Rod A. Wing

Methylation-sensitive linking libraries enhance gene-enriched sequencing of complex genomes and map DNA methylation domains (2008)

Nelson, William, Luo, Meizhong, Ma, Jianxin, Estep, Matt, Estill, James, He, Ruifeng, ...

Abstract Background Many plant genomes are resistant to whole-genome assembly due to an abundance of repetitive sequence, leading to the development of gene-rich sequencing techniques. Two such...

Bioinformatics Whole-Genome Validation of High-Information-Content (2008)

William M. Nelson, Arvindk. Bharti, Fusheng Wei, Galina Fuks, Hyeran Kim, Rod A. Wing, ...

Fluorescent-based high-information-content fingerprinting (HICF) techniques have recently been developed for physical mapping. These techniques make use of automated capillary DNA sequencing...

A fruitful outcome to the papaya genome project (2008)

Wei, Fusheng, Wing, Rod A

Abstract The draft genome sequence of a transgenic virus-resistant papaya marks the first genome sequence of a commercially important transgenic crop plant.

The Amborellagenome: an evolutionary reference for plant biology (2008)

Soltis, Douglas E, Albert, Victor A, Leebens-Mack, Jim, Palmer, Jeffrey D, Wing, Rod A, DePamphilis, Claude W, ...

Abstract The nuclear genome sequence of Amborella trichopoda , the sister species to all other extant angiosperms, will be an exceptional resource for plant genomics.

Construction, alignment and analysis of twelve framework physical maps that represent the ten genome types of the genus Oryza (2008)

Kim, HyeRan, Hurwitz, Bonnie, Yu, Yeisoo, Collura, Kristi, Gill, Navdeep, SanMiguel, Phillip, ...

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...

The Subtelomere of Oryza sativa Chromosome 3 Short Arm as a Hot Bed of New Gene Origination in Rice (2008)

Fan, Chuanzhu, Zhang, Yong, Yu, Yeisoo, Rounsley, Steve, Long, Manyuan, Wing, Rod A.

Despite general observations of non-random genomic distribution of new genes, it is unclear whether or not new genes preferentially occur in certain genomic regions driven by related molecular...

A Phylogenetic Analysis of Indel Dynamics in the Cotton Genus (2008)

Grover, Corrinne E., Yu, Yeisoo, Wing, Rod A., Paterson, Andrew H., Wendel, Jonathan F.

Genome size evolution is a dynamic process involving counterbalancing mechanisms whose actions vary across lineages and over time. Whereas the primary mechanism of expansion, transposable element...

Transposable element distribution, abundance and role in genome size variation in the genus Oryza (2007)

Zuccolo, Andrea, Sebastian, Aswathy, Talag, Jayson, Yu, Yeisoo, Kim, HyeRan, Collura, Kristi, ...

Abstract Background The genus Oryza is composed of 10 distinct genome types, 6 diploid and 4 polyploid, and includes the world's most important food crop – rice ( Oryza sativa [AA]). Genome size...

Physical and Genetic Structure of the Maize Genome Reflects Its Complex Evolutionary History (2007)

Fusheng Wei, Ed Coe, William Nelson, Arvind K. Bharti, Fred Engler, Ed Butler, ...

Maize (Zea mays L.) is one of the most important cereal crops and a model for the study of genetics, evolution, and domestication. To better understand maize genome organization and to build a...

Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana (2007)

Itoh, Takeshi, Tanaka, Tsuyoshi, Barrero, Roberto A., Yamasaki, Chisato, Fujii, Yasuyuki, Hilton, Phillip B., ...

We present here the annotation of the complete genome of rice Oryza sativa L. ssp. japonica cultivar Nipponbare. All functional annotations for proteins and non-protein-coding RNA (npRNA) candidates...

A bacterial artificial chromosome library for Biomphalaria glabrata   , intermediate snail host of Schistosoma mansoni   (2007)

Coen M Adema, Mei-Zhong Luo, Ben Hanelt, Lynn A Hertel, Jennifer J Marshall, Si-Ming Zhang, ...

To provide a novel resource for analysis of the genome of Biomphalaria glabrata   , members of the international Biomphalaria glabrata Genome Initiative (biology.unm.edu/biomphalaria-genome.html),...

Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana (2007)

Itoh, Takeshi, Tanaka, Tsuyoshi, Barrero, Roberto A., Yamasaki, Chisato, Fujii, Yasuyuki, Hilton, Phillip B., ...

We present here the annotation of the complete genome of rice Oryza sativa L. ssp. japonica cultivar Nipponbare. All functional annotations for proteins and non-protein-coding RNA (npRNA) candidates...

A bacterial artificial chromosome library for Biomphalaria glabrata, intermediate snail host of Schistosoma mansoni (2006)

Adema,Coen M, Luo,Mei-Zhong, Hanelt,Ben, Hertel,Lynn A, Marshall,Jennifer J, Zhang,Si-Ming, ...

To provide a novel resource for analysis of the genome of Biomphalaria glabrata, members of the international Biomphalaria glabrata Genome Initiative (biology.unm.edu/biomphalaria-genome.html),...

Uneven chromosome contraction and expansion in the maize genome (2006)

Bruggmann, Rémy, Bharti, Arvind K., Gundlach, Heidrun, Lai, Jinsheng, Young, Sarah, Pontaroli, Ana C., ...

Maize (Zea mays or corn), both a major food source and an important cytogenetic model, evolved from a tetraploid that arose about 4.8 million years ago (Mya). As a result, maize has extensive...

Differential lineage-specific amplification of transposable elements is responsible for genome size variation in Gossypium (2006)

Hawkins, Jennifer S., Kim, HyeRan, Nason, John D., Wing, Rod A., Wendel, Jonathan F.

The DNA content of eukaryotic nuclei (C-value) varies ∼200,000-fold, but there is only a ∼20-fold variation in the number of protein-coding genes. Hence, most C-value variation is ascribed to the...

Doubling genome size without polyploidization: Dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice (2006)

Piegu, Benoit, Guyot, Romain, Picault, Nathalie, Roulin, Anne, Saniyal, Abhijit, Kim, Hyeran, ...

Retrotransposons are the main components of eukaryotic genomes, representing up to 80% of some large plant genomes. These mobile elements transpose via a “copy and paste” mechanism, thus...

Differential lineage-specific amplification of transposable elements is responsible for genome size variation in Gossypium (2006)

Hawkins, Jennifer S., Kim, HyeRan, Nason, John D., Wing, Rod A., Wendel, Jonathan F.

The DNA content of eukaryotic nuclei (C-value) varies ∼200,000-fold, but there is only a ∼20-fold variation in the number of protein-coding genes. Hence, most C-value variation is ascribed to the...

Doubling genome size without polyploidization: Dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice (2006)

Piegu, Benoit, Guyot, Romain, Picault, Nathalie, Roulin, Anne, Saniyal, Abhijit, Kim, Hyeran, ...

Retrotransposons are the main components of eukaryotic genomes, representing up to 80% of some large plant genomes. These mobile elements transpose via a “copy and paste” mechanism, thus...

Uneven chromosome contraction and expansion in the maize genome (2006)

Bruggmann, Rémy, Bharti, Arvind K., Gundlach, Heidrun, Lai, Jinsheng, Young, Sarah, Pontaroli, Ana C., ...

Maize (Zea mays or corn), both a major food source and an important cytogenetic model, evolved from a tetraploid that arose about 4.8 million years ago (Mya). As a result, maize has extensive...

The Oryza bacterial artificial chromosome library resource: Construction and analysis of 12 deep-coverage large-insert BAC libraries that represent the 10 genome types of the genus Oryza (2006)

Ammiraju, Jetty S.S., Luo, Meizhong, Goicoechea, José L., Wang, Wenming, Kudrna, Dave, Mueller, Christopher, ...

Rice (Oryza sativa L.) is the most important food crop in the world and a model system for plant biology. With the completion of a finished genome sequence we must now functionally characterize the...

The Oryza bacterial artificial chromosome library resource: Construction and analysis of 12 deep-coverage large-insert BAC libraries that represent the 10 genome types of the genus Oryza (2005)

Ammiraju, Jetty S.S., Luo, Meizhong, Goicoechea, José L., Wang, Wenming, Kudrna, Dave, Mueller, Christopher, ...

Rice (Oryza sativa L.) is the most important food crop in the world and a model system for plant biology. With the completion of a finished genome sequence we must now functionally characterize the...

