Toward a unified genetic map of higher plants, transcending the monocot–dicot divergence

Paterson, Andrew H.; Lan, Tian; Reischmann, Kim P.; Chang, C. H.; Lin, Yi Ru; Liu, Sin-Chieh; Burow, Mark D.; Kowalski, S. P.; Katsar, Catherine S.; Delmonte, Terrye A.; Feldmann, Kenneth A.; Schertz, K. F.; Wendel, Jonathan F.

doi:10.1038/ng1296-380

Cited by 170 publications

(112 citation statements)

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“…Nonrandom patterns of gene expression are found among proximally located rice (Ma et al, 2005) and Arabidopsis (Ren et al, 2007) genes. While a comparative study to date found no microsynteny between the two species in these domains (Ren et al, 2007), inferences about monocot-dicot synteny are much more complicated than was realized before the availability of whole-genome sequences (Paterson et al, 1996), due largely to multiple paleopolyploidies and associated gene losses. While monocot-dicot synteny is difficult to discern, synteny blocks in the grasses often comprise entire chromosomes or chromosome arms and offer little resolution to discern chance persistence from the preservation of gene order by selection.…”

Section: Distinguishing Features Of the Cerealsmentioning

confidence: 99%

Comparative Genomics of Grasses Promises a Bountiful Harvest

Paterson

Bowers²,

Feltus³

et al. 2009

Plant Physiology

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Section: Distinguishing Features Of the Cerealsmentioning

confidence: 99%

Comparative Genomics of Grasses Promises a Bountiful Harvest

Paterson

Bowers²,

Feltus³

et al. 2009

Plant Physiology

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“…Curiously, even in the relatively "conservative" Poaceae, certain lineages appear to be rapidly evolving. The genomes of rye and wheat appear to differ by ‫ف‬ 13 chromosomal rearrangements after only ‫ف‬ 6 million years of divergence (Devos et al, 1992a(Devos et al, , 1992b, a rate of reshuffling more than twice the average calculated for nine taxa (Paterson et al, 1996) and exceeded only by the Brassica-Arabidopsis lineage.…”

Section: The Poaceaementioning

confidence: 99%

Comparative Genomics of Plant Chromosomes

et al. 2000

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FOUNDATIONS OF COMPARATIVE GENOMICSComparative genomics, the study of the similarities and differences in structure and function of hereditary information across taxa, uses molecular tools to investigate many notions that long preceded identification of DNA as the hereditary molecule. Vavilov's (1922) law of homologous series in variation was an early suggestion of the similarities in the genetic blueprints of many (plant) species. Genetic analysis based on morphological and isoenzyme markers hinted at parallel arrangements of genes along the chromosomes of various taxa. These hints were later borne out at the DNA level, in seminal investigations of nightshades (Tanksley et al., 1988; Bonierbale et al., 1988) and grasses (Hulbert et al., 1990).Over the past two decades, multiple investigations of many additional taxa have delivered two broad messages: (1) In most plants, the evolution of the small but essential portion of the genome that actually encodes the organism's genes has proceeded relatively slowly; as a result, taxa that have been reproductively isolated for millions of years have retained recognizable intragenic DNA sequences as well as similar arrangements of genes along the chromosomes. (2) A wide range of factors, such as ancient chromosomal or segmental duplications, mobility of DNA sequences, gene deletion, and localized rearrangements, has been superimposed on the relatively slow tempo of chromosomal evolution and causes many deviations from colinearity. COMPARATIVE MAPS IN CROP TAXA The BrassicaceaeThe Brassicaceae comprise 360 genera, organized into 13 tribes (Shultz, 1936; Al-Shehbaz, 1973). The most economically important species are in the genus Brassica (tribe Brassiceae), six species of which are cultivated worldwide.

