Genome evolution: extinction,continuation or explosion?

Darwin recognised the processes of speciation and the frequent extinction of species. We now understand many of the genome-scale processes occurring during evolution involving mutations, amplification, loss or homogenisation of DNA sequences; rearrangement, fusion and fission of chromosomes; and horizontal transfer of genes or genomes, including processes involving hybridisation and polyploidy. DNA sequence information, combined with appropriate informatic tools and experimental approaches such as generation of synthetic hybrids, comparison of genotypes across environments, and modelling of genomic responses, is now letting us link genome behaviour with its consequences. The understanding of genome evolution will be of critical value both for conservation of the biodiversity of the plant kingdom and addressing the challenges of breeding new and more sustainable crops to feed the human population.     

Allele mining in diverse accessions of tropical grasses to improve forage quality and reduce environmental impact

Background and AimsThe C₄Urochloa species (syn. Brachiaria) and Megathyrsus maximus (syn. Panicum maximum) are used as pasture for cattle across vast areas in tropical agriculture systems in Africa and South America. A key target for variety improvement is forage quality: enhanced digestibility could decrease the amount of land required per unit production, and enhanced lipid content could decrease methane emissions from cattle. For these traits, loss-of-function (LOF) alleles in known gene targets are predicted to improve them, making a reverse genetics approach of allele mining feasible. We therefore set out to look for such alleles in diverse accessions of Urochloa species and Megathyrsus maximus from the genebank collection held at the CIAT.MethodsWe studied allelic diversity of 20 target genes (11 for digestibility, nine for lipid content) in 104 accessions selected to represent genetic diversity and ploidy levels of U. brizantha, U. decumbens, U. humidicola, U. ruziziensis and M. maximum. We used RNA sequencing and then bait capture DNA sequencing to improve gene models in a U. ruziziensis reference genome to assign polymorphisms with high confidence.Key ResultsWe found 953 non-synonymous polymorphisms across all genes and accessions; within these, we identified seven putative LOF alleles with high confidence, including those in the non-redundant SDP1 and BAHD01 genes present in diploid and tetraploid accessions. These LOF alleles could respectively confer increased lipid content and digestibility if incorporated into a breeding programme.ConclusionsWe demonstrated a novel, effective approach to allele discovery in diverse accessions using a draft reference genome from a single species. We used this to find gene variants in a collection of tropical grasses that could help reduce the environmental impact of cattle production.     

Supervised Lowess normalization of comparative genome hybridization data – application to lactococcal strain comparisons

Background

Visualising the evolutionary history of a set of sequences is a challenge for molecular phylogenetics. One approach is to use undirected graphs, such as median networks, to visualise phylogenies where reticulate relationships such as recombination or homoplasy are displayed as cycles. Median networks contain binary representations of sequences as nodes, with edges connecting those sequences differing at one character; hypothetical ancestral nodes are invoked to generate a connected network which contains all most parsimonious trees. Quasi-median networks are a generalisation of median networks which are not restricted to binary data, although phylogenetic information contained within the multistate positions can be lost during the preprocessing of data. Where the history of a set of samples contain frequent homoplasies or recombination events quasi-median networks will have a complex topology. Graph reduction or pruning methods have been used to reduce network complexity but some of these methods are inapplicable to datasets in which recombination has occurred and others are procedurally complex and/or result in disconnected networks.

Results

We address the problems inherent in construction and reduction of quasi-median networks. We describe a novel method of generating quasi-median networks that uses all characters, both binary and multistate, without imposing an arbitrary ordering of the multistate partitions. We also describe a pruning mechanism which maintains at least one shortest path between observed sequences, displaying the underlying relations between all pairs of sequences while maintaining a connected graph.

Conclusion

Application of this approach to 5S rDNA sequence data from sea beet produced a pruned network within which genetic isolation between populations by distance was evident, demonstrating the value of this approach for exploration of evolutionary relationships.     

Evaluation of the Inheritance of the Complex Vertebral Malformation Syndrome by Breeding Studies

To investigate the congenital complex vertebral malformation syndrome (CVM) in Holstein calves, two breeding studies were performed including 262 and 363 cows, respectively. Cows were selected from the Danish Cattle Database based on pedigree and insemination records. Selected cows were progeny of sires with an established heterozygous CVM genotype and pregnant after insemination with semen from another sire with heterozygous CVM genotype. Following calving the breeders should state, if the calf was normal and was requested to submit dead calves for necropsy. In both studies, significantly fewer CVM affected calves than expected were obtained; a finding probably reflecting extensive intrauterine mortality in CVM affected foetuses. The findings illustrate increased intrauterine mortality as a major potential bias in observational studies of inherited disorders.     