Incongruent Patterns of Local and Global Genome Size Evolution in Cotton (2004)

Grover, Corrinne E., Kim, HyeRan, Wing, Rod A., Paterson, Andrew H., Wendel, Jonathan F.

Genome sizes in plants vary over several orders of magnitude, reflecting a combination of differentially acting local and global forces such as biases in indel accumulation and transposable element...

Structural features of the rice chromosome 4 centromere (2004)

Zhang, Yu, Huang, Yuchen, Zhang, Lei, Li, Ying, Lu, Tingting, Lu, Yiqi, ...

A complete sequence of a chromosome centromere is necessary for fully understanding centromere function. We reported the sequence structures of the first complete rice chromosome centromere through...

Incongruent Patterns of Local and Global Genome Size Evolution in Cotton (2004)

Grover, Corrinne E., Kim, HyeRan, Wing, Rod A., Paterson, Andrew H., Wendel, Jonathan F.

Genome sizes in plants vary over several orders of magnitude, reflecting a combination of differentially acting local and global forces such as biases in indel accumulation and transposable element...

Rate Variation Among Nuclear Genes and the Age of Polyploidy in Gossypium (2003)

Senchina, David S., Alvarez, Ines, Cronn, Richard C., Liu, Bao, Rong, Junkang, Noyes, Richard D., ...

Molecular evolutionary rate variation in Gossypium (cotton) was characterized using sequence data for 48 nuclear genes from both genomes of allotetraploid cotton, models of its diploid progenitors,...

Rate Variation among Nuclear Genes and the Age of Polyploidy in Gossypium (2003)

Senchina, David S., Alvarez, Ines, Cronn, Richard C., Liu, Bao, Rong, Junkang, Noyes, Richard D., ...

Molecular evolutionary rate variation in Gossypium (cotton) was characterized using sequence data for 48 nuclear genes from both genomes of allotetraploid cotton, models of its diploid progenitors,...

Rate Variation among Nuclear Genes and the Age of Polyploidy in Gossypium (2003)

Senchina, David S., Alvarez, Ines, Cronn, Richard C., Liu, Bao, Rong, Junkang, Noyes, Richard D., ...

Molecular evolutionary rate variation in Gossypium (cotton) was characterized using sequence data for 48 nuclear genes from both genomes of allotetraploid cotton, models of its diploid progenitors,...

A BAC library for grape and strategies for the development of a physical framework for the grape genome (2002)

Tomkins, Jeffrey P, Peterson, Daniel G, Yang, Tae-Jin, Main, Dorrie, Ablett, Effie M, Henry, Robert J, ...

We have constructed a grape BAC library using the cultivar Syrah. The library contains 55,296 clones stored in 144 384-well microtiter plates. A random sampling of 381 BACs indicated an average...

A BAC library for grape and strategies for the development of a physical framework for the grape genome (2002)

Tomkins, Jeffrey P, Peterson, Daniel G, Yang, Tae-Jin, Main, Dorrie, Ablett, Effie M, Henry, Robert J, ...

We have constructed a grape BAC library using the cultivar Syrah. The library contains 55,296 clones stored in 144 384-well microtiter plates. A random sampling of 381 BACs indicated an average...

MagnaportheDB: a federated solution for integrating physical and genetic map data with BAC end derived sequences for the rice blast fungus Magnaporthe grisea (2002)

Martin, Stanton L., Blackmon, Barbara P., Rajagopalan, Ravi, Houfek, Thomas D., Sceeles, Robert G., Denn, Sheila O., ...

We have created a federated database for genome studies of Magnaporthe grisea, the causal agent of rice blast disease, by integrating end sequence data from BAC clones, genetic marker data and BAC...

A BAC library for grape and strategies for the development of a physical framework for the grape genome (2002)

Tomkins, Jeffrey P, Peterson, Daniel G, Yang, Tae-Jin, Main, Dorrie, Ablett, Effie M, Henry, Robert J, ...

We have constructed a grape BAC library using the cultivar Syrah. The library contains 55,296 clones stored in 144 384-well microtiter plates. A random sampling of 381 BACs indicated an average...

Grape (vitis vinifera L.) BAC library construction, preliminary STC analysis, and Identification of Clones Associated with Flavonoid and Stilbene biosynthesis (2001)

Tomkins, Jeffrey P, Peterson, Daniel G, Yang, Tae-Jin, Ablett, Effie F, Henry, Robert J, Lee, L Slade, ...

