Showing papers by "Alex Widmer published in 2011"

Plant centromeric retrotransposons: a structural and cytogenetic perspective

Abstract: Background The centromeric and pericentromeric regions of plant chromosomes are colonized by Ty3/gypsy retrotransposons, which, on the basis of their reverse transcriptase sequences, form the chromovirus CRM clade. Despite their potential importance for centromere evolution and function, they have remained poorly characterized. In this work, we aimed to carry out a comprehensive survey of CRM clade elements with an emphasis on their diversity, structure, chromosomal distribution and transcriptional activity.

Genetic analysis of post-mating reproductive barriers in hybridizing European Populus species

Abstract: Molecular genetic analyses of experimental crosses provide important information on the strength and nature of post-mating barriers to gene exchange between divergent populations, which are topics of great interest to evolutionary geneticists and breeders. Although not a trivial task in long-lived organisms such as trees, experimental interspecific recombinants can sometimes be created through controlled crosses involving natural F1's. Here, we used this approach to understand the genetics of post-mating isolation and barriers to introgression in Populus alba and Populus tremula, two ecologically divergent, hybridizing forest trees. We studied 86 interspecific backcross (BC1) progeny and >350 individuals from natural populations of these species for up to 98 nuclear genetic markers, including microsatellites, indels and single nucleotide polymorphisms, and inferred the origin of the cytoplasm of the cross with plastid DNA. Genetic analysis of the BC1 revealed extensive segregation distortions on six chromosomes, and >90% of these (12 out of 13) favored P. tremula donor alleles in the heterospecific genomic background. Since selection was documented during early diploid stages of the progeny, this surprising result was attributed to epistasis, cyto-nuclear coadaptation, heterozygote advantage at nuclear loci experiencing introgression or a combination of these. Our results indicate that gene flow across ‘porous' species barriers affects these poplars and aspens beyond neutral, Mendelian expectations and suggests the mechanisms responsible. Contrary to expectations, the Populus sex determination region is not protected from introgression. Understanding the population dynamics of the Populus sex determination region will require tests based on natural interspecific hybrid zones.

Comparative high-throughput transcriptome sequencing and development of SiESTa, the Silene EST annotation database

Abstract: The genus Silene is widely used as a model system for addressing ecological and evolutionary questions in plants, but advances in using the genus as a model system are impeded by the lack of available resources for studying its genome. Massively parallel sequencing cDNA has recently developed into an efficient method for characterizing the transcriptomes of non-model organisms, generating massive amounts of data that enable the study of multiple species in a comparative framework. The sequences generated provide an excellent resource for identifying expressed genes, characterizing functional variation and developing molecular markers, thereby laying the foundations for future studies on gene sequence and gene expression divergence. Here, we report the results of a comparative transcriptome sequencing study of eight individuals representing four Silene and one Dianthus species as outgroup. All sequences and annotations have been deposited in a newly developed and publicly available database called SiESTa, the Silene EST annotation database. A total of 1,041,122 EST reads were generated in two runs on a Roche GS-FLX 454 pyrosequencing platform. EST reads were analyzed separately for all eight individuals sequenced and were assembled into contigs using TGICL. These were annotated with results from BLASTX searches and Gene Ontology (GO) terms, and thousands of single-nucleotide polymorphisms (SNPs) were characterized. Unassembled reads were kept as singletons and together with the contigs contributed to the unigenes characterized in each individual. The high quality of unigenes is evidenced by the proportion (49%) that have significant hits in similarity searches with the A. thaliana proteome. The SiESTa database is accessible at http://www.siesta.ethz.ch . The sequence collections established in the present study provide an important genomic resource for four Silene and one Dianthus species and will help to further develop Silene as a plant model system. The genes characterized will be useful for future research not only in the species included in the present study, but also in related species for which no genomic resources are yet available. Our results demonstrate the efficiency of massively parallel transcriptome sequencing in a comparative framework as an approach for developing genomic resources in diverse groups of non-model organisms.

Introgression in peripheral populations and colonization shape the genetic structure of the coastal shrub Armeria pungens

Abstract: The coastal shrub Armeria pungens has a disjunct Atlantic-Mediterranean distribution. The historic range expansion underlying this distribution was investigated using the nuclear internal transcribed spacer region, three plastid regions (namely trnL-F, trnS-fM and matK) and morphometric data. A highly diverse ancestral lineage was identified in southwest Portugal. More recently, two areas have been colonized: (1) Corsica and Sardinia, where disjunct Mediterranean populations have been established as a result of the long-distance dispersal of Portuguese genotypes, and (2) the southern part of the Atlantic range, Gulf of Cadiz, where a distinct lineage showing no genetic differentiation among populations occurs. Genetic consequences of colonization seem to have been more severe in the Gulf of Cadiz than in Corsica-Sardinia. Although significant genetic divergence is associated with low plastid diversity in the Gulf of Cadiz, in Corsica-Sardinia, the loss of plastid haplotypes was not accompanied by divergence from disjunct Portuguese source populations. In addition, in its northernmost and southernmost populations, A. pungens exhibited evidence for ancient or ongoing introgression from sympatric congeners. Introgression might have created novel genotypes able to expand beyond the latitudinal margins of the species or, alternatively, these genotypes may be the result of surfing of alleles from other species in demographic equilibrium into peripheral populations of A. pungens. Our results highlight the evolutionary significance of genetic drift following the colonization of new areas and the key role of introgression in range expansion.