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...
Xu, Jian-Hong, Messing, Joachim
Comparative analyses of the sequence of entire genomes have shown that gene duplications, chromosomal segmental duplications, or even whole genome duplications (WGD) have played prominent roles in...
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...
Sequence-indexed mutations in maize using the UniformMu transposon-tagging population (2007)
Settles, A Mark, Holding, David R, Tan, Bao, Latshaw, Susan P, Liu, Juan, Suzuki, Masaharu, ...
Abstract Background Gene knockouts are a critical resource for functional genomics. In Arabidopsis, comprehensive knockout collections were generated by amplifying and sequencing genomic DNA flanking...
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...
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...
Maize haplotype with a helitron-amplified cytidine deaminase gene copy (2006)
Xu, Jian-Hong, Messing, Joachim
Abstract Background Genetic maps are based on recombination of orthologous gene sequences between different strains of the same species. Therefore, it was unexpected to find extensive...
Retrotranspositions in orthologous regions of closely related grass species (2006)
Du, Chunguang, Swigoňová, Zuzana, Messing, Joachim
Abstract Background Retrotransposons are commonly occurring eukaryotic transposable elements (TEs). Among these, long terminal repeat (LTR) retrotransposons are the most abundant TEs and can comprise...
On the Tetraploid Origin of the Maize Genome (2006)
Zuzana Swigonova, Jinsheng Lai, Jianxin Ma, Wusirika Ramakrishna, Victor Llaca, Jeffrey L. Bennetzen, ...
Data from cytological and genetic mapping studies suggest that maize arose as a tetraploid. Two previous studies investigating the most likely mode of maize origin arrived at different conclusions....
Wusirika Ramakrishna, Jianxin Ma, Phillip SanMiguel, John Emberton, Jorge Dubcovsky, Bryan A Shiloff, ...
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...
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...
On the Tetraploid Origin of the Maize Genome (2004)
Zuzana Swigonova, Jinsheng Lai, Jianxin Ma, Wusirika Ramakrishna, Victor Llaca, Jeffrey L. Bennetzen, ...
Data from cytological and genetic mapping studies suggest that maize arose as a tetraploid. Two previous studies investigating the most likely mode of maize origin arrived at different conclusions....
Close Split of Sorghum and Maize Genome Progenitors (2004)
Swigonová, Zuzana, Lai, Jinsheng, Ma, Jianxin, Ramakrishna, Wusirika, Llaca, Victor, Bennetzen, Jeffrey L., ...
It is generally believed that maize (Zea mays L. ssp. mays) arose as a tetraploid; however, the two progenitor genomes cannot be unequivocally traced within the genome of modern maize. We have taken...
Gene Loss and Movement in the Maize Genome (2004)
Lai, Jinsheng, Ma, Jianxin, Swigonová, Zuzana, Ramakrishna, Wusirika, Linton, Eric, Llaca, Victor, ...
Maize (Zea mays L. ssp. mays), one of the most important agricultural crops in the world, originated by hybridization of two closely related progenitors. To investigate the fate of its genes after...
Characterization of the Maize Endosperm Transcriptome and Its Comparison to the Rice Genome (2004)
Lai, Jinsheng, Dey, Nrisingha, Kim, Cheol-Soo, Bharti, Arvind K., Rudd, Stephen, Mayer, Klaus F.X., ...
The cereal endosperm is a major organ of the seed and an important component of the world's food supply. To understand the development and physiology of the endosperm of cereal seeds, we focused on...
Washida, Haruhiko, Sugino, Aya, Messing, Joachim, Esen, Asim, Okita, Thomas W.
Plant storage proteins are synthesized and stored in different compartments of the plant endomembrane system. Developing maize seeds synthesize and accumulate prolamin (zein) and 11S globulin...
Expression of the sorghum 10-member kafirin gene cluster in maize endosperm (2004)
Song, Rentao, Segal, Gregorio, Messing, Joachim
Functional analysis of chromosomal segments containing linked genes requires the insertion of contiguous genomic sequences from bacterial artificial chromosomes (BACs) into the genome. Therefore, we...
