Comparisons of pollen coat genes across Brassicaceae species reveal rapid evolution by repeat expansion and diversification. (1/26)

Reproductive genes and traits evolve rapidly in many organisms, including mollusks, algae, and primates. Previously we demonstrated that a family of glycine-rich pollen surface proteins (GRPs) from Arabidopsis thaliana and Brassica oleracea had diverged substantially, making identification of homologous genes impossible despite a separation of only 20 million years. Here we address the molecular genetic mechanisms behind these changes, sequencing the eight members of the GRP cluster, along with 11 neighboring genes in four related species, Arabidopsis arenosa, Olimarabidopsis pumila, Capsella rubella, and Sisymbrium irio. We found that GRP genes change more rapidly than their neighbors; they are more repetitive and have undergone substantially more insertion/deletion events while preserving repeat amino acid composition. Genes flanking the GRP cluster had an average K(a)/K(s) approximately 0.2, indicating strong purifying selection. This ratio rose to approximately 0.5 in the first GRP exon, indicating relaxed selective constraints. The repetitive nature of the second GRP exon makes alignment difficult; even so, K(a)/K(s) within the Arabidopsis genus demonstrated an increase that correlated with exon length. We conclude that rapid GRP evolution is primarily due to duplication, deletion, and divergence of repetitive sequences. GRPs may mediate pollen recognition and hydration by female cells, and divergence of these genes could correlate with or even promote speciation. We tested cross-species interactions, showing that the ability of A. arenosa stigmas to hydrate pollen correlated with GRP divergence and identifying A. arenosa as a model for future studies of pollen recognition.  (+info)

The Arabidopsis genome sequence as a tool for genome analysis in Brassicaceae. A comparison of the Arabidopsis and Capsella rubella genomes. (2/26)

The annotated Arabidopsis genome sequence was exploited as a tool for carrying out comparative analyses of the Arabidopsis and Capsella rubella genomes. Comparison of a set of random, short C. rubella sequences with the corresponding sequences in Arabidopsis revealed that aligned protein-coding exon sequences differ from aligned intron or intergenic sequences in respect to the degree of sequence identity and the frequency of small insertions/deletions. Molecular-mapped markers and expressed sequence tags derived from Arabidopsis were used for genetic mapping in a population derived from an interspecific cross between Capsella grandiflora and C. rubella. The resulting eight Capsella linkage groups were compared to the sequence maps of the five Arabidopsis chromosomes. Fourteen colinear segments spanning approximately 85% of the Arabidopsis chromosome sequence maps and 92% of the Capsella genetic linkage map were detected. Several fusions and fissions of chromosomal segments as well as large inversions account for the observed arrangement of the 14 colinear blocks in the analyzed genomes. In addition, evidence for small-scale deviations from genome colinearity was found. Colinearity between the Arabidopsis and Capsella genomes is more pronounced than has been previously reported for comparisons between Arabidopsis and different Brassica species.  (+info)

Isolation and molecular characterization of a new CRT binding factor gene from Capsella bursa-pastoris. (3/26)

A new CRT binding factor (CBF) gene designated Cbcbf25 was cloned from Capsella bursa-pastoris, a wild grass, by the rapid amplification of cDNA ends (RACE). The full-length cDNA of Cbcbf25 was 898 bp with a 669 bp open reading frame (ORF) encoding a putative DRE/CRT (LTRE)-binding protein of 223 amino acids. The predicted CbCBF25 protein contained a potential nuclear localization signal (NLS) in its N-terminal region followed by an AP2 DNA-binding motif and a possible acidic activation domain in the C-terminal region. Bioinformatic analysis revealed that Cbcbf25 has a high level of similarity with other CBF genes like cbf1, cbf2, and cbf3 from Arabidopsis thaliana, and Bncbf5, Bncbf7, Bncbf16, and Bncbf17 from Brassica napus. A cold acclimation assay showed that Cbcbf25 was expressed immediately after cold triggering, but this expression was transient, suggesting that it concerns cold acclimation. Our study implies that Cbcbf25 is an analogue of other CBF genes and may participate in cold-response, by for example, controlling the expression of cold-regulated genes or increasing the freezing tolerance of plants.  (+info)

Comparative genome analyses of Arabidopsis spp.: inferring chromosomal rearrangement events in the evolutionary history of A. thaliana. (4/26)

Comparative genome analysis is a powerful tool that can facilitate the reconstruction of the evolutionary history of the genomes of modern-day species. The model plant Arabidopsis thaliana with its n = 5 genome is thought to be derived from an ancestral n = 8 genome. Pairwise comparative genome analyses of A. thaliana with polyploid and diploid Brassicaceae species have suggested that rapid genome evolution, manifested by chromosomal rearrangements and duplications, characterizes the polyploid, but not the diploid, lineages of this family. In this study, we constructed a low-density genetic linkage map of Arabidopsis lyrata ssp. lyrata (A. l. lyrata; n = 8, diploid), the closest known relative of A. thaliana (MRCA approximately 5 Mya), using A. thaliana-specific markers that resolve into the expected eight linkage groups. We then performed comparative Bayesian analyses using raw mapping data from this study and from a Capsella study to infer the number and nature of rearrangements that distinguish the n = 8 genomes of A. l. lyrata and Capsella from the n = 5 genome of A. thaliana. We conclude that there is strong statistical support in favor of the parsimony scenarios of 10 major chromosomal rearrangements separating these n = 8 genomes from A. thaliana. These chromosomal rearrangement events contribute to a rate of chromosomal evolution higher than previously reported in this lineage. We infer that at least seven of these events, common to both sets of data, are responsible for the change in karyotype and underlie genome reduction in A. thaliana.  (+info)

