The ‘inner circle’ of the cereal genomes

Bolot, Stéphanie; Abrouk, Michaël; Quraishi, Umar Masood; Stein, Nils; Messing, Joachim; Feuillet, Catherine; Salse, Jérôme

doi:10.1016/j.pbi.2008.10.011

Cited by 144 publications

(115 citation statements)

References 41 publications

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“…The grasses originated 55-70 million years ago (mya) and subsequently diversified to include all the major cereal crop species in addition to nearly 10,000 nondomesticated relatives (Fig. 1A;Kellogg 2001;Bolot et al 2009). The maize genome originated 4.8 mya via the segmental allotetraploidization of two progenitor genomes that themselves diverged from a sorghum progenitor~11.9 mya (Gaut and Doebley 1997;Swigonova et al 2004).…”

Section: Background Informationmentioning

confidence: 99%

Maize (Zea mays): A Model Organism for Basic and Applied Research in Plant Biology

Strable¹,

Scanlon²

2009

Cold Spring Harb Protoc

131

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INTRODUCTIONZea mays ssp. mays is one of the world’s most important crop plants, boasting a multibillion dollar annual revenue. In addition to its agronomic importance, maize has been a keystone model organism for basic research for nearly a century. Within the cereals, which include other plant model species such as rice (Oryza sativa), sorghum (Sorghum bicolor), wheat (Triticum spp.), and barley (Hordeum vulgare), maize is the most thoroughly researched genetic system. Several attributes of the maize plant, including a vast collection of mutant stocks, large heterochromatic chromosomes, extensive nucleotide diversity, and genic colinearity within related grasses, have positioned this species as a centerpiece for genetic, cytogenetic, and genomic research. As a model organism, maize is the subject of such far-ranging biological investigations as plant domestication, genome evolution, developmental physiology, epigenetics, pest resistance, heterosis, quantitative inheritance, and comparative genomics. These and other studies will be advanced by the completed sequencing and annotation of the maize gene space, which will be realized during 2009. Here we present an overview of the use of maize as a model system and provide links to several protocols that enable its genetic and genomic analysis.

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Section: Background Informationmentioning

confidence: 99%

Maize (Zea mays): A Model Organism for Basic and Applied Research in Plant Biology

Strable¹,

Scanlon²

2009

Cold Spring Harb Protoc

131

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“…Integration of the independent analyses of the duplications within and synteny between the 5 major cereal genomes [hereafter referred to r for rice, m for maize, s for sorghum, and t for the Triticeae (wheat and barley)] allowed us to the characterize more precisely the seven shared duplications identified recently among the ancestral grass chromosomal groups (15,22). These paleoduplications were found on the following chromosome pair combinations: t4-t5/r11-r12/s5-s8/m2-m4-m1-m3-m10, t1-t3/r5-r1/s9-s3/ m6-m8-m3, t1-t4/r10-r3/s1/m1-m5-m9, t2-t4/r7-r3/s2-s1/m2-m7-m1-m9-m5, t2-t6/r4-r2/s6-s4/m2-m10-m4-m5, t5-t7/r9-r8/s2-s7/m2-m7-m1-m4-m10-m6, and t6-t7/r2-r6/s4-s10/m4-m5-m6-m9 (Table S1 of ancestral shared duplications and recent lineage-specific duplications (Fig.…”

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Reconstruction of monocotelydoneous proto-chromosomes reveals faster evolution in plants than in animals

