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

Lifeng Lin; Gary J. Pierce; John E. Bowers; James C. Estill; Rosana O. Compton; Lisa K. Rainville; Changsoo Kim; Cornelia Lemke; Junkang Rong; Haibao Tang; Xiyin Wang; Michele Braidotti; Amy H. Chen; Kristen Chicola; Kristi Collura; Ethan Epps; Wolfgang Golser; Corrinne Grover; Jennifer Ingles; Santhosh Karunakaran; Dave Kudrna; Jaime Olive; Nabila Tabassum; Eareana Um; Marina Wissotski; Yeisoo Yu; Andrea Zuccolo; Mehboob ur Rahman; Daniel G. Peterson; Rod A. Wing; Jonathan F. Wendel; Andrew H. Paterson

doi:10.1186/1471-2164-11-395

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

Lifeng Lin, Gary J. Pierce, John E. Bowers, James C. Estill, Rosana O. Compton, Lisa K. Rainville, Changsoo Kim, Cornelia Lemke, Junkang Rong, Haibao Tang, Xiyin Wang, Michele Braidotti, Amy H. Chen, Kristen Chicola, Kristi Collura, Ethan Epps, Wolfgang Golser, Corrinne Grover, Jennifer Ingles, Santhosh KarunakaranDave Kudrna, Jaime Olive, Nabila Tabassum, Eareana Um, Marina Wissotski, Yeisoo Yu, Andrea Zuccolo, Mehboob ur Rahman, Daniel G. Peterson, Rod A. Wing, Jonathan F. Wendel, Andrew H. Paterson

Research output: Contribution to journal › Article › peer-review

48 Scopus citations

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. © 2010 Lin et al; licensee BioMed Central Ltd.

Original language	English (US)
Journal	BMC Genomics
Volume	11
Issue number	1
DOIs	https://doi.org/10.1186/1471-2164-11-395
State	Published - Jun 22 2010
Externally published	Yes

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10.1186/1471-2164-11-395

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Lin, L., Pierce, G. J., Bowers, J. E., Estill, J. C., Compton, R. O., Rainville, L. K., Kim, C., Lemke, C., Rong, J., Tang, H., Wang, X., Braidotti, M., Chen, A. H., Chicola, K., Collura, K., Epps, E., Golser, W., Grover, C., Ingles, J., ... Paterson, A. H. (2010). A draft physical map of a D-genome cotton species (Gossypium raimondii). BMC Genomics, 11(1). https://doi.org/10.1186/1471-2164-11-395

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title = "A draft physical map of a D-genome cotton species (Gossypium raimondii)",

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. {\textcopyright} 2010 Lin et al; licensee BioMed Central Ltd.",

author = "Lifeng Lin and Pierce, {Gary J.} and Bowers, {John E.} and Estill, {James C.} and Compton, {Rosana O.} and Rainville, {Lisa K.} and Changsoo Kim and Cornelia Lemke and Junkang Rong and Haibao Tang and Xiyin Wang and Michele Braidotti and Chen, {Amy H.} and Kristen Chicola and Kristi Collura and Ethan Epps and Wolfgang Golser and Corrinne Grover and Jennifer Ingles and Santhosh Karunakaran and Dave Kudrna and Jaime Olive and Nabila Tabassum and Eareana Um and Marina Wissotski and Yeisoo Yu and Andrea Zuccolo and {ur Rahman}, Mehboob and Peterson, {Daniel G.} and Wing, {Rod A.} and Wendel, {Jonathan F.} and Paterson, {Andrew H.}",

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Lin, L, Pierce, GJ, Bowers, JE, Estill, JC, Compton, RO, Rainville, LK, Kim, C, Lemke, C, Rong, J, Tang, H, Wang, X, Braidotti, M, Chen, AH, Chicola, K, Collura, K, Epps, E, Golser, W, Grover, C, Ingles, J, Karunakaran, S, Kudrna, D, Olive, J, Tabassum, N, Um, E, Wissotski, M, Yu, Y, Zuccolo, A, ur Rahman, M, Peterson, DG, Wing, RA, Wendel, JF & Paterson, AH 2010, 'A draft physical map of a D-genome cotton species (Gossypium raimondii)', BMC Genomics, vol. 11, no. 1. https://doi.org/10.1186/1471-2164-11-395

TY - JOUR

T1 - A draft physical map of a D-genome cotton species (Gossypium raimondii)

AU - Lin, Lifeng

AU - Pierce, Gary J.

AU - Bowers, John E.

AU - Estill, James C.

AU - Compton, Rosana O.

AU - Rainville, Lisa K.

AU - Kim, Changsoo

AU - Lemke, Cornelia

AU - Rong, Junkang

AU - Tang, Haibao

AU - Wang, Xiyin

AU - Braidotti, Michele

AU - Chen, Amy H.

AU - Chicola, Kristen

AU - Collura, Kristi

AU - Epps, Ethan

AU - Golser, Wolfgang

AU - Grover, Corrinne

AU - Ingles, Jennifer

AU - Karunakaran, Santhosh

AU - Kudrna, Dave

AU - Olive, Jaime

AU - Tabassum, Nabila

AU - Um, Eareana

AU - Wissotski, Marina

AU - Yu, Yeisoo

AU - Zuccolo, Andrea

AU - ur Rahman, Mehboob

AU - Peterson, Daniel G.

AU - Wing, Rod A.

AU - Wendel, Jonathan F.

AU - Paterson, Andrew H.

N1 - Generated from Scopus record by KAUST IRTS on 2019-11-20

PY - 2010/6/22

Y1 - 2010/6/22

N2 - 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. © 2010 Lin et al; licensee BioMed Central Ltd.

AB - 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. © 2010 Lin et al; licensee BioMed Central Ltd.

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DO - 10.1186/1471-2164-11-395

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VL - 11

JO - BMC Genomics

JF - BMC Genomics

IS - 1

ER -

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

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