Wusirika Ramakrishna, Jianxin Ma, Phillip SanMiguel, John Emberton, Jorge Dubcovsky, Bryan A Shiloff, ...
Trans replication and high copy numbers of wheat dwarf virus vectors in maize cells (1992)
Timmermans, Marija C.P., Das, O.Prem, Messing, Joachim
The replication of shuttle vectors derived from Wheat Dwarf Virus, a monopartlte geminivirus, was studied in cultured maize endosperm cells, and In the Black Mexican Sweet (BMS) maize cell line....
A new allele of the duplicated 27kD zein locus of maize generated by homologous recombination (1991)
Das, O.Prem, Poliak, Eduard, Ward, Kathleen, Messing, Joachim
The 27kD zein storage protein locus in many Inbred lines of maize consists of a tandem duplication of 12kb, with an expressed gene In each repeat, termed A and B. A single-copy allele with only the A...
Replication of a geminivirus derived shuttle vector in maize endosperm cells (1991)
Ugaki, Masashi, Ueda, Takashi, Timmermans, Marja C.P., Vieira, Jeffrey, EIIiston, Keith O., Messing, Joachim
A maize (Zea mays L.) endosperm cell culture has been shown to efficiently replicate DNA sequences derived from wheat dwarf virus (WDV), a monopartrte monocot geminivirus. To analyze sequences...
Sequence analysis of zein cDNAs obtained by an efficient mRNA cloning method (1983)
Heidecker, Gisela, Messing, Joachim
A cDNA library was generated from mRNA Isolated from the developing endosperm of W22 maize inbred. cDNA clones for zeln, the maize storage protein family, were isolated and analyzed by DNA...
Apple II software for M13 shotgun DNA sequencing (1982)
Larson, Roger, Messing, Joachim
A set of programs is presented for the reconstruction of a DNA sequence from data generated by the M13 shotgun sequencing technique. Once the sequence has been established and stored other programs...
A system for shotgun DNA sequencing (1981)
Messing, Joachim, Crea, Roberto, Seeburg, Peter H.
A multipurpose cloning site has been introduced into the gene for β-galactosidase (β-D-galactosidegalactohydrolase, EC 3.21.23) on the single-stranded DNA phage M13mp2 (Gronenborn, B. and Messing,...
Gardner, Richard C., Howarth, Alan J., Hahn, Peter, Brown-Luedi, Marianne, Shepherd, Robert J., Messing, Joachim
We have determined the complete primary structure (8031 base pairs) of an infectious clone of cauliflower mosaic virus strain CM1841. The sequence was obtained using the strategy of cloning shotgun...
The primary structure of a plant storage protein: zein (1981)
Geraghty, Dan, Peifer, Mark A., Rubenstein, Irwin, Messing, Joachim
The protein sequence of a representative of the zeins, the major storage proteins of maize, has been derived from the nucleotide sequence of a zein cDNA clone. This cDNA was sequenced both by the...
Untersuchungen zur Replikation des plasmids 15 in Escherichia coli /--von Joachim Messing,... (1974)
Inaug.-Diss. : Pharm. : Munchen : 1974.
Importance of anchor genomes for any plant genome project
Messing, Joachim, Llaca, Victor
Progress in agricultural and environmental technologies is hampered by a slower rate of gene discovery in plants than animals. The vast pool of genes in plants, however, will be an important resource...
Gene expression of a gene family in maize based on noncollinear haplotypes
Song, Rentao, Messing, Joachim
Genomic regions of nearly every species diverged into different haplotypes, mostly based on point mutations, small deletions, and insertions that do not affect the collinearity of genes within a...
Contiguous Genomic DNA Sequence Comprising the 19-kD Zein Gene Family from Maize1
Song, Rentao, Messing, Joachim
A new approach has been undertaken to analyze the sequences and linear organization of the 19-kD zein genes in maize (Zea mays). A high-coverage, large-insert genomic library of the inbred line B73...
