Preventievarkensziekten.nl

Livestock Research en de GD hebben een analysetool ontwikkeld, waarmee varkenshouders de specifieke risicofactoren voor het bedrijf in kaart kunnen brengen: www.preventievarkensziekten.nl. Deze tool kan bijdragen aan een planmatig diergezondheidmanagement, waarbij de veehouder zich bewust is van de bedrijfsrisico’s en de nadruk legt op het voorkómen van ziekten

DNA sequence evolution in fast evolving mitochondrial DNA nad1 exons in Geraniaceae and Plantaginaceae

Previously, nucleotide substitution rates in mitochondrial DNA of Geraniaceae and Plantaginaceae have been shown to be exceptionally high compared with other angiosperm mtDNA lineages. It has also been shown that mtDNA introns were lost in Geraniaceae and Plantaginaceae. In this study we compile 127 DNA sequences from two partial exons of the mtDNA nad1 gene in Geraniaceae, Plantaginaceae, and other angiosperm groups for which rate accelerations have not been reported, to assess the extent and nature of the nucleotide substitution rate acceleration. Whereas Litorella appears to have undergone a rate acceleration comparable to that observed in Plantago, the Geraniacean sister group representative Hypseocharis biloba has not, indicating that the rate change has occurred between the split of Hypseocharis and the rest of the Geraniaceae. Silent/non-silent rate ratios ¿ have decreased threefold in the "fast mtDNA" clades compared with other angiosperms, whereas their codon usage bias is around 20% lower. Absence of RNA editing in Geraniacean and Plantago mtDNA genes is confirmed. Possible causes for the exceptional substitution rate accelerations observed in these lineages are discussed in terms of the retroprocessing process or the possibility of affected mitochondrial DNA polymerase ¿ proofreading accuracy contro

Annonaceae substitution rates - a codon model perspective

The Annonaceae includes cultivated species of economic interest and represents an important source of information for better understanding the evolution of tropical rainforests. In phylogenetic analyses of DNA sequence data that are used to address evolutionary questions, it is imperative to use appropriate statistical models. Annonaceae are cases in point: Two sister clades, the subfamilies Annonoideae and Malmeoideae, contain the majority of Annonaceae species diversity. The Annonoideae generally show a greater degree of sequence divergence compared to the Malmeoideae, resulting in stark differences in branch lengths in phylogenetic trees. Uncertainty in how to interpret and analyse these differences has led to inconsistent results when estimating the ages of clades in Annonaceae using molecular dating techniques. We ask whether these differences may be attributed to inappropriate modelling assumptions in the phylogenetic analyses. Specifically, we test for (clade-specific) differences in rates of non-synonymous and synonymous substitutions. A high ratio of nonsynonymous to synonymous substitutions may lead to similarity of DNA sequences due to convergence instead of common ancestry, and as a result confound phylogenetic analyses. We use a dataset of three chloroplast genes (rbcL, matK, ndhF) for 129 species representative of the family. We find that differences in branch lengths between major clades are not attributable to different rates of non-synonymous and synonymous substitutions. The differences in evolutionary rate between the major clades of Annonaceae pose a challenge for current molecular dating techniques that should be seen as a warning for the interpretation of such results in other organisms

How to Open the Treasure Chest? Optimising DNA Extraction from Herbarium Specimens

Herbarium collections are potentially an enormous resource for DNA studies, but the use of herbarium specimens in molecular studies has thus far been slowed down by difficulty in obtaining amplifiable DNA. Here we compare a set of commercially available DNA extraction protocols and their performance in terms of DNA purity and yield, and PCR amplification success as measured by using three differentially sized markers, the rbcL barcoding marker (cpDNA), the LEAFY exon 3 (nrDNA), and the trnL(UAA) P6 loop (cpDNA). Results reveal large differences between extraction methods, where DNA purity rather than yield is shown to be strongly correlated with PCR success. Amplicon size shows similarly strong correlation with PCR success, with the shortest fragment showing the highest success rate (78%, P6 loop, 10–143 base pairs (bp)) and the largest fragment the lowest success (10%, rbcL, 670 bp). The effect of specimen preparation method on PCR success was also tested. Results show that drying method strongly affects PCR success, especially the availability of fragments longer than 250 bp, where longer fragments are more available for PCR amplification in air dried material compared to alcohol dried specimens. Results from our study indicate that projects relying on poor-quality starting material such as herbarium or scat samples should focus on extracting pure DNA and aim to amplify short target regions

Using multi-locus allelic sequence data to estimate genetic divergence among four Lilium (Liliaceae) cultivars

