Construction, Alignment and Analysis of Twelve Framework Physical Maps that Represent the Ten Genome Types of the Genus Oryza

HyeRan Kim; Bonnie Hurwitz; Yeisoo Yu; Kristi Collura; Navdeep Gill; Phillip SanMiguel; James C. Mullikin; Christopher Maher; William Nelson; Marina Wissotski; Michele Braidotti; David Kudrna; José Luis Goicoechea; Lincoln Stein; Doreen Ware; Scott A. Jackson; Carol Soderlund; Rod A. Wing

doi:10.1186/gb-2008-9-2-r45

Construction, Alignment and Analysis of Twelve Framework Physical Maps that Represent the Ten Genome Types of the Genus Oryza

HyeRan Kim
, Bonnie Hurwitz
, Yeisoo Yu
, Kristi Collura
, Navdeep Gill
, Phillip SanMiguel
, James C. Mullikin
, Christopher Maher
, William Nelson
, Marina Wissotski
, Michele Braidotti
, David Kudrna
, José Luis Goicoechea
, Lincoln Stein
, Doreen Ware
, Scott A. Jackson
, Carol Soderlund
, Rod A. Wing

Department of Biological Sciences

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

78 Scopus citations

Abstract

We describe the establishment and analysis of a genus-wide comparative framework composed of 12 bacterial artificial chromosome fingerprint and end-sequenced physical maps representing the 10 genome types of Oryza aligned to the O. sativa ssp. japonica reference genome sequence. Over 932 Mb of end sequence was analyzed for repeats, simple sequence repeats, miRNA and single nucleotide variations, providing the most extensive analysis of Oryza sequence to date.

Original language	American English
Article number	R45
Journal	Genome Biology
Volume	9
DOIs	https://doi.org/10.1186/gb-2008-9-2-r45
State	Published - Feb 28 2008

Keywords

Chromosomes, Artificial, Bacterial/genetics
Genetic Variation
Genome, Plant
MicroRNAs/genetics
Oryza/genetics
Physical Chromosome Mapping
Repetitive Sequences, Nucleic Acid/genetics
Sequence Alignment
Sequence Analysis, DNA/methods

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10.1186/gb-2008-9-2-r45License: CC BY

Construction Alignment and Analysis of Twelve Framework Physical

http://nsuworks.nova.edu/cnso_bio_facarticles/1234

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Kim, H., Hurwitz, B., Yu, Y., Collura, K., Gill, N., SanMiguel, P., Mullikin, J. C., Maher, C., Nelson, W., Wissotski, M., Braidotti, M., Kudrna, D., Goicoechea, J. L., Stein, L., Ware, D., Jackson, S. A., Soderlund, C., & Wing, R. A. (2008). Construction, Alignment and Analysis of Twelve Framework Physical Maps that Represent the Ten Genome Types of the Genus Oryza. Genome Biology, 9, Article R45. https://doi.org/10.1186/gb-2008-9-2-r45

Kim, H, Hurwitz, B, Yu, Y, Collura, K, Gill, N, SanMiguel, P, Mullikin, JC, Maher, C, Nelson, W, Wissotski, M, Braidotti, M, Kudrna, D, Goicoechea, JL, Stein, L, Ware, D, Jackson, SA, Soderlund, C & Wing, RA 2008, 'Construction, Alignment and Analysis of Twelve Framework Physical Maps that Represent the Ten Genome Types of the Genus Oryza', Genome Biology, vol. 9, R45. https://doi.org/10.1186/gb-2008-9-2-r45

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abstract = "We describe the establishment and analysis of a genus-wide comparative framework composed of 12 bacterial artificial chromosome fingerprint and end-sequenced physical maps representing the 10 genome types of Oryza aligned to the O. sativa ssp. japonica reference genome sequence. Over 932 Mb of end sequence was analyzed for repeats, simple sequence repeats, miRNA and single nucleotide variations, providing the most extensive analysis of Oryza sequence to date.",

keywords = "Chromosomes, Artificial, Bacterial/genetics, Genetic Variation, Genome, Plant, MicroRNAs/genetics, Oryza/genetics, Physical Chromosome Mapping, Repetitive Sequences, Nucleic Acid/genetics, Sequence Alignment, Sequence Analysis, DNA/methods",

author = "HyeRan Kim and Bonnie Hurwitz and Yeisoo Yu and Kristi Collura and Navdeep Gill and Phillip SanMiguel and Mullikin, \{James C.\} and Christopher Maher and William Nelson and Marina Wissotski and Michele Braidotti and David Kudrna and Goicoechea, \{Jos{\'e} Luis\} and Lincoln Stein and Doreen Ware and Jackson, \{Scott A.\} and Carol Soderlund and Wing, \{Rod A.\}",

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doi = "10.1186/gb-2008-9-2-r45",

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AU - Kim, HyeRan

AU - Hurwitz, Bonnie

AU - Yu, Yeisoo

AU - Collura, Kristi

AU - Gill, Navdeep

AU - SanMiguel, Phillip

AU - Mullikin, James C.

AU - Maher, Christopher

AU - Nelson, William

AU - Wissotski, Marina

AU - Braidotti, Michele

AU - Kudrna, David

AU - Goicoechea, José Luis

AU - Stein, Lincoln

AU - Ware, Doreen

AU - Jackson, Scott A.

AU - Soderlund, Carol

AU - Wing, Rod A.

PY - 2008/2/28

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N2 - We describe the establishment and analysis of a genus-wide comparative framework composed of 12 bacterial artificial chromosome fingerprint and end-sequenced physical maps representing the 10 genome types of Oryza aligned to the O. sativa ssp. japonica reference genome sequence. Over 932 Mb of end sequence was analyzed for repeats, simple sequence repeats, miRNA and single nucleotide variations, providing the most extensive analysis of Oryza sequence to date.

AB - We describe the establishment and analysis of a genus-wide comparative framework composed of 12 bacterial artificial chromosome fingerprint and end-sequenced physical maps representing the 10 genome types of Oryza aligned to the O. sativa ssp. japonica reference genome sequence. Over 932 Mb of end sequence was analyzed for repeats, simple sequence repeats, miRNA and single nucleotide variations, providing the most extensive analysis of Oryza sequence to date.

KW - Chromosomes, Artificial, Bacterial/genetics

KW - Genetic Variation

KW - Genome, Plant

KW - MicroRNAs/genetics

KW - Oryza/genetics

KW - Physical Chromosome Mapping

KW - Repetitive Sequences, Nucleic Acid/genetics

KW - Sequence Alignment

KW - Sequence Analysis, DNA/methods

U2 - 10.1186/gb-2008-9-2-r45

DO - 10.1186/gb-2008-9-2-r45

M3 - Article

C2 - 18304353

SN - 1474-760X

VL - 9

JO - Genome Biology

JF - Genome Biology

M1 - R45

ER -

Construction, Alignment and Analysis of Twelve Framework Physical Maps that Represent the Ten Genome Types of the Genus Oryza

Abstract

Keywords

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