We have constructed a grape BAC library using the cultivar Syrah. The library contains 55,296 clones stored in 144 384-well microtiter plates. A random sampling of 381 BACs indicated an average...

Development of genomic resources for grape: BAC library construction preliminary STC analysis and identification of clones associated with flavonoid and stilbene biosynthesis (2001)

Tomkins, Jeffrey P, Peterson, Daniel G, Yang, Tae-Jin, Main, Dorrie, Lee, L Slade, Henry, Robert J, ...

We have constructed a grape BAC library using the cultivar Syrah. The library contains 55,296 clones stored in 144 384-well microtiter plates. A random sampling of 381 BACs indicated an average...

Grape (vitis vinifera L.) BAC library construction, preliminary STC analysis, and Identification of Clones Associated with Flavonoid and Stilbene biosynthesis (2001)

Tomkins, Jeffrey P, Peterson, Daniel G, Yang, Tae-Jin, Ablett, Effie F, Henry, Robert J, Lee, L Slade, ...

We have constructed a grape BAC library using the cultivar Syrah. The library contains 55,296 clones stored in 144 384-well microtiter plates. A random sampling of 381 BACs indicated an average...

Toward a Cytological Characterization of the Rice Genome (2001)

Cheng, Zhukuan, Buell, C. Robin, Wing, Rod A., Gu, Minghong, Jiang, Jiming

A Marker-Dense Physical Map of the Bradyrhizobium japonicum Genome (2001)

Tomkins, Jeffrey P., Wood, Todd C., Stacey, Minviluz G., Loh, John T., Judd, Adam, Goicoechea, Jose L., ...

Development of genomic resources for grape: BAC library construction preliminary STC analysis and identification of clones associated with flavonoid and stilbene biosynthesis (2001)

Tomkins, Jeffrey P, Peterson, Daniel G, Yang, Tae-Jin, Main, Dorrie, Lee, L Slade, Henry, Robert J, ...

We have constructed a grape BAC library using the cultivar Syrah. The library contains 55,296 clones stored in 144 384-well microtiter plates. A random sampling of 381 BACs indicated an average...

Development of genomic resources for grape: BAC library construction preliminary STC analysis and identification of clones associated with flavonoid and stilbene biosynthesis (2001)

Tomkins, Jeffrey P, Peterson, Daniel G, Yang, Tae-Jin, Main, Dorrie, Lee, L Slade, Henry, Robert J, ...

We have constructed a grape BAC library using the cultivar Syrah. The library contains 55,296 clones stored in 144 384-well microtiter plates. A random sampling of 381 BACs indicated an average...

Grape (vitis vinifera L.) BAC library construction, preliminary STC analysis, and Identification of Clones Associated with Flavonoid and Stilbene biosynthesis (2001)

Tomkins, Jeffrey P, Peterson, Daniel G, Yang, Tae-Jin, Ablett, Effie F, Henry, Robert J, Lee, L Slade, ...

We have constructed a grape BAC library using the cultivar Syrah. The library contains 55,296 clones stored in 144 384-well microtiter plates. A random sampling of 381 BACs indicated an average...

A new approach for the identification and cloning of genes: the pBACwich system using Cre/lox site-specific recombination (2000)

Choi, Sangdun, Begum, Dilara, Koshinsky, Heather, Ow, David W., Wing, Rod A.

With current plant transformation methods (Agrobacterium, biolistics and protoplast fusion), insertion of DNA into the genome occurs randomly and in many instances at multiple sites. Associated...

Locus-specific contig assembly in highly-duplicated genomes, using the BAC-RF method (2000)

Lin, Yann-rong, Draye, Xavier, Qian, Xiaoyin, Ren, Shuzin, Zhu, Ling-hua, Tomkins, Jeff, ...

Polyploidy, the presence of multiple sets of chromosomes that are similar but not identical, complicates both chromosome walking and assembly of sequence-ready contigs for many plant taxa including a...

Rice Transposable Elements: A Survey of 73,000 Sequence-Tagged-Connectors (2000)

Mao, Long, Wood, Todd C., Yu, Yeisoo, Budiman, Muhammad A., Tomkins, Jeff, Woo, Sung-sick, ...