Salse

Abrouk

Bolot

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

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Paleogenomics seeks to reconstruct ancestral genomes from the genes of today's species. The characterization of paleo-duplications represented by 11,737 orthologs and 4,382 paralogs identified in five species belonging to three of the agronomically most important subfamilies of grasses, that is, Ehrhartoideae (rice) Panicoideae (sorghum, maize), and Pooideae (wheat, barley), permitted us to propose a model for an ancestral genome with a minimal size of 33.6 Mb structured in five proto-chromosomes containing at least 9,138 predicted proto-genes. It appears that only four major evolutionary shuffling events (␣, ␤, ␥, and ␦) explain the divergence of these five cereal genomes during their evolution from a common paleo-ancestor. Comparative analysis of ancestral gene function with rice as a reference indicated that five categories of genes were preferentially modified during evolution. Furthermore, alignments between the five grass proto-chromosomes and the recently identified seven eudicot proto-chromosomes indicated that additional very active episodes of genome rearrangements and gene mobility occurred during angiosperm evolution. If one compares the pace of primate evolution of 90 million years (233 species) to 60 million years of the Poaceae (10,000 species), change in chromosome structure through speciation has accelerated significantly in plants.grasses ͉ paleogenomics P aleogenomics, the study of ancestral genome structures, allows the identification and characterization of mechanisms (e.g., duplications, translocations, and inversions) that have shaped genome species during their evolution and provides a framework to better integrate results from genetics, genomics, and comparative analyses. Studies of fossils and lower taxa organisms [Neanderthal (1), Echinoderms (2), Mammoth (3), Sponge (4), and Moss (5)] have yielded unprecedented information on the evolution of animal species and the relationships between them. When fossil DNA is not available, paleogenomics can be performed through largescale comparative analyses of actual species and through ancestor modeling.In silico colinearity studies and ancestral genome reconstruction in mammals have been facilitated by a generally moderate reshuffling of chromosomal segments since their divergence from a common ancestor Ϸ130 million years ago (mya) (6-9). Recently, Nakatani et al. (10) provided an integrated view of vertebrate paleogenomics with an ancestor of 10 to 13 proto-chromosomes. In contrast to mammals, paleogenomics has been poorly investigated in plants as angiosperm species have undergone serial whole genome or segmental duplications, diploidization, small-scale rearrangements (translocations, gene conversions), and gene copying events that make comparative studies between and within the monocotyledon (mainly grasses) and eudicot families very challenging. For the eudicots, two scenarios based on comparisons between the grape, Arabidopsis thaliana, and poplar genome sequences have been proposed recently. In the first one, the eudicots were proposed t...

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“…This strategy is supported by a significant level of colinearity between Poaceae genomes (Moore et al, 1995;Bolot et al, 2009). Moreover, high-quality reference genome sequences for both rice and sorghum (Sorghum bicolor) are available (Sasaki and Sederoff, 2003;Paterson et al, 2009) and provide a platform for large-scale implementation of this approach.…”

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Gene Content and Virtual Gene Order of Barley Chromosome 1H

et al. 2009

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Chromosome 1H (approximately 622 Mb) of barley (Hordeum vulgare) was isolated by flow sorting and shotgun sequenced by GSFLX pyrosequencing to 1.3-fold coverage. Fluorescence in situ hybridization and stringent sequence comparison against genetically mapped barley genes revealed 95% purity of the sorted chromosome 1H fraction. Sequence comparison against the reference genomes of rice (Oryza sativa) and sorghum (Sorghum bicolor) and against wheat (Triticum aestivum) and barley expressed sequence tag datasets led to the estimation of 4,600 to 5,800 genes on chromosome 1H, and 38,000 to 48,000 genes in the whole barley genome. Conserved gene content between chromosome 1H and known syntenic regions of rice chromosomes 5 and 10, and of sorghum chromosomes 1 and 9 was detected on a per gene resolution. Informed by the syntenic relationships between the two reference genomes, genic barley sequence reads were integrated and ordered to deduce a virtual gene map of barley chromosome 1H. We demonstrate that synteny-based analysis of low-pass shotgun sequenced flow-sorted Triticeae chromosomes can deliver linearly ordered high-resolution gene inventories of individual chromosomes, which complement extensive Triticeae expressed sequence tag datasets. Thus, integration of genomic, transcriptomic, and synteny-derived information represents a major step toward developing reference sequences of chromosomes and complete genomes of the most important plant tribe for mankind.

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The ‘inner circle’ of the cereal genomes

Cited by 144 publications

References 41 publications

Maize (Zea mays): A Model Organism for Basic and Applied Research in Plant Biology

Maize (Zea mays): A Model Organism for Basic and Applied Research in Plant Biology

Reconstruction of monocotelydoneous proto-chromosomes reveals faster evolution in plants than in animals

Gene Content and Virtual Gene Order of Barley Chromosome 1H

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