A high density physical map of chromosome 1BL supports evolutionary studies,map-based cloning and sequencing in wheat

Background

As for other major crops, achieving a complete wheat genome sequence is essential for the application of genomics to breeding new and improved varieties. To overcome the complexities of the large, highly repetitive and hexaploid wheat genome, the International Wheat Genome Sequencing Consortium established a chromosome-based strategy that was validated by the construction of the physical map of chromosome 3B. Here, we present improved strategies for the construction of highly integrated and ordered wheat physical maps, using chromosome 1BL as a template, and illustrate their potential for evolutionary studies and map-based cloning.

Results

Using a combination of novel high throughput marker assays and an assembly program, we developed a high quality physical map representing 93% of wheat chromosome 1BL, anchored and ordered with 5,489 markers including 1,161 genes. Analysis of the gene space organization and evolution revealed that gene distribution and conservation along the chromosome results from the superimposition of the ancestral grass and recent wheat evolutionary patterns, leading to a peak of synteny in the central part of the chromosome arm and an increased density of non-collinear genes towards the telomere. With a density of about 11 markers per Mb, the 1BL physical map provides 916 markers, including 193 genes, for fine mapping the 40 QTLs mapped on this chromosome.

Conclusions

Here, we demonstrate that high marker density physical maps can be developed in complex genomes such as wheat to accelerate map-based cloning, gain new insights into genome evolution, and provide a foundation for reference sequencing.     

Evaluation and classification of RING-finger domains encoded by the <Emphasis Type="Italic">Arabidopsis</Emphasis> genome

Background

In computational analysis, the RING-finger domain is one of the most frequently detected domains in the Arabidopsis proteome. In fact, it is more abundant in Arabidopsis than in other eukaryotic genomes. However, computational analysis might classify ambiguous domains of the closely related PHD and LIM motifs as RING domains by mistake. Thus, we set out to define an ordered set of Arabidopsis RING domains by evaluating predicted domains on the basis of recent structural data.

Results

Inspection of the proteome with a current InterPro release predicts 446 RING domains. We evaluated each detected domain and as a result eliminated 59 false positives. The remaining 387 domains were grouped by cluster analysis and according to their metal-ligand arrangement. We further defined novel patterns for additional computational analyses of the proteome. They were based on recent structural data that enable discrimination between the related RING, PHD and LIM domains. These patterns allow us to predict with different degrees of certainty whether a particular domain is indeed likely to form a RING finger.

Conclusions

In summary, 387 domains have a significant potential to form a RING-type cross-brace structure. Many of these RING domains overlap with predicted PHD domains; however, the RING domain signature mostly prevails. Thus, the abundance of PHD domains in Arabidopsis has been significantly overestimated. Cluster analysis of the RING domains defines groups of proteins, which frequently show significant similarity outside the RING domain. These groups document a common evolutionary origin of their members and potentially represent genes of overlapping functionality.

     

Adaptive phosphate uptake behaviour of phytoplankton to environmental phosphate fluctuations

When phytoplankton growth in lakes is limited by the available phosphate, the external phosphate concentration fluctuates around a threshold value at which available energy is insufficient to drive phosphate incorporation into a polyphosphate pool. As a result, occasional increases in the external concentration are experienced by phytoplankton as a series of phosphate pulses. Based on [(32) P] phosphate uptake experiments with lake phytoplankton, we show that a community is able to process information about the experienced pattern of phosphate pulses via a complex regulation of the kinetic and energetic properties of cellular phosphate uptake systems. As a result, physiological adaptation to alterations of ambient phosphate concentration depends on the pattern of phosphate fluctuations to which the community had been exposed during its previous growth. In this process, the entire community exhibits coherent uptake behaviour with respect to a common threshold value. Thereby, different threshold values result from different antecedent pulse patterns, apparently unrestrained by the amount of previously stored phosphate. The coherent behaviour observed contradicts the basic assumptions of the competitive exclusion principle and provides an alternative perspective for explaining the paradoxical coexistence of many phytoplankton species.     

Distribution,functional impact,and origin mechanisms of copy number variation in the barley genome

Background

There is growing evidence for the prevalence of copy number variation (CNV) and its role in phenotypic variation in many eukaryotic species. Here we use array comparative genomic hybridization to explore the extent of this type of structural variation in domesticated barley cultivars and wild barleys.

