PoMaMo—a comprehensive database for potato genome data

A database for potato genome data (PoMaMo, Potato Maps and More) was established. The database contains molecular maps of all twelve potato chromosomes with about 1000 mapped elements, sequence data, putative gene functions, results from BLAST analysis, SNP and InDel information from different diploid and tetraploid potato genotypes, publication references, links to other public databases like GenBank (http://www.ncbi.nlm.nih.gov/) or SGN (Solanaceae Genomics Network, http://www.sgn.cornell.edu/), etc. Flexible search and data visualization interfaces enable easy access to the data via internet (https://gabi.rzpd.de/PoMaMo.html). The Java servlet tool YAMB (Yet Another Map Browser) was designed to interactively display chromosomal maps. Maps can be zoomed in and out, and detailed information about mapped elements can be obtained by clicking on an element of interest. The GreenCards interface allows a text-based data search by marker-, sequence- or genotype name, by sequence accession number, gene function, BLAST Hit or publication reference. The PoMaMo database is a comprehensive database for different potato genome data, and to date the only database containing SNP and InDel data from diploid and tetraploid potato genotypes

On the Importance of Being Ernst Mayr: “Darwin's apostle” died at the age of 100

Ernst Mayr lived for a century and accomplished more than several lifetimes worth of science in different biological disciplines, most notably evolutionary biology. Axel Meyer reflects on this remarkable ma

Conservation and co-option in developmental programmes: the importance of homology relationships

One of the surprising insights gained from research in evolutionary developmental biology (evo-devo) is that increasing diversity in body plans and morphology in organisms across animal phyla are not reflected in similarly dramatic changes at the level of gene composition of their genomes. For instance, simplicity at the tissue level of organization often contrasts with a high degree of genetic complexity. Also intriguing is the observation that the coding regions of several genes of invertebrates show high sequence similarity to those in humans. This lack of change (conservation) indicates that evolutionary novelties may arise more frequently through combinatorial processes, such as changes in gene regulation and the recruitment of novel genes into existing regulatory gene networks (co-option), and less often through adaptive evolutionary processes in the coding portions of a gene. As a consequence, it is of great interest to examine whether the widespread conservation of the genetic machinery implies the same developmental function in a last common ancestor, or whether homologous genes acquired new developmental roles in structures of independent phylogenetic origin. To distinguish between these two possibilities one must refer to current concepts of phylogeny reconstruction and carefully investigate homology relationships. Particularly problematic in terms of homology decisions is the use of gene expression patterns of a given structure. In the future, research on more organisms other than the typical model systems will be required since these can provide insights that are not easily obtained from comparisons among only a few distantly related model species

Implementing large genomic single nucleotide polymorphism data sets in phylogenetic network reconstructions: A case study of particularly rapid radiations of cichlid fish

The Midas cichlids of the Amphilophus citrinellus spp. species complex from Nicaragua (13 species) are an extraordinary example of adaptive and rapid radiation (⁠37K SNPs from 19 ingroup lineages) and present estimated phylogenetic networks for this extremely young and fast-evolving radiation of cichlid fish. We demonstrate that the MSNC is more appropriate than the multispecies coalescent alone for the analysis of this rapid radiation.Fil: Olave, Melisa. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto Argentino de Investigaciones de las Zonas Áridas. Provincia de Mendoza. Instituto Argentino de Investigaciones de las Zonas Áridas. Universidad Nacional de Cuyo. Instituto Argentino de Investigaciones de las Zonas Áridas; Argentina. University of Konstanz; AlemaniaFil: Meyer, Axel. University Of Konstanz; Alemani

Phylogenomic analyses of KCNA gene clusters in vertebrates: why do gene clusters stay intact?

