The ABC's of comparative genomics in the Brassicaceae: building blocks of crucifer genomes

Schranz, M. Eric; Lysak, Martin A.; Mitchell-Olds, Thomas

doi:10.1016/j.tplants.2006.09.002

Cited by 515 publications

(589 citation statements)

References 52 publications

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“…The Arabidopsis thaliana genome has been subdivided into 21 conserved segments (i.e., genomic blocks) (Parkin et al 2005), which have been duplicated and rearranged to form the entire B. napus genome (Schranz et al 2006). Our molecular cytogenetic map was able to identify the corresponding homoeologous chromosomes or regions between the A and C genomes, and we optimized hybridization conditions to avoid detecting ancient paralogous segments indicative of ancient polyploidy events (Lysak et al 2005;Lysak 2009).…”

Section: Discussionmentioning

confidence: 99%

Karyotype and Identification of All Homoeologous Chromosomes of AllopolyploidBrassica napusand Its Diploid Progenitors

2011

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Investigating recombination of homoeologous chromosomes in allopolyploid species is central to understanding plant breeding and evolution. However, examining chromosome pairing in the allotetraploid Brassica napus has been hampered by the lack of chromosome-specific molecular probes. In this study, we establish the identification of all homoeologous chromosomes of allopolyploid B. napus by using robust molecular cytogenetic karyotypes developed for the progenitor species Brassica rapa (A genome) and Brassica oleracea (C genome). The identification of every chromosome among these three Brassica species utilized genetically mapped bacterial artificial chromosomes (BACs) from B. rapa as probes for fluorescent in situ hybridization (FISH). With this BAC-FISH data, a second karyotype was developed using two BACs that contained repetitive DNA sequences and the ubiquitous ribosomal and pericentromere repeats. Using this diagnostic probe mix and a BAC that contained a C-genome repeat in two successive hybridizations allowed for routine identification of the corresponding homoeologous chromosomes between the A and C genomes of B. napus. When applied to the B. napus cultivar Stellar, we detected one chromosomal rearrangement relative to the parental karyotypes. This robust novel chromosomal painting technique will have biological applications for the understanding of chromosome pairing, homoeologous recombination, and genome evolution in the genus Brassica and will facilitate new applied breeding technologies that rely upon identification of chromosomes.

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Section: Discussionmentioning

confidence: 99%

Karyotype and Identification of All Homoeologous Chromosomes of AllopolyploidBrassica napusand Its Diploid Progenitors

2011

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“…We chose background genes that are involved in different physiological processes and unlinked, i.e., situated on different ancestral chromosomes (AK) (Schranz et al 2006) in C. rubella (Table 1). For each gene, both homeologs, i.e., the two loci duplicated by polyploidy, were sequenced.…”

Section: Methodsmentioning

confidence: 99%

Splicing Variation at a FLOWERING LOCUS C Homeolog Is Associated With Flowering Time Variation in the Tetraploid Capsella bursa-pastoris

et al. 2009

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The long-term fates of duplicate genes are well studied both empirically and theoretically, but how the short-term evolution of duplicate genes contributes to phenotypic variation is less well known. Here, we have studied the genetic basis of flowering time variation in the disomic tetraploid Capsella bursa-pastoris. We sequenced four duplicate candidate genes for flowering time and 10 background loci in samples from western Eurasia and China. Using a mixed-model approach that accounts for population structure, we found that polymorphisms at one homeolog of two candidate genes, FLOWERING LOCUS C (FLC) and CRYPTOCHROME1 (CRY1), were associated with natural flowering time variation. No potentially causative polymorphisms were found in the coding region of CRY1; however, at FLC two splice site polymorphisms were associated with early flowering. Accessions harboring nonconsensus splice sites expressed an alternatively spliced transcript or did not express this FLC homeolog. Our results are consistent with the function of FLC as a major repressor of flowering in Arabidopsis thaliana and imply that nonfunctionalization of duplicate genes could provide an important source of phenotypic variation.

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“…The Brassicaceae are an ideal family for the identification of CNSs owing to their relatively small genome sizes, robust phylogeny 23 and wealth of genomic data. So far, the genomes of six crucifer species have been partially or completely sequenced, including those of (i) the model 8 9 2 VOLUME 45 | NUMBER 8 | AUGUST 2013 Nature GeNetics A r t i c l e s plant A. thaliana 24 ; (ii) Arabidopsis lyrata, a congener of A. thaliana with a more ancestral karyotype and genome size 25 ; (iii) Capsella rubella, which falls in the sister group to the genus Arabidopsis 26 ; (iv) Brassica rapa (Chinese cabbage 27 ), one of the several closely related Brassica crop species in the tribe Brassiceae that share a recent genome triplication event (Br-α) 28 ; (v) Eutrema salsugineum (previously Thellungiella halophila) of the tribe Eutremeae, an extremophile adapted to saline habitats 29 ; and (vi) Schrenkiella parvula (previously Thellungiella parvula) 30 , another extremophile of uncertain tribal placement.…”

Section: A R T I C L E Smentioning

confidence: 99%

An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions

et al. 2013

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Despite the central importance of noncoding DNA to gene regulation and evolution, understanding of the extent of selection on plant noncoding DNA remains limited compared to that of other organisms. Here we report sequencing of genomes from three Brassicaceae species (Leavenworthia alabamica, Sisymbrium irio and Aethionema arabicum) and their joint analysis with six previously sequenced crucifer genomes. Conservation across orthologous bases suggests that at least 17% of the Arabidopsis thaliana genome is under selection, with nearly one-quarter of the sequence under selection lying outside of coding regions. Much of this sequence can be localized to approximately 90,000 conserved noncoding sequences (CNSs) that show evidence of transcriptional and post-transcriptional regulation. Population genomics analyses of two crucifer species, A. thaliana and Capsella grandiflora, confirm that most of the identified CNSs are evolving under medium to strong purifying selection. Overall, these CNSs highlight both similarities and several key differences between the regulatory DNA of plants and other species.

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The ABC's of comparative genomics in the Brassicaceae: building blocks of crucifer genomes

Cited by 515 publications

References 52 publications

Karyotype and Identification of All Homoeologous Chromosomes of AllopolyploidBrassica napusand Its Diploid Progenitors

Karyotype and Identification of All Homoeologous Chromosomes of AllopolyploidBrassica napusand Its Diploid Progenitors

Splicing Variation at a FLOWERING LOCUS C Homeolog Is Associated With Flowering Time Variation in the Tetraploid Capsella bursa-pastoris

An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions

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