A Deep-Coverage Tomato BAC Library and Prospects Toward Development of an STC Framework for Genome Sequencing (2000)

Budiman, Muhammad A., Mao, Long, Wood, Todd C., Wing, Rod A.

Construction and characterization of bacterial artificial chromosome library of Sorghum bicolor (1994)

Woo, Sung-Sick, Jiang, Jiming, Gill, Bikram S., Paterson, Andrew H., Wing, Rod A.

The construction of representative large insert DNA libraries is critical for the analysis of complex genomes. The predominant vector system for such work is the yeast artificial chromosome (YAC)...

PCR amplification from single seeds, facilitating DNA marker-assisted breeding (1993)

Wang, Guo-Liang, Wing, Rod A., Paterson, Andrew H.

Isolation of molecular markers from specific chromosomal intervals using DNA pools from existing mapping populations (1991)

Giovannoni, James J., Wing, Rod A., Ganal, Martin W., Tanksley, Steven D.

We present a general method for isolating molecular markers specific to any region of a chromosome using existing mapping populations. Two pools of DNA from individuals homozygous for opposing...

Toward Integration of Comparative Genetic, Physical, Diversity, and Cytomolecular Maps for Grasses and Grains, Using the Sorghum Genome as a Foundation1

Draye, Xavier, Lin, Yann-Rong, Qian, Xiao-yin, Bowers, John E., Burow, Gloria B., Morrell, Peter L., ...

The small genome of sorghum (Sorghum bicolor L. Moench.) provides an important template for study of closely related large-genome crops such as maize (Zea mays) and sugarcane (Saccharum spp.), and is...

MagnaportheDB: a federated solution for integrating physical and genetic map data with BAC end derived sequences for the rice blast fungus Magnaporthe grisea

Martin, Stanton L., Blackmon, Barbara P., Rajagopalan, Ravi, Houfek, Thomas D., Sceeles, Robert G., Denn, Sheila O., ...

We have created a federated database for genome studies of Magnaporthe grisea, the causal agent of rice blast disease, by integrating end sequence data from BAC clones, genetic marker data and BAC...

A new approach for the identification and cloning of genes: the pBACwich system using Cre/lox site-specific recombination

Choi, Sangdun, Begum, Dilara, Koshinsky, Heather, Ow, David W., Wing, Rod A.

With current plant transformation methods (Agrobacterium, biolistics and protoplast fusion), insertion of DNA into the genome occurs randomly and in many instances at multiple sites. Associated...

Locus-specific contig assembly in highly-duplicated genomes, using the BAC-RF method

Lin, Yann-rong, Draye, Xavier, Qian, Xiaoyin, Ren, Shuzin, Zhu, Ling-hua, Tomkins, Jeff, ...

Polyploidy, the presence of multiple sets of chromosomes that are similar but not identical, complicates both chromosome walking and assembly of sequence-ready contigs for many plant taxa including a...

Sequence and Analysis of the Tomato JOINTLESS Locus1

Mao, Long, Begum, Dilara, Goff, Stephen A., Wing, Rod A.

A 119-kb bacterial artificial chromosome from the JOINTLESS locus on the tomato (Lycopersicon esculentum) chromosome 11 contained 15 putative genes. Repetitive sequences in this region include one...

An Integrated Physical and Genetic Map of the Rice Genome

Chen, Mingsheng, Presting, Gernot, Barbazuk, W. Brad, Goicoechea, Jose Luis, Blackmon, Barbara, Fang, Guangchen, ...

Rice was chosen as a model organism for genome sequencing because of its economic importance, small genome size, and syntenic relationship with other cereal species. We have constructed a bacterial...

Genome Dynamics and Evolution of the Mla (Powdery Mildew) Resistance Locus in BarleyW⃞

Wei, Fusheng, Wing, Rod A., Wise, Roger P.

Genes that confer defense against pathogens often are clustered in the genome and evolve via diverse mechanisms. To evaluate the organization and content of a major defense gene complex in cereals,...

The chloroplast genome exists in multimeric forms

Deng, Xing-Wang, Wing, Rod A., Gruissem, Wilhelm

Chloroplast DNA conformation was analyzed by pulse-field gel electrophoresis. We found that spinach leaf chloroplast DNA molecules exist in at least four distinct forms with the apparent molecular...

