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 ∼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.[Supplemental material is available online at www.genome.org. The following individuals kindly provided reagents, samples, or unpublished information as indicated in the paper: C. Langley.]Comparative genome analysis can be a powerful tool to address questions pertaining to the evolution of the structure of genomes (Paterson and Bennetzen 2001). In plant families that include model taxa, such as the Brassicaceae, the Solanaceae, and the Poaceae, comparative mapping studies allow evolutionary inferences related to the nature and number of rearrangements that distinguish the genomes of the model species from those of their less well-studied relatives (Bonierbale et al. 1988;Ahn and Tanksley 1993;Prince et al. 1993;Chittendan et al. 1994;Kurata et al. 1994;Periera et al. 1994;Lagercrantz and Lydiate 1996;Gale and Devos 1998;Lagercrantz 1998;Doganlar et al. 2002). Not only do such inferences facilitate the transfer of knowledge from model taxa to their relatives, but they also provide insight into the process of genome restructuring that can lead to reproductive isolation and ultimately speciation (Rieseberg 2001;Hall et al. 2002). The larger the number of taxa analyzed within a family, the more comprehensive the information is for inferring the nature of ancestral genomes and the evolutionary history that led to the speciation of the members of that family.The Brassicaceae (or Cruciferae) is a dicot family divided into 13 tribes with a total of 360 genera (Al-Shehbaz 1973) including th...
Models of codon substitution are developed that incorporate physicochemical properties of amino acids. When amino acid sites are inferred to be under positive selection, these models suggest the nature and extent of the physicochemical properties selected for. This is accomplished by first partitioning the codons based on some property of the amino acids they code for, and then using this partition to parametrize the rates of property-conserving and property-altering base substitutions at the codon level by means of finite mixtures of Markov models that also account for codon and transition:transversion biases. Here, we apply this method to two positively-selected receptors involved in ligand-recognition; the class-I alleles of the human Major Histocompatibility Complex (MHC) of known structure and the S-locus Receptor Kinase (SRK) of the sporophytic self-incompatibility system (SSI) in cruciferous plants (Brassicaceae), whose structure is unknown. Through likelihood ratio tests we demonstrate that the positively selected MHC and SRK proteins are under physico-
It is estimated that 5 million years of evolution separate Arabidopsis thaliana from its close relative Arabidopsis lyrata. The two taxa differ by many characteristics, and together they exemplify the differentiation of angiosperms into self-fertilizing and cross-fertilizing species as well as annual and perennial species. Despite their disparate life histories, the two species can be crossed to produce viable and vigorous hybrids exhibiting heterotic effects. Although pollen sterile, the hybrids produce viable ovules and were used as female parent in backcrosses to both parental species. The resulting backcross plants exhibited transgressive variation for a number of interesting developmental and growth traits as well as negative nuclear/ cytoplasmic interactions. Moreover, the genesis of a fertile amphidiploid neospecies, apparently by spontaneous somatic doubling in an interspecific hybrid, was observed in the laboratory. The mechanisms responsible for the generation of amphiploids and the subsequent evolution of amphiploid genomes can now be studied through direct observation using the large arsenal of molecular tools available for Arabidopsis.Plant growth and development have traditionally been studied by generating relevant mutations or by analyzing naturally occurring variants within a species. In only a few cases has the tremendous interspecies variation that was generated over the millions of years of evolution been used. In recent years, it has been increasingly recognized that natural variability is a major resource that could complement traditional approaches. Thus, in the model plant Arabidopsis, intraspecific genetic variation has been noted among different geographical isolates, and this variation, which is largely quantitative in nature, is being subjected to analytical methods developed for the analysis of quantitative trait loci in crop plants (for review, see Alonso-Blanco and Koornneef, 2000). However, the enormous store of natural variation that is manifest in interspecies differences has remained largely untapped.Wide crosses and interspecific hybridizations have been used to investigate the genetic basis of complex traits that differentiate varieties within a species as well as related species in several plant families (Doebley et al
No abstract
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
hi@scite.ai
10624 S. Eastern Ave., Ste. A-614
Henderson, NV 89052, USA
Copyright © 2024 scite LLC. All rights reserved.
Made with 💙 for researchers
Part of the Research Solutions Family.