Analyses of Synteny Between <i>Arabidopsis thaliana</i> and Species in the Asteraceae Reveal a Complex Network of Small Syntenic Segments and Major Chromosomal Rearrangements

Timms, Lee; Jimenez, Rosmery; Chase, Mike; Lavelle, Dean; McHale, Leah K.; Kozik, Alexander; Lai, Zhao; Heesacker, Adam; Knapp, Steven J.; Rieseberg, Loren H.; Michelmore, Richard W.; Kesseli, Rick

doi:10.1534/genetics.105.049205

Cited by 30 publications

(18 citation statements)

References 52 publications

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“…The current study demonstrates that these COSII genes can also be used for comparative mapping across plant families-at least for the closely related plant families Solanaceae (tomato) and Rubiaceae (coffee). Understanding the modes and consequences of genome evolution across higher level taxa (such as families) may provide new insights into angiosperm diversification (Timms et al 2006). The current study, comparing the genomes of coffee and tomato, represents one of the few cases in which synteny could be well-deciphered across plant families.…”

Section: Discussionmentioning

confidence: 99%

High resolution synteny maps allowing direct comparisons between the coffee and tomato genomes

Lefebvre-Pautigny

Philippot

et al. 2010

Tree Genetics & Genomes

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Tomato (Solanum lycopersicum) and coffee (Coffea canephora) belong to the sister families Solanaceae and Rubiaceae, respectively. We report herein the mapping of a common set of 257 Conserved Ortholog Set II genes in the genomes of both species. The mapped markers are well distributed across both genomes allowing the first syntenic comparison between species from these two families. The majority (75%) of the synteny blocks are short (<4 cM); however, some extend up to 50 cM. In an effort to further characterize the synteny between these two genomes, we took advantage of the available sequence for the tomato genome to show that tomato chromosome 7 is syntenic to half of the two coffee linkage groups E and F with the putative break point in tomato localized to the boundary of the heterochromatin and euchromatin on the long arm. In addition to the new insight on genome conservation and evolution between the plant families Solanaceae and Rubiaceae, the comparative maps presented herein provide a translational tool by which coffee researchers may take benefit of DNA sequence and genetic information from tomato and vice versa. It is thus expected that these comparative genome information will help to facilitate and expedite genetic and genomic research in coffee.

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Section: Discussionmentioning

confidence: 99%

High resolution synteny maps allowing direct comparisons between the coffee and tomato genomes

Lefebvre-Pautigny

Philippot

et al. 2010

Tree Genetics & Genomes

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“…For example, the rice genome sequence has been used to facilitate map-based cloning in wheat and barley [25]. Unfortunately, while comparative analyses have revealed extensive co-linearity between closely related taxa [26][27][28], the length of conserved regions decreases dramatically with increasing evolutionary distance [29][30][31].…”

Section: Introductionmentioning

confidence: 99%

Crop evolution: from genetics to genomics

Burke

Burger

Chapman

2007

Current Opinion in Genetics & Development

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“…The rearrangement events in the evolutionary history of the genus Arabidopsis has been outlined by examining the level of synteny between the linkage maps of the Arabidopsis species and the Arabidopsis genome sequence (Yogeeswaran et al 2005;Hansson et al 2006). The major chromosomal rearrangements between Arabidopsis and Asteraceae (Timms et al 2006) and the structural divergence of the genic regions between Arabidopsis and Brassica (Suwabe et al 2006;Town et al 2006) also have been demonstrated by using the complete Arabidopsis reference sequence.…”

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

et al. 2007

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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 34,224 fingerprints, onto the O. sativa genome sequence. The level of conservation of each chromosome between the two species was determined by calculating a ratio of BES alignments. The alignment result suggests more divergence of intergenic and repeat regions in comparison to gene-rich regions. Further, this characteristic enabled localization of heterochromatic and euchromatic regions for each chromosome of both species. The alignment identified 16 locations containing expansions, contractions, inversions, and transpositions. By aligning 40% of the punctata BES on the map, 87% of the punctata FPC map covered 98% of the O. sativa genome sequence. The genome size of O. punctata was estimated to be 8% larger than that of O. sativa with individual chromosome differences of 1.5-16.5%. The sum of expansions and contractions observed in regions .500 kb were similar, suggesting that most of the contractions/ expansions contributing to the genome size difference between the two species are small, thus preserving the macro-collinearity between these species, which diverged $2 million years ago. C OMPARATIVE genome analysis is proving to be an excellent tool, not only to discover genes and understand their functions, but also to unravel the evolutionary relationships between species. Since related species are derived from recent common ancestors, it comes as no surprise that in both dicots and monocots extensive genetic collinearity was found when related species were mapped using common RFLP probe sets (Bonierbale et al. 1988;Hulbert et al. 1990;Ahn and Tanksley 1993;Jena et al. 1994). While extensive collinearity seems to be limited to the genus level among dicots (Tanksley et al.1988), sufficient collinearity exists to allow rough alignment of genetic maps across entire genomes throughout the entire cereal clade (Moore et al. 1995). The complete sequences of the model organisms Arabidopsis and rice (Arabi- Although rice is considered a model plant and placed at the center of the cereal crop syntenic circle (Moore et al. 1995; Gale and Devos 1998a,b;Devos 2005), only a few genomewide comparative analyses as yet have been performed using the rice genome sequence as a reference. The sorghum genome was compared to the rice genome sequence using two sorghum physical maps integrated with genetic markers and BAC hybridization data (Bowers et al. 2005). Various local rearrangements between other cereals and rice have been reported in sequence-level comparisons using the rice genome sequence as the reference (Chen et al. 1998;Goff et al. 2002;Bennetzen and Ma 2003;Sorrells Sequence data from this article have been deposited with the EMBL/GenBank Data Libraries under accession nos. CW502583-CW509125, CW514009-539178, CW620733-CW624836, CW628185-633039, CW672722-CW676096, CW691361-692844, CW748472-CW754418, CW775494-CW77843...

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Analyses of Synteny Between Arabidopsis thaliana and Species in the Asteraceae Reveal a Complex Network of Small Syntenic Segments and Major Chromosomal Rearrangements

Cited by 30 publications

References 52 publications

High resolution synteny maps allowing direct comparisons between the coffee and tomato genomes

High resolution synteny maps allowing direct comparisons between the coffee and tomato genomes

Crop evolution: from genetics to genomics

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

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