Comparative Sequence Analysis of the Sorghum Rph Region and the Maize Rp1 Resistance Gene Complex
Ramakrishna, Wusirika, Emberton, John, SanMiguel, Phillip, Ogden, Matthew, Llaca, Victor, Messing, Joachim, ...
A 268-kb chromosomal segment containing sorghum (Sorghum bicolor) genes that are orthologous to the maize (Zea mays) Rp1 disease resistance (R) gene complex was sequenced. A region of approximately...
Mosaic Organization of Orthologous Sequences in Grass Genomes
Song, Rentao, Llaca, Victor, Messing, Joachim
Although comparative genetic mapping studies show extensive genome conservation among grasses, recent data provide many exceptions to gene collinearity at the DNA sequence level. Rice, sorghum, and...
Dual Regulated RNA Transport Pathways to the Cortical Region in Developing Rice Endosperm
Hamada, Shigeki, Ishiyama, Keiki, Sakulsingharoj, Chotipa, Choi, Sang-Bong, Wu, Yujia, Wang, Changlin, ...
Prolamine and glutelin RNAs are localized to two subdomains of the cortical endoplasmic reticulum (ER), the protein body ER and the cisternal ER, in developing rice seeds. The addition of nearly...
Sequence, Regulation, and Evolution of the Maize 22-kD α Zein Gene Family
Song, Rentao, Llaca, Victor, Linton, Eric, Messing, Joachim
We have isolated and sequenced all 23 members of the 22-kD α zein (z1C) gene family of maize. This is one of the largest plant gene families that has been sequenced from a single genetic background...
Pattern of diversity in the genomic region near the maize domestication gene tb1
Clark, Richard M., Linton, Eric, Messing, Joachim, Doebley, John F.
Domesticated maize and its wild ancestor (teosinte) differ strikingly in morphology and afford an opportunity to examine the connection between strong selection and diversity in a major crop species....
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...
Close Split of Sorghum and Maize Genome Progenitors
Swigoňová, Zuzana, Lai, Jinsheng, Ma, Jianxin, Ramakrishna, Wusirika, Llaca, Victor, Bennetzen, Jeffrey L., ...
It is generally believed that maize (Zea mays L. ssp. mays) arose as a tetraploid; however, the two progenitor genomes cannot be unequivocally traced within the genome of modern maize. We have taken...
Gene Loss and Movement in the Maize Genome
Lai, Jinsheng, Ma, Jianxin, Swigoňová, Zuzana, Ramakrishna, Wusirika, Linton, Eric, Llaca, Victor, ...
Maize (Zea mays L. ssp. mays), one of the most important agricultural crops in the world, originated by hybridization of two closely related progenitors. To investigate the fate of its genes after...
Characterization of the Maize Endosperm Transcriptome and Its Comparison to the Rice Genome
Lai, Jinsheng, Dey, Nrisingha, Kim, Cheol-Soo, Bharti, Arvind K., Rudd, Stephen, Mayer, Klaus F.X., ...
The cereal endosperm is a major organ of the seed and an important component of the world's food supply. To understand the development and physiology of the endosperm of cereal seeds, we focused on...
Expression of the sorghum 10-member kafirin gene cluster in maize endosperm
Song, Rentao, Segal, Gregorio, Messing, Joachim
Functional analysis of chromosomal segments containing linked genes requires the insertion of contiguous genomic sequences from bacterial artificial chromosomes (BACs) into the genome. Therefore, we...
Gene movement by Helitron transposons contributes to the haplotype variability of maize
Lai, Jinsheng, Li, Yubin, Messing, Joachim, Dooner, Hugo K.
Different maize inbred lines are polymorphic for the presence or absence of genic sequences at various allelic chromosomal locations. In the bz genomic region, located in 9S, sequences homologous to...
