcentral.com/1471-2164/11/395en
dc.rights© 2010 Lin et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0)en
dc.titleA draft physical map of a D-genome cotton species (Gossypium raimondii)en
dc.typeArticleen
dc.identifier.eissn1471-2164en
dc.contributor.departmentPlant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30605, USAen
dc.contributor.departmentDepartment of Ecology, Evolution, & Organismal Biology, Iowa State University, Ames, IA 50011, USAen
dc.contributor.departmentArizona Genomics Institute, School of Plant Sciences and BIO5 Institute for Collaborative Research, University of Arizona, Tucson, AZ 85721, USAen
dc.contributor.departmentNational Institute for Biotechnology & Genetic Engineering (NIBGE), Faisalabad, Pakistanen
dc.contributor.departmentLife Sciences & Biotechnology Institute, Mississippi State University, Mississippi State, MS 39762 USAen
dc.contributor.departmentDepartment of Plant Biology, University of Georgia, Athens, GA, 30602, USAen
dc.contributor.departmentSchool of Agriculture and Food Sciences, Zhejiang Forestry University, Lin'an, Hangzhou, Zhejiang, 311300, Chinaen
dc.contributor.departmentDepartment of Plant and Microbiology, College of Natural Resources, University of California, Berkeley, CA, USAen
dc.identifier.journalBMC Genomicsen
dc.description.collectioninformationThis item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at repository@u.library.arizona.edu.en
dc.eprint.versionFinal published versionen
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