Wheat Neocentromeres Found in F1 Triticale × Tritordeum Hybrids (AABBRH<Superscript>ch</Superscript>) After 5-Azacytidine Treatment

The DNA hypomethylation effect of 5-azacytine (5-AC; a cytosine analog) is widely known. This agent has been used for rRNA gene expression studies of Triticeae amphiploids and hybrids regarding rye rRNA genes suppression caused by the wheat nucleolar dominance phenomenon. However, this situation is reverted by 5-AC treatment which activates rye rRNA gene expression as it has been intensively observed in triticale. For nucleolar dominance studies, we produced F1 multigeneric hybrids (AABBRH^ch; 2n = 6x = 42) from crosses between the triticale cultivar ‘Corgo’ (AABBRR; 2n = 6x = 42) and the tritordeum cultivars HT9 and HT31 (AABBH^chH^ch; 2n = 6x = 42). The hybrid seeds were germinated in a low concentration of 5-AC (treatment) and in distilled water (nontreated control plants). Silver nitrate staining performed in one 5-AC-treated F1 hybrid revealed a reduced number of interphase cells with seven nucleoli, metaphases with eight Ag-NORs, and neocentromeres in the long arm of three wheat chromosomes. Nontreated hybrids presented six Ag-NORs per mitotic metaphase cell and a maximum of six nucleoli per interphase because of the 1R Ag-NOR suppression. No neocentromere was found in the control F1 hybrid plants. Both treated and nontreated seedlings were subsequently evaluated by fluorescent in situ hybridization performed with genomic and repetitive DNA probes to identify H^ch and rye genomes, to confirm Ag-NORs location, and to detect inactive rDNA loci. DAPI counterstaining was also helpful for the detection of neocentromeres in the long arm of three wheat chromosomes. This study allowed us to suggest that 5-AC treatment specifically induced wheat neocentromeres in the F1 multigeneric triticale × tritordeum hybrids.     

Different patterns in molecular evolution of the Triticeae

A huge part of the genomes of most Triticeae species is formed by different families of repetitive DNA sequences. In this paper the phylogenetic distribution of two major classes of the repeats, retrotransposons and tandemly organized DNA sequences, are considered and compared with the evolution of gene-rich regions and generally accepted Triticeae phylogenetic relationships. In Hordeum, LTR-containing retrotransposons are dispersed along the chromosomes and are consistent with the existing picture of the phylogeny of Hordeum. Another retrotransposon class, LINEs, have evolved independently from LTR-retrotransposons. Different retrotransposon classes appear to have competed for genome space during the evolution of Hordeum. Another class of repeats, tandemly organized DNA sequences, tends to cluster at the functionally important regions of chromosomes, centromeres and telomeres. The distribution of a number of tandem DNA families in Triticeae is not congruent with generally accepted phylogenetic relationships. While natural selection is the dominant factor determining the structure of genic regions we suggest that the contribution of random events is important in the evolution of repetitive DNA sequences. The interplay of stochastic processes, molecular drive, and selection determines the structure of chromosomal regions, notably at centromeres and telomeres, stabilizing and differentiating species-specific karyotypes. Thus, the evolution of these regions may occur largely independently of the evolution of gene-rich regions.     

Molecular cytogenetic analysis and centromeric satellite organization of a novel 8;11 translocation in sheep: a possible intermediate in biarmed chromosome evolution

During analysis of genome organization in sheep (Ovis aries, 2n = 54, XY/XX), we found a novel chromosomal translocation in an animal expected to be normal, adding to the six centric fusions previously reported. The translocation was identified as t(8;11) by G-banding and was shown to be centric, involving whole chromosome arms by chromosome painting with probes for Chromosomes (Chrs) 8 and 11. Satellite I and a newly isolated satellite II clone was used to characterize the centromeric regions of both the novel and the three pairs of evolutionarily derived biarmed chromosomes. The novel t(8;11) showed satellite I proximal on both arms with satellite II covering the centromere, while the evolutionarily derived fusion leading to Chrs 2 and 3 showed the opposite configuration, not obviously derived by a simple fusion. Chr 1 has lost the satellite I hybridization patterns. The novel t(8;11) provides strong evidence for an intermediate step in evolution of the biarmed chromosomes in sheep.