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 Evolution of the r/b Chromosomal Regions in Rice, Maize and Sorghum
Swigoňová, Zuzana, Bennetzen, Jeffrey L., Messing, Joachim
The r1 and b1 genes of maize, each derived from the chromosomes of two progenitors that hybridized >4.8 million years ago (MYA), have been a rich source for studying transposition, recombination,...
DNA Rearrangement in Orthologous Orp Regions of the Maize, Rice and Sorghum Genomes
Ma, Jianxin, SanMiguel, Phillip, Lai, Jinsheng, Messing, Joachim, Bennetzen, Jeffrey L.
The homeologous Orp1 and Orp2 regions of maize and the orthologous regions in sorghum and rice were compared by generating sequence data for >486 kb of genomic DNA. At least three genic...
A new opaque variant of maize by a single dominant RNA-interference-inducing transgene.
Segal, Gregorio, Song, Rentao, Messing, Joachim
In maize, alpha-zeins, the main protein components of seed stores, are major determinants of nutritional imbalance when maize is used as the sole food source. Mutations like opaque-2 (o2) are used in...
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...
Importance of anchor genomes for any plant genome project
Messing, Joachim, Llaca, Victor
Progress in agricultural and environmental technologies is hampered by a slower rate of gene discovery in plants than animals. The vast pool of genes in plants, however, will be an important resource...
Gene expression of a gene family in maize based on noncollinear haplotypes
Song, Rentao, Messing, Joachim
Genomic regions of nearly every species diverged into different haplotypes, mostly based on point mutations, small deletions, and insertions that do not affect the collinearity of genes within a...
Contiguous Genomic DNA Sequence Comprising the 19-kD Zein Gene Family from Maize1
Song, Rentao, Messing, Joachim
A new approach has been undertaken to analyze the sequences and linear organization of the 19-kD zein genes in maize (Zea mays). A high-coverage, large-insert genomic library of the inbred line B73...
Comparative Sequence Analysis of the Sorghum Rph Region and the Maize Rp1 Resistance Gene Complex
Ramakrishna, Wusirika, Emberton, John, SanMiguel, Phillip, Ogden, Matthew, Llaca, Victor, Messing, Joachim, ...
A 268-kb chromosomal segment containing sorghum (Sorghum bicolor) genes that are orthologous to the maize (Zea mays) Rp1 disease resistance (R) gene complex was sequenced. A region of approximately...
Mosaic Organization of Orthologous Sequences in Grass Genomes
Song, Rentao, Llaca, Victor, Messing, Joachim
Although comparative genetic mapping studies show extensive genome conservation among grasses, recent data provide many exceptions to gene collinearity at the DNA sequence level. Rice, sorghum, and...
Dual Regulated RNA Transport Pathways to the Cortical Region in Developing Rice Endosperm
Hamada, Shigeki, Ishiyama, Keiki, Sakulsingharoj, Chotipa, Choi, Sang-Bong, Wu, Yujia, Wang, Changlin, ...
Prolamine and glutelin RNAs are localized to two subdomains of the cortical endoplasmic reticulum (ER), the protein body ER and the cisternal ER, in developing rice seeds. The addition of nearly...
Sequence, Regulation, and Evolution of the Maize 22-kD α Zein Gene Family
Song, Rentao, Llaca, Victor, Linton, Eric, Messing, Joachim
We have isolated and sequenced all 23 members of the 22-kD α zein (z1C) gene family of maize. This is one of the largest plant gene families that has been sequenced from a single genetic background...
Pattern of diversity in the genomic region near the maize domestication gene tb1
Clark, Richard M., Linton, Eric, Messing, Joachim, Doebley, John F.
Domesticated maize and its wild ancestor (teosinte) differ strikingly in morphology and afford an opportunity to examine the connection between strong selection and diversity in a major crop species....
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...
Close Split of Sorghum and Maize Genome Progenitors
Swigoňová, Zuzana, Lai, Jinsheng, Ma, Jianxin, Ramakrishna, Wusirika, Llaca, Victor, Bennetzen, Jeffrey L., ...