Evolution of the self-incompatibility system in the Brassicaceae: identification of S-locus receptor kinase (SRK) in self-incompatible Capsella grandiflora. (5/26)

Self-incompatibility (SI) has been well studied in the genera Brassica and Arabidopsis, which have become models for investigation into the SI system. To understand the evolution of the SI system in the Brassicaceae, comparative analyses of the S-locus in genera other than Brassica and Arabidopsis are necessary. We report the identification of six putative S-locus receptor kinase genes (SRK) in natural populations of Capsella grandiflora, an SI species from a genus which is closely related to Arabidopsis. These S-alleles display striking similarities to the Arabidopsis lyrata SRK alleles in sequence and structure. Our phylogenetic analysis supports the scenario of differing SI evolution along the two lineages (The Brassica lineage and Arabidopsis/Capsella lineage). Our results also argue that the ancestral S-locus lacked the SLG gene (S-locus glycoprotein) and that the diversification of S-alleles predates the separation of Arabidopsis and Capsella.  (+info)

Catching a 'hopeful monster': shepherd's purse (Capsella bursa-pastoris) as a model system to study the evolution of flower development. (6/26)

Capsella is a small genus within the mustard family (Brassicaceae). Its three species, however, show many evolutionary trends also observed in other Brassicaceae (including Arabidopsis) and far beyond, including transitions from a diploid, self-incompatible, obligatory outcrossing species with comparatively large and attractive flowers but a restricted distribution to a polyploid, self-compatible, predominantly selfing, invasive species with floral reductions. All these evolutionary transitions may have contributed to the fact that Capsella bursa-pastoris (shepherd's purse) has become one of the most widely distributed flowering plants on our planet. In addition, Capsella bursa-pastoris shows a phenomenon that, although rare, could be of great evolutionary importance, specifically the occurrence of a homeotic variety found in relatively stable populations in the wild. Several lines of evidence suggest that homeotic changes played a considerable role in floral evolution, but how floral homeotic varieties are established in natural populations has remained a highly controversial topic among evolutionary biologists. Due to its close relationship with the model plant Arabidopsis thaliana, numerous experimental tools are available for studying the genus Capsella, and further tools are currently being developed. Hence, Capsella provides great opportunities to investigate the evolution of flower development from molecular developmental genetics to field ecology and biogeography, and from morphological refinements to major structural transitions.  (+info)

Epigenetic mechanisms for breakdown of self-incompatibility in interspecific hybrids. (7/26)

As a major agent of rapid speciation, interspecific hybridization has played an important role in plant evolution. When hybridization involves species that exhibit self-incompatibility (SI), this prezygotic barrier to self-fertilization must be overcome or lost to allow selfing. How SI, a normally dominant trait, is lost in nascent hybrids is not known, however. Here we demonstrate that hybrid self-fertility can result from epigenetic changes in expression of the S-locus genes that determine specificity in the SI response. We analyzed loss of SI in synthetic hybrids produced by crossing self-fertile and self-incompatible species in each of two crucifer genera. We show that SI is lost in the stigmas of A. thaliana-lyrata hybrids and their neo-allotetraploid derivatives and in the pollen of C. rubella-grandiflora hybrids and their homoploid progenies. Aberrant processing of S-locus receptor kinase gene transcripts as detected in Arabidopsis hybrids and suppression of the S-locus cysteine-rich protein gene as observed in Capsella hybrids are two reversible mechanisms by which SI might break down upon interspecific hybridization to generate self-fertile hybrids in nature.  (+info)

Differential expression of genes important for adaptation in Capsella bursa-pastoris (Brassicaceae). (8/26)

Understanding the genetic basis of natural variation is of primary interest for evolutionary studies of adaptation. In Capsella bursa-pastoris, a close relative of Arabidopsis (Arabidopsis thaliana), variation in flowering time is correlated with latitude, suggestive of an adaptation to photoperiod. To identify pathways regulating natural flowering time variation in C. bursa-pastoris, we have studied gene expression differences between two pairs of early- and late-flowering C. bursa-pastoris accessions and compared their response to vernalization. Using Arabidopsis microarrays, we found a large number of significant differences in gene expression between flowering ecotypes. The key flowering time gene FLOWERING LOCUS C (FLC) was not differentially expressed prior to vernalization. This result is in contrast to those in Arabidopsis, where most natural flowering time variation acts through FLC. However, the gibberellin and photoperiodic flowering pathways were significantly enriched for gene expression differences between early- and late-flowering C. bursa-pastoris. Gibberellin biosynthesis genes were down-regulated in late-flowering accessions, whereas circadian core genes in the photoperiodic pathway were differentially expressed between early- and late-flowering accessions. Detailed time-series experiments clearly demonstrated that the diurnal rhythm of CIRCADIAN CLOCK-ASSOCIATED1 (CCA1) and TIMING OF CAB EXPRESSION1 (TOC1) expression differed between flowering ecotypes, both under constant light and long-day conditions. Differential expression of flowering time genes was biologically validated in an independent pair of flowering ecotypes, suggesting a shared genetic basis or parallel evolution of similar regulatory differences. We conclude that genes involved in regulation of the circadian clock, such as CCA1 and TOC1, are strong candidates for the evolution of adaptive flowering time variation in C. bursa-pastoris.  (+info)

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