A Deep-Coverage Tomato BAC Library and Prospects Toward Development of an STC Framework for Genome Sequencing

Budiman, Muhammad A., Mao, Long, Wood, Todd C., Wing, Rod A.

Recently a new strategy using BAC end sequences as sequence-tagged connectors (STCs) was proposed for whole-genome sequencing projects. In this study, we present the construction and detailed...

Rice Transposable Elements: A Survey of 73,000 Sequence-Tagged-Connectors

Mao, Long, Wood, Todd C., Yu, Yeisoo, Budiman, Muhammad A., Tomkins, Jeff, Woo, Sung-sick, ...

As part of an international effort to sequence the rice genome, the Clemson University Genomics Institute is developing a sequence-tagged-connector (STC) framework. This framework includes the...

A Marker-Dense Physical Map of the Bradyrhizobium japonicum Genome

Tomkins, Jeffrey P., Wood, Todd C., Stacey, Minviluz G., Loh, John T., Judd, Adam, Goicoechea, Jose L., ...

Bacterial artificial chromosome (BAC) clones are effective mapping and sequencing reagents for use with a wide variety of small and large genomes. This report describes the development of a physical...

Toward a Cytological Characterization of the Rice Genome

Cheng, Zhukuan, Buell, C. Robin, Wing, Rod A., Gu, Minghong, Jiang, Jiming

Rice (Oryza sativa L.) will be the first major crop, as well as the first monocot plant species, to be completely sequenced. Integration of DNA sequence-based maps with cytological maps will be...

A New Resource for Cereal Genomics: 22K Barley GeneChip Comes of Age1

Close, Timothy J., Wanamaker, Steve I., Caldo, Rico A., Turner, Stacy M., Ashlock, Daniel A., Dickerson, Julie A., ...

In recent years, access to complete genomic sequences, coupled with rapidly accumulating data related to RNA and protein expression patterns, has made it possible to determine comprehensively how...

Structural features of the rice chromosome 4 centromere

Zhang, Yu, Huang, Yuchen, Zhang, Lei, Li, Ying, Lu, Tingting, Lu, Yiqi, ...

A complete sequence of a chromosome centromere is necessary for fully understanding centromere function. We reported the sequence structures of the first complete rice chromosome centromere through...

Incongruent Patterns of Local and Global Genome Size Evolution in Cotton

Grover, Corrinne E., Kim, HyeRan, Wing, Rod A., Paterson, Andrew H., Wendel, Jonathan F.

Genome sizes in plants vary over several orders of magnitude, reflecting a combination of differentially acting local and global forces such as biases in indel accumulation and transposable element...

Sequence composition and genome organization of maize

Messing, Joachim, Bharti, Arvind K., Karlowski, Wojciech M., Gundlach, Heidrun, Kim, Hye Ran, Yu, Yeisoo, ...

Zea mays L. ssp. mays, or corn, one of the most important crops and a model for plant genetics, has a genome ≈80% the size of the human genome. To gain global insight into the organization of its...

Large-Scale Identification of Expressed Sequence Tags Involved in Rice and Rice Blast Fungus Interaction1

Jantasuriyarat, Chatchawan, Gowda, Malali, Haller, Karl, Hatfield, Jamie, Lu, Guodong, Stahlberg, Eric, ...

To better understand the molecular basis of the defense response against the rice blast fungus (Magnaporthe grisea), a large-scale expressed sequence tag (EST) sequencing approach was used to...

Construction of a bacterial artificial chromosome library from the spikemoss Selaginella moellendorffii: a new resource for plant comparative genomics

Wang, Wenming, Tanurdzic, Milos, Luo, Meizhong, Sisneros, Nicholas, Kim, Hye Ran, Weng, Jing-Ke, ...

Comparative physical mapping links conservation of microsynteny to chromosome structure and recombination in grasses

Bowers, John E., Arias, Miguel A., Asher, Rochelle, Avise, Jennifer A., Ball, Robert T., Brewer, Gene A., ...

Nearly finished sequences for model organisms provide a foundation from which to explore genomic diversity among other taxonomic groups. We explore genome-wide microsynteny patterns between the rice...

Whole-Genome Validation of High-Information-Content Fingerprinting1

Nelson, William M., Bharti, Arvind K., Butler, Ed, Wei, Fusheng, Fuks, Galina, Kim, HyeRan, ...