Next Generation Sequencing (NGS) may enable estimating relationships among genotypes using allelic variation of multiple nuclear genes simultaneously. We explored the potential and caveats of this strategy in four genetically distant Lilium cultivars to estimate their genetic divergence from transcriptome sequences using three approaches: POFAD (Phylogeny of Organisms from Allelic Data, uses allelic information of sequence data), RAxML (Randomized Accelerated Maximum Likelihood, tree building based on concatenated consensus sequences) and Consensus Network (constructing a network summarizing among gene tree conflicts). Twenty six gene contigs were chosen based on the presence of orthologous sequences in all cultivars, seven of which also had an orthologous sequence in Tulipa, used as out-group. The three approaches generated the same topology. Although the resolution offered by these approaches is high, in this case there was no extra benefit in using allelic information. We conclude that these 26 genes can be widely applied to construct a species tree for the genus Lilium

Phylogeny, morphological evolution, and speciation of endemic brassicaceae genera in the cape flora of southern Africa

Heliophila (ca. 73 spp.), the ditypic Cycloptychis and Thlaspeocarpa, and the monotypic Schlechteria, Silicularia, Brachycarpaea, and Chamira are endemic to the Cape region of South Africa, where they are the dominant genera of Brassicaceae. They may be regarded as the most diversified Brassicaceae lineage in every aspect of habit, leaf, flower, and fruit morphology. The characters used in the separation of these genera and their species, especially fruit type (silique vs. silicle), dehiscence (dehiscent vs. indehiscent), compression (latiseptate vs. angustiseptate), and cotyledonary type (spirolobal, diplecolobal, twice conduplicate), have been used extensively in the delimitation of tribes. The relationship and taxonomic limits among these genera are unclear and controversial. The present ITS study demonstrates the monophyly of tribe Heliophileae, with Chamira as sister clade. The other five smaller genera above are nested within two of the three main lineages of Heliophila, to which they should be reduced to synonymy. The current study reveals parallel evolution of fruit characters often used heavily in the traditional classification schemes of the family. However, the arrangement of species into three main clades largely corresponds with the distribution of morphological characters (e.g., habit, leaf shape, seed structure, inflorescence type, and presence/absence of basal appendages on the pedicels, petals, and staminal filaments) not adequately accounted for in previous studies. Estimation of divergence times of the main lineages of Heliophila is in agreement with recent estimations in other plant groups, all of which date the diversification against a background of aridification in the Pliocene and Pleistocene. Species of one main clade are perennial, microphyllous shrubs/subshrubs typically restricted to poor sandstone soils in the southwestern and western parts of the Cape Floristic Region of South Africa. Species of the other two clades are predominantly annuals that grow in more arid regions of Namibia and Namaqualand, as well as in the above sandstone areas of the Cape Region. The adaptive significance of various floral structures is discussed in terms of their possible role in the rapid diversification within Heliophila

Genomic Treasure Troves: Complete Genome Sequencing of Herbarium and Insect Museum Specimens

Unlocking the vast genomic diversity stored in natural history collections would create unprecedented opportunities for genome-scale evolutionary, phylogenetic, domestication and population genomic studies. Many researchers have been discouraged from using historical specimens in molecular studies because of both generally limited success of DNA extraction and the challenges associated with PCR-amplifying highly degraded DNA. In today's next-generation sequencing (NGS) world, opportunities and prospects for historical DNA have changed dramatically, as most NGS methods are actually designed for taking short fragmented DNA molecules as templates. Here we show that using a standard multiplex and paired-end Illumina sequencing approach, genome-scale sequence data can be generated reliably from dry-preserved plant, fungal and insect specimens collected up to 115 years ago, and with minimal destructive sampling. Using a reference-based assembly approach, we were able to produce the entire nuclear genome of a 43-year-old Arabidopsis thaliana (Brassicaceae) herbarium specimen with high and uniform sequence coverage. Nuclear genome sequences of three fungal specimens of 22–82 years of age (Agaricus bisporus, Laccaria bicolor, Pleurotus ostreatus) were generated with 81.4–97.9% exome coverage. Complete organellar genome sequences were assembled for all specimens. Using de novo assembly we retrieved between 16.2–71.0% of coding sequence regions, and hence remain somewhat cautious about prospects for de novo genome assembly from historical specimens. Non-target sequence contaminations were observed in 2 of our insect museum specimens. We anticipate that future museum genomics projects will perhaps not generate entire genome sequences in all cases (our specimens contained relatively small and low-complexity genomes), but at least generating vital comparative genomic data for testing (phylo)genetic, demographic and genetic hypotheses, that become increasingly more horizontal. Furthermore, NGS of historical DNA enables recovering crucial genetic information from old type specimens that to date have remained mostly unutilized and, thus, opens up a new frontier for taxonomic research as well