Comparative Genomics of<i>Brassica oleracea</i>and<i>Arabidopsis thaliana</i>Reveal Gene Loss, Fragmentation, and Dispersal after Polyploidy

Town, Christopher D.; Cheung, Foo; Maiti, Rama; Crabtree, Jonathan; Haas, Brian J.; Wortman, Jennifer; Hine, Erin; Althoff, Ryan; Arbogast, Tamara S.; Tallon, Luke J.; Vigouroux, Marielle; Trick, Martin; Bancroft, Ian

doi:10.1105/tpc.106.041665

Cited by 378 publications

(338 citation statements)

References 55 publications

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“…A loss of paralogous gene copies was documented herein for all three single-copy nuclear genes and all analyzed species. Extensive gene loss was also found in the mesopolyploid genomes of B. rapa (Yang et al, 2006) and B. oleracea (Town et al, 2006).…”

Section: Diploidization: Retention Versus Loss Of Genomic Blocksmentioning

confidence: 89%

Fast Diploidization in Close Mesopolyploid Relatives ofArabidopsis

et al. 2010

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Mesopolyploid whole-genome duplication (WGD) was revealed in the ancestry of Australian Brassicaceae species with diploid-like chromosome numbers (n = 4 to 6). Multicolor comparative chromosome painting was used to reconstruct complete cytogenetic maps of the cryptic ancient polyploids. Cytogenetic analysis showed that the karyotype of the Australian Camelineae species descended from the eight ancestral chromosomes (n = 8) through allopolyploid WGD followed by the extensive reduction of chromosome number. Nuclear and maternal gene phylogenies corroborated the hybrid origin of the mesotetraploid ancestor and suggest that the hybridization event occurred ;6 to 9 million years ago.The four, five, and six fusion chromosome pairs of the analyzed close relatives of Arabidopsis thaliana represent complex mosaics of duplicated ancestral genomic blocks reshuffled by numerous chromosome rearrangements. Unequal reciprocal translocations with or without preceeding pericentric inversions and purported end-to-end chromosome fusions accompanied by inactivation and/or loss of centromeres are hypothesized to be the main pathways for the observed chromosome number reduction. Our results underline the significance of multiple rounds of WGD in the angiosperm genome evolution and demonstrate that chromosome number per se is not a reliable indicator of ploidy level.

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Section: Diploidization: Retention Versus Loss Of Genomic Blocksmentioning

confidence: 89%

Fast Diploidization in Close Mesopolyploid Relatives ofArabidopsis

et al. 2010

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“…If miRNA gene clusters existed before polyploidization, genome duplication events would produce duplicated miRNA clusters, a situation analogous to the protein-coding gene blocks [42]. Segmental duplication may also occur during chromosomal recombination and shuffling.…”

Section: Additional Expansion Of Mirna Gene Families Via Segmental Dumentioning

confidence: 99%

Evolution of plant microRNA gene families

Mao

2006

Cell Res

147

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MicroRNAs (miRNAs) are important post-transcriptional regulators of their target genes in plants and animals. miRNAs are usually 20-24 nucleotides long. Despite their unusually small sizes, the evolutionary history of miRNA gene families seems to be similar to their protein-coding counterparts. In contrast to the small but abundant miRNA families in the animal genomes, plants have fewer but larger miRNA gene families. Members of plant miRNA gene families are often highly similar, suggesting recent expansion via tandem gene duplication and segmental duplication events. Although many miRNA genes are conserved across plant species, the same gene family varies significantly in size and genomic organization in different species, which may cause dosage effects and spatial and temporal differences in target gene regulations. In this review, we summarize the current progress in understanding the evolution of plant miRNA gene families.

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“…With more than 300 additional genera, Brassica species alone includes many important vegetables that are widely used in the cuisine of many cultures (B. rapa: Chinese cabbage, Pak-choi and turnip; B. oleracea: broccoli, cabbage and cauliflower) as well as oilseed crops (B. napus, B. rapa, B. juncea and B. carinata) which provide collectively 12% of world edible vegetable oil production 5 . The six widely cultivated Brassica species are also a classical example of the importance of polyploidy in botanical evolution, described by the "U's triangle" 6 , with the three diploid oleracea 7 and B. rapa 8 since its divergence from the A. thaliana lineage 13-17 MYA 9,10 or more 11 .…”

Section: Introductionmentioning

confidence: 99%

The genome of the mesopolyploid crop species Brassica rapa

Wang¹,

Wang²,

Wang³

et al. 2011

Nat Genet

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The genome of the mesopolyploid crop species Brassica rapaThe Brassica rapa Genome Sequencing Project Consortium 1 Abstract:The Brassicaceae family which includes Arabidopsis thaliana, is a natural priority for reaching beyond botanical models to more deeply sample angiosperm genomic and functional diversity. Here we report the draft genome sequence and its annoation of Brassica rapa, one of the two ancestral species of oilseed rape. We modeled 41,174 protein-coding genes in the B. rapa genome. B. rapa has experienced only the second genome triplication reported to date, with its close relationship to A. thaliana providing a useful outgroup for investigating many consequences of triplication for its structural and functional evolution. The extent of gene loss (fractionation) among triplicated genome segments varies, with one copy containing a greater proportion of genes expected to have been present in its ancestor (70%) than the remaining two (46% and 36%). Both a generally rapid evolutionary rate, and specific copy number amplifications of particular gene families, may contribute to the remarkable propensity of Brassica species for the development of new morphological variants. The B. rapa genome provides a new resource for comparative and evolutionary analysis of the Brassicaceae genomes and also a platform for genetic improvement of Brassica oil and vegetable crops.2

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Comparative Genomics ofBrassica oleraceaandArabidopsis thalianaReveal Gene Loss, Fragmentation, and Dispersal after Polyploidy

Cited by 378 publications

References 55 publications

Fast Diploidization in Close Mesopolyploid Relatives ofArabidopsis

Fast Diploidization in Close Mesopolyploid Relatives ofArabidopsis

Evolution of plant microRNA gene families

The genome of the mesopolyploid crop species Brassica rapa

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