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“…Few attempts to analyze genome colinearity between more distantly related species have been reported (Paterson et al, 1996;Devos et al, 1999;van Dodeweerd et al, 1999;Ku et al, 2000). The low degree of sequence homology in distantly related species hampers the unambiguous recognition of orthologous sequences, a prerequisite for studying colinearity relationships between species.…”

Section: Introductionmentioning

confidence: 99%

“…Tomato and Arabidopsis were chosen for such a comparative analysis because these species are representatives of two major clades of the eudicots, the asterids and rosids, respectively (Soltis et al, 1999). Colinear chromosome segments between distantly related species are expected to be small (Paterson et al, 1996); therefore, a microsynteny approach was taken to search for colinearity between the tomato and Arabidopsis genomes. The sequence of a region of the tomato genome spanning five genes including the Lateral suppressor gene (Schumacher et al, 1999) was determined.…”

Section: Introductionmentioning

confidence: 99%

“…Comparing the genetic maps of Arabidopsis and different Brassica species also has revealed many colinear chromosome segments for species belonging to the Brassicaceae family (reviewed in Schmidt, 2000). The results of the first microsynteny studies using sequencelevel resolution in the Poaceae (Chen et al, 1997;Messing and Llaca, 1998;Tikhonov et al, 1999) and Brassicaceae families (Grant et al, 1998;Acarkan et al, 2000) support the view that genome colinearity can be observed at the level of genes.Few attempts to analyze genome colinearity between more distantly related species have been reported (Paterson et al, 1996;Devos et al, 1999;van Dodeweerd et al, 1999;Ku et al, 2000). The low degree of sequence homology in distantly related species hampers the unambiguous 1 These authors contributed equally to this work.…”

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Comparative Sequence Analysis Reveals Extensive Microcolinearity in the Lateral Suppressor Regions of the Tomato, Arabidopsis, and Capsella Genomes

Rossberg¹,

Theres

Acarkan³

et al. 2001

Plant Cell

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A 57-kb region of tomato chromosome 7 harboring five different genes was compared with the sequence of the Arabidopsis genome to search for microsynteny between the genomes of these two species. For all five genes, homologous sequences could be identified in a 30-kb region located on Arabidopsis chromosome 1. Only two inversion events distinguish the arrangement of the five genes in tomato from that in Arabidopsis. Inversions were not detected when the arrangement of the five Arabidopsis genes was compared with the arrangement in the orthologous region of Capsella, a plant closely related to Arabidopsis. These results provide evidence for microcolinearity between closely and distantly related dicotyledonous species. The degree of microcolinearity found can be exploited to localize orthologous genes in Arabidopsis and tomato in an unambiguous way. INTRODUCTIONArabidopsis, a small crucifer, has been adopted as a model in plant genome analysis. The small genome size of 125 Mbp and a low number of repetitive elements facilitated the assembly of comprehensive molecular marker and clone contig maps for the five Arabidopsis chromosomes (reviewed in Schmidt, 1998). Sequence analysis of the genome has been completed (The Arabidopsis Genome Initiative, 2000). The 430-Mbp rice genome is a model for monocotyledonous plants, and the rice genome project aims to decipher the entire genomic sequence for this species (Sasaki and Burr, 2000). Equally detailed studies are not feasible for many other plant genomes at present, especially given the large genome sizes of most crop plants. It needs to be established if and how information generated on the Arabidopsis and rice genomes can be used for the study of other plant genomes.Comparative genetic mapping experiments yielded evidence for the conservation of gene repertoire and colinear chromosome segments for related species. An extensive conservation of marker order was found for the 12 tomato and potato chromosomes, and five chromosomal inversions could explain differences in marker organization (Tanksley et al., 1992). For the Poaceae family, a remarkable degree of genome conservation could be established even between species that diverged as long as 60 million years ago and that differ considerably in genome size (reviewed in Gale and Devos, 1998). Comparing the genetic maps of Arabidopsis and different Brassica species also has revealed many colinear chromosome segments for species belonging to the Brassicaceae family (reviewed in Schmidt, 2000). The results of the first microsynteny studies using sequencelevel resolution in the Poaceae (Chen et al., 1997;Messing and Llaca, 1998;Tikhonov et al., 1999) and Brassicaceae families (Grant et al., 1998;Acarkan et al., 2000) support the view that genome colinearity can be observed at the level of genes.Few attempts to analyze genome colinearity between more distantly related species have been reported (Paterson et al., 1996;Devos et al., 1999;van Dodeweerd et al., 1999;Ku et al., 2000). The low degree of sequence homology in distantl...

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Toward a unified genetic map of higher plants, transcending the monocot–dicot divergence

Cited by 170 publications

References 30 publications

Comparative Genomics of Grasses Promises a Bountiful Harvest

Comparative Genomics of Grasses Promises a Bountiful Harvest

Comparative Genomics of Plant Chromosomes

Comparative Sequence Analysis Reveals Extensive Microcolinearity in the Lateral Suppressor Regions of the Tomato, Arabidopsis, and Capsella Genomes

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