Results

A collection of 14 barley genotypes including eight cultivars and six wild barleys were used for comparative genomic hybridization. CNV affects 14.9% of all the sequences that were assessed. Higher levels of CNV diversity are present in the wild accessions relative to cultivated barley. CNVs are enriched near the ends of all chromosomes except 4H, which exhibits the lowest frequency of CNVs. CNV affects 9.5% of the coding sequences represented on the array and the genes affected by CNV are enriched for sequences annotated as disease-resistance proteins and protein kinases. Sequence-based comparisons of CNV between cultivars Barke and Morex provided evidence that DNA repair mechanisms of double-strand breaks via single-stranded annealing and synthesis-dependent strand annealing play an important role in the origin of CNV in barley.

Conclusions

We present the first catalog of CNVs in a diploid Triticeae species, which opens the door for future genome diversity research in a tribe that comprises the economically important cereal species wheat, barley, and rye. Our findings constitute a valuable resource for the identification of CNV affecting genes of agronomic importance. We also identify potential mechanisms that can generate variation in copy number in plant genomes.     

Tropical Asian species show that the Old World clade of ‘spiny solanums’ (Solanum subgenus Leptostemonum pro parte: Solanaceae) is not monophyletic

The tropical Asian taxa of the species‐rich genus Solanum (Solanaceae) have been less well studied than their highly diverse New World relatives. Most of these tropical Asian species, including the cultivated brinjal eggplant/aubergine and its wild progenitor, are part of the largest monophyletic Solanum lineage, the ‘spiny solanums’ (subgenus Leptostemonum or the Leptostemonum clade). Here we present the first phylogenetic analysis of spiny solanums that includes broad sampling of the tropical Asian species, with 42 of the 56 currently recognized species represented. Two nuclear and three plastid regions [internal transcribed spacer (ITS), waxy, ndhF‐rpL32, trnS‐trnG and trnT‐trnF] were amplified and used to reconstruct phylogenetic relationships using maximum likelihood and Bayesian methods. Our analyses show that Old World spiny solanums do not resolve in a single clade, but are part of three unrelated lineages, suggesting at least three independent introductions from the New World. We identify and describe several monophyletic groups in Old World solanums that have not been previously recognized. Some of these lineages are coherent in terms of morphology and geography, whereas others show considerable morphological variation and enigmatic distribution patterns. Tropical Asia occupies a key position in the biogeography of Old World spiny solanums, with tropical Asian taxa resolved as the closest relatives of diverse groups of species from Australia and Africa.     

Molecular phylogenetics of Sarcolaenaceae (Malvales), Madagascar's largest endemic plant family

With 72 species belonging to ten genera, Sarcolaenaceae are the largest and most diverse of Madagascar's endemic plant families. Comprising shrubs and trees, with members found in nearly all of this island nation's biogeographic regions, they are characterised by the presence of a distinctive extra‐floral involucre that is more or less accrescent, partially or completely covering or enveloping the fruit. We present the first molecular phylogenetic study of Sarcolaenaceae, using broad sampling that encompasses the family's taxonomic and morphological diversity, including 46 species representing all ten genera and sequence data from one nuclear marker (ITS) and three plastid regions (psaA‐ORF170, psbA‐trnH and rbcL), to reconstruct phylogenetic relationships using Bayesian inference and maximum likelihood. Results confirm the monophyly of Sarcolaenaceae and of eight of the ten genera; the monophyly of Rhodolaena remains ambiguous, although the taxa sampled were recovered in two well supported clades that are coherent in terms of morphology and geography. Only a single species of Eremolaena was available for study. The phylogenetic backbone of Sarcolaenaceae is not fully resolved, making it difficult to identify potential morphological synapomorphies or ecological preferences between and within genera. In the family, two monophyletic groups were, however, found [Pentachlaena + Eremolaena + Perrierodendron (Clade A) and Xyloolaena + Leptolaena + Sarcolaena + Mediusella + Xerochlamys (Clade B)] that are consistent with previous results based on morphology. Expanded species sampling and data from additional, more quickly evolving markers will be needed to produce a fully resolved phylogenetic tree for Sarcolaenaceae, which could then serve as a basis for exploring macroevolutionary patterns and processes in this remarkable family and reconstructing its biogeographic history.