<p>Abstract</p> <p>Background</p> <p>Gene clusters are of interest for the understanding of genome evolution since they provide insight in large-scale duplications events as well as patterns of individual gene losses. Vertebrates tend to have multiple copies of gene clusters that typically are only single clusters or are not present at all in genomes of invertebrates. We investigated the genomic architecture and conserved non-coding sequences of vertebrate <it>KCNA </it>gene clusters. <it>KCNA </it>genes encode shaker-related voltage-gated potassium channels and are arranged in two three-gene clusters in tetrapods. Teleost fish are found to possess four clusters. The two tetrapod <it>KNCA </it>clusters are of approximately the same age as the <it>Hox </it>gene clusters that arose through duplications early in vertebrate evolution. For some genes, their conserved retention and arrangement in clusters are thought to be related to regulatory elements in the intergenic regions, which might prevent rearrangements and gene loss. Interestingly, this hypothesis does not appear to apply to the <it>KCNA </it>clusters, as too few conserved putative regulatory elements are retained.</p> <p>Results</p> <p>We obtained <it>KCNA </it>coding sequences from basal ray-finned fishes (sturgeon, gar, bowfin) and confirmed that the duplication of these genes is specific to teleosts and therefore consistent with the fish-specific genome duplication (FSGD). Phylogenetic analyses of the genes suggest a basal position of the only intron containing <it>KCNA </it>gene in vertebrates (<it>KCNA7</it>). Sistergroup relationships of <it>KCNA1/2 </it>and <it>KCNA3/6 </it>support that a large-scale duplication gave rise to the two clusters found in the genome of tetrapods. We analyzed the intergenic regions of <it>KCNA </it>clusters in vertebrates and found that there are only a few conserved sequences shared between tetrapods and teleosts or between paralogous clusters. The orthologous teleost clusters, however, show sequence conservation in these regions.</p> <p>Conclusion</p> <p>The lack of overall conserved sequences in intergenic regions suggests that there are either other processes than regulatory evolution leading to cluster conservation or that the ancestral regulatory relationships among genes in <it>KCNA </it>clusters have been changed together with their regulatory sites.</p

Phylogeography, colonization and population history of the Midas cichlid species complex (Amphilophus spp.) in the Nicaraguan crater lakes

<p>Abstract</p> <p>Background</p> <p>Elucidation of the mechanisms driving speciation requires detailed knowledge about the phylogenetic relationships and phylogeography of the incipient species within their entire ranges as well as their colonization history. The Midas cichlid species complex <it>Amphilophus </it>spp. has been proven to be a powerful model system for the study of ecological specialization, sexual selection and the mechanisms of sympatric speciation. Here we present a comprehensive and integrative phylogeographic analysis of the complete Midas Cichlid species complex in Nicaragua (> 2000 individuals) covering the entire distributional range, using two types of molecular markers (the mitochondrial DNA control region and 15 microsatellites). We investigated the majority of known lake populations of this species complex and reconstructed their colonization history in order to distinguish between alternative speciation scenarios.</p> <p>Results</p> <p>We found that the large lakes contain older and more diverse Midas Cichlid populations, while all crater lakes hold younger and genetically less variable species assemblages. The large lakes appear to have repeatedly acted as source populations for all crater lakes, and our data indicate that faunal exchange among crater lakes is extremely unlikely. Despite their very recent (often only a few thousand years old) and common origin from the two large Nicaraguan lakes, all crater lake Midas Cichlid radiations underwent independent, but parallel, evolution, and comprise distinct genetic units. Indeed several of these crater lakes contain multiple genetically distinct incipient species that most likely arose through sympatric speciation. Several crater lake radiations can be traced back to a single ancestral line, but some appear to have more than one founding lineage. The timing of the colonization(s) of each crater lake differs, although most of them occurred more (probably much more) recently than 20,000 years ago.</p> <p>Conclusion</p> <p>The genetic differentiation of the crater lake populations is directly related to the number of founding lineages, but independent of the timing of colonization. Interestingly, levels of phenotypic differentiation, and speciation events, appeared independent of both factors.</p

Fragile DNA contributes to repeated evolution

Sequence features that affect DNA fragility might facilitate fast, repeated evolution by elevating mutation rates at genomic hotspots.Non peer reviewe

Divergent allometric trajectories in gene expression and coexpression produce species differences in sympatrically speciating Midas cichlid fish

The mechanisms of speciation without geographic isolation (i.e., sympatric speciation) remain debated. This is due in part to the fact that the genomic landscape that could promote or hinder species divergence in the presence of gene flow is still largely unknown. However, intensive research is now centered on understanding the genetic architecture of adaptive traits associated with this process as well as how gene expression might affect these traits. Here, using RNAseq data, we investigated gene expression of sympatrically speciating benthic and limnetic Neotropical cichlid fishes at two developmental stages. First, we identified groups of co-expressed genes (modules) at each stage. While there are a few large and well-preserved modules, most of the other modules are not preserved across life stages. Second, we show that later in development more and larger co-expression modules are associated with divergence between benthic and limnetic fish compared to the earlier life stage. This divergence between benthic and limnetic fish in co-expression mirrors divergence in overall expression between benthic and limnetic fish, which is more pronounced later in life. Our results reveal that already at one-day post-hatch benthic and limnetic fish diverge in (co)expression, and that this divergence becomes more substantial when fish are free-swimming but still unlikely to have divergent swimming and feeding habits. More importantly, our study describes how the co-expression of several genes through development, as opposed to individual genes, is associated with benthic-limnetic species differences, and how two morphogenetic trajectories diverge as fish grow older.publishe