Fluorescent-based high-information-content fingerprinting (HICF) techniques have recently been developed for physical mapping. These techniques make use of automated capillary DNA sequencing...

Structure and Architecture of the Maize Genome1[W]

Haberer, Georg, Young, Sarah, Bharti, Arvind K., Gundlach, Heidrun, Raymond, Christina, Fuks, Galina, ...

Maize (Zea mays or corn) plays many varied and important roles in society. It is not only an important experimental model plant, but also a major livestock feed crop and a significant source of...

The Oryza bacterial artificial chromosome library resource: Construction and analysis of 12 deep-coverage large-insert BAC libraries that represent the 10 genome types of the genus Oryza

Ammiraju, Jetty S.S., Luo, Meizhong, Goicoechea, José L., Wang, Wenming, Kudrna, Dave, Mueller, Christopher, ...

Rice (Oryza sativa L.) is the most important food crop in the world and a model system for plant biology. With the completion of a finished genome sequence we must now functionally characterize the...

Dasheng: a recently amplified nonautonomous long terminal repeat element that is a major component of pericentromeric regions in rice.

Jiang, Ning, Bao, Zhirong, Temnykh, Svetlana, Cheng, Zhukuan, Jiang, Jiming, Wing, Rod A, ...

A new and unusual family of LTR elements, Dasheng, has been discovered in the genome of Oryza sativa following database searches of approximately 100 Mb of rice genomic sequence and 78 Mb of BAC-end...

A 3347-locus genetic recombination map of sequence-tagged sites reveals features of genome organization, transmission and evolution of cotton (Gossypium).

Rong, Junkang, Abbey, Colette, Bowers, John E, Brubaker, Curt L, Chang, Charlene, Chee, Peng W, ...

We report genetic maps for diploid (D) and tetraploid (AtDt) Gossypium genomes composed of sequence-tagged sites (STS) that foster structural, functional, and evolutionary genomic studies. The maps...

Comparative population genetics of the panicoid grasses: sequence polymorphism, linkage disequilibrium and selection in a diverse sample of sorghum bicolor.

Hamblin, Martha T, Mitchell, Sharon E, White, Gemma M, Gallego, Javier, Kukatla, Rakesh, Wing, Rod A, ...

Levels of genetic variation and linkage disequilibrium (LD) are critical factors in association mapping methods as well as in identification of loci that have been targets of selection. Maize, an...

Construction of a nurse shark (Ginglymostoma cirratum) bacterial artificial chromosome (BAC) library and a preliminary genome survey

Luo, Meizhong, Kim, HyeRan, Kudrna, Dave, Sisneros, Nicholas B, Lee, So-Jeong, Mueller, Christopher, ...

Integration of hybridization-based markers (overgos) into physical maps for comparative and evolutionary explorations in the genus Oryza and in Sorghum

Hass-Jacobus, Barbara L, Futrell-Griggs, Montona, Abernathy, Brian, Westerman, Rick, Goicoechea, Jose-Luis, Stein, Joshua, ...

Uneven chromosome contraction and expansion in the maize genome

Bruggmann, Rémy, Bharti, Arvind K., Gundlach, Heidrun, Lai, Jinsheng, Young, Sarah, Pontaroli, Ana C., ...

Maize (Zea mays or corn), both a major food source and an important cytogenetic model, evolved from a tetraploid that arose about 4.8 million years ago (Mya). As a result, maize has extensive...

Differential lineage-specific amplification of transposable elements is responsible for genome size variation in Gossypium

Hawkins, Jennifer S., Kim, HyeRan, Nason, John D., Wing, Rod A., Wendel, Jonathan F.

The DNA content of eukaryotic nuclei (C-value) varies ∼200,000-fold, but there is only a ∼20-fold variation in the number of protein-coding genes. Hence, most C-value variation is ascribed to the...

Doubling genome size without polyploidization: Dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice

Piegu, Benoit, Guyot, Romain, Picault, Nathalie, Roulin, Anne, Saniyal, Abhijit, Kim, Hyeran, ...

Retrotransposons are the main components of eukaryotic genomes, representing up to 80% of some large plant genomes. These mobile elements transpose via a “copy and paste” mechanism, thus...