It is generally believed that maize (Zea mays L. ssp. mays) arose as a tetraploid; however, the two progenitor genomes cannot be unequivocally traced within the genome of modern maize. We have taken...
Gene Loss and Movement in the Maize Genome
Lai, Jinsheng, Ma, Jianxin, Swigoňová, Zuzana, Ramakrishna, Wusirika, Linton, Eric, Llaca, Victor, ...
Maize (Zea mays L. ssp. mays), one of the most important agricultural crops in the world, originated by hybridization of two closely related progenitors. To investigate the fate of its genes after...
Characterization of the Maize Endosperm Transcriptome and Its Comparison to the Rice Genome
Lai, Jinsheng, Dey, Nrisingha, Kim, Cheol-Soo, Bharti, Arvind K., Rudd, Stephen, Mayer, Klaus F.X., ...
The cereal endosperm is a major organ of the seed and an important component of the world's food supply. To understand the development and physiology of the endosperm of cereal seeds, we focused on...
Expression of the sorghum 10-member kafirin gene cluster in maize endosperm
Song, Rentao, Segal, Gregorio, Messing, Joachim
Functional analysis of chromosomal segments containing linked genes requires the insertion of contiguous genomic sequences from bacterial artificial chromosomes (BACs) into the genome. Therefore, we...
Gene movement by Helitron transposons contributes to the haplotype variability of maize
Lai, Jinsheng, Li, Yubin, Messing, Joachim, Dooner, Hugo K.
Different maize inbred lines are polymorphic for the presence or absence of genic sequences at various allelic chromosomal locations. In the bz genomic region, located in 9S, sequences homologous to...
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...
Structure and Evolution of the r/b Chromosomal Regions in Rice, Maize and Sorghum
Swigoňová, Zuzana, Bennetzen, Jeffrey L., Messing, Joachim
The r1 and b1 genes of maize, each derived from the chromosomes of two progenitors that hybridized >4.8 million years ago (MYA), have been a rich source for studying transposition, recombination,...
DNA Rearrangement in Orthologous Orp Regions of the Maize, Rice and Sorghum Genomes
Ma, Jianxin, SanMiguel, Phillip, Lai, Jinsheng, Messing, Joachim, Bennetzen, Jeffrey L.
The homeologous Orp1 and Orp2 regions of maize and the orthologous regions in sorghum and rice were compared by generating sequence data for >486 kb of genomic DNA. At least three genic...
A new opaque variant of maize by a single dominant RNA-interference-inducing transgene.
Segal, Gregorio, Song, Rentao, Messing, Joachim
In maize, alpha-zeins, the main protein components of seed stores, are major determinants of nutritional imbalance when maize is used as the sole food source. Mutations like opaque-2 (o2) are used in...
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...
Sequence-indexed mutations in maize using the UniformMu transposon-tagging population
Settles, A Mark, Holding, David R, Tan, Bao Cai, Latshaw, Susan P, Liu, Juan, Suzuki, Masaharu, ...
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...
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...
Ramakrishna, Wusirika, Ma, Jianxin, SanMiguel, Phillip, Emberton, John, Dubcovsky, Jorge, Shiloff, Bryan A, ...
On the Tetraploid Origin of the Maize Genome
Swigonova, Zuzana, Lai, Jinsheng, Ma, Jianxin, Ramakrishna, Wusirika, Llaca, Victor, Bennetzen, Jeffrey L., ...
Data from cytological and genetic mapping studies suggest that maize arose as a tetraploid. Two previous studies investigating the most likely mode of maize origin arrived at different conclusions....
Xu, Jian-Hong, Messing, Joachim
Zea mays, commonly known as corn, is perhaps the most greatly produced crop in terms of tonnage and a major food, feed, and biofuel resource. Here we analyzed its prolamin gene family, encoding the...
Goettel, Wolfgang, Messing, Joachim
An important objective in genome research is to relate genome structure to gene function. Sequence comparisons among orthologous and paralogous genes and their allelic variants can reveal sequences...