Physical and Genetic Structure of the Maize Genome Reflects Its Complex Evolutionary History

Wei, Fusheng, Coe, Ed, Nelson, William, Bharti, Arvind K, Engler, Fred, Butler, Ed, ...

Maize (Zea mays L.) is one of the most important cereal crops and a model for the study of genetics, evolution, and domestication. To better understand maize genome organization and to build a...

Comparative Physical Mapping Between Oryza sativa (AA Genome Type) and O. punctata (BB Genome Type)

Kim, HyeRan, Miguel, Phillip San, Nelson, William, Collura, Kristi, Wissotski, Marina, Walling, Jason G., ...

A comparative physical map of the AA genome (Oryza sativa) and the BB genome (O. punctata) was constructed by aligning a physical map of O. punctata, deduced from 63,942 BAC end sequences (BESs) and...

Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana

Itoh, Takeshi, Tanaka, Tsuyoshi, Barrero, Roberto A., Yamasaki, Chisato, Fujii, Yasuyuki, Hilton, Phillip B., ...

We present here the annotation of the complete genome of rice Oryza sativa L. ssp. japonica cultivar Nipponbare. All functional annotations for proteins and non-protein-coding RNA (npRNA) candidates...

Genomic and Genetic Characterization of Rice Cen3 Reveals Extensive Transcription and Evolutionary Implications of a Complex Centromere[W][OA]

Yan, Huihuang, Ito, Hidetaka, Nobuta, Kan, Ouyang, Shu, Jin, Weiwei, Tian, Shulan, ...

The centromere is the chromosomal site for assembly of the kinetochore where spindle fibers attach during cell division. In most multicellular eukaryotes, centromeres are composed of long tracts of...

Transposable element distribution, abundance and role in genome size variation in the genus Oryza

Zuccolo, Andrea, Sebastian, Aswathy, Talag, Jayson, Yu, Yeisoo, Kim, HyeRan, Collura, Kristi, ...

Evolutionary History and Positional Shift of a Rice Centromere

Ma, Jianxin, Wing, Rod A., Bennetzen, Jeffrey L., Jackson, Scott A.

Rice centromere 8 was previously proposed to be an “immature” centromere that recently arose from a genic region. Our comparative genomics analysis indicates that Cen8 was formed at its current...

Construction, alignment and analysis of twelve framework physical maps that represent the ten genome types of the genus Oryza

Kim, HyeRan, Hurwitz, Bonnie, Yu, Yeisoo, Collura, Kristi, Gill, Navdeep, SanMiguel, Phillip, ...

Bacterial artificial chromosome (BAC) fingerprint and end-sequenced physical maps representing the ten genome types of Oryza are presented

The Amborella genome: an evolutionary reference for plant biology

Soltis, Douglas E, Albert, Victor A, Leebens-Mack, Jim, Palmer, Jeffrey D, Wing, Rod A, DePamphilis, Claude W, ...

The nuclear genome sequence of Amborella trichopoda, the sister species to all other extant angiosperms, will be an exceptional resource for plant genomics.

A fruitful outcome to the papaya genome project

Wei, Fusheng, Wing, Rod A

Papaya provides the first draft genome sequence of a transgenic fruit.

Methylation-sensitive linking libraries enhance gene-enriched sequencing of complex genomes and map DNA methylation domains

Nelson, William, Luo, Meizhong, Ma, Jianxin, Estep, Matt, Estill, James, He, Ruifeng, ...

Dynamic Evolution of Oryza Genomes Is Revealed by Comparative Genomic Analysis of a Genus-Wide Vertical Data Set[W][OA]

Ammiraju, Jetty S.S., Lu, Fei, Sanyal, Abhijit, Yu, Yeisoo, Song, Xiang, Jiang, Ning, ...

Oryza (23 species; 10 genome types) contains the world's most important food crop — rice. Although the rice genome serves as an essential tool for biological research, little is known about the...

Comparative sequence analysis of MONOCULM1-orthologous regions in 14 Oryza genomes

Lu, Fei, Ammiraju, Jetty S. S., Sanyal, Abhijit, Zhang, Shengli, Song, Rentao, Chen, Jinfeng, ...

Comparative genomics is a powerful tool to decipher gene and genome evolution. Placing multiple genome comparisons in a phylogenetic context improves the sensitivity of evolutionary inferences. In...