Design of a bovine low-density SNP array optimized for imputation

The Illumina BovineLD BeadChip was designed to support imputation to higher density genotypes in dairy and beef breeds by including single-nucleotide polymorphisms (SNPs) that had a high minor allele frequency as well as uniform spacing across the genome except at the ends of the chromosome where densities were increased. The chip also includes SNPs on the Y chromosome and mitochondrial DNA loci that are useful for determining subspecies classification and certain paternal and maternal breed lineages. The total number of SNPs was 6,909. Accuracy of imputation to Illumina BovineSNP50 genotypes using the BovineLD chip was over 97% for most dairy and beef populations. The BovineLD imputations were about 3 percentage points more accurate than those from the Illumina GoldenGate Bovine3K BeadChip across multiple populations. The improvement was greatest when neither parent was genotyped. The minor allele frequencies were similar across taurine beef and dairy breeds as was the proportion of SNPs that were polymorphic. The new BovineLD chip should facilitate low-cost genomic selection in taurine beef and dairy cattle.     

Mycorrhizal symbiosis stimulates endoreduplication in angiosperms

Symbiotic and parasitic relationships can alter the degree of endoreduplication in plant cells, and a limited number of studies have documented this occurrence in root cells colonized by arbuscular mycorrhizal (AM) fungi. However, this phenomenon has not been tested in a wide range of plant species, including species that are non-endopolyploid and those that do not associate with AM fungi. We grew 37 species belonging to 16 plant families, with a range of genome sizes and a range in the degree of endopolyploidy. The endoreduplication index (EI) was compared between plants that were inoculated with Glomus irregulare and plants that were not inoculated. Of the species colonized with AM fungi, 22 of the 25 species had a significant increase in endopolyploid root nuclei over non-mycorrhizal plants, including species that do not normally exhibit endopolyploidy. Changes in the EI were strongly correlated (R(2) = 0.619) with the proportion of root length colonized by arbuscules. No change was detected in the EI for the 12 non-mycorrhizal species. This work indicates that colonization by symbiotic fungi involves a mechanism to increase nuclear DNA content in roots across many angiosperm groups and is likely linked to increased metabolism and protein production.     

Comparison of different delivery systems of DNA vaccination for the induction of protection against tuberculosis in mice and guinea pigs

The great challenges for researchers working in the field of vaccinology are optimizing DNA vaccines for use in humans or large animals and creating effective single-dose vaccines using appropriated controlled delivery systems. Plasmid DNA encoding the heat-shock protein 65 (hsp65) (DNAhsp65) has been shown to induce protective and therapeutic immune responses in a murine model of tuberculosis (TB). Despite the success of naked DNAhsp65-based vaccine to protect mice against TB, it requires multiple doses of high amounts of DNA for effective immunization. In order to optimize this DNA vaccine and simplify the vaccination schedule, we coencapsulated DNAhsp65 and the adjuvant trehalose dimycolate (TDM) into biodegradable poly (DL-lactide-co-glycolide) (PLGA) microspheres for a single dose administration. Moreover, a single-shot prime-boost vaccine formulation based on a mixture of two different PLGA microspheres, presenting faster and slower release of, respectively, DNAhsp65 and the recombinant hsp65 protein was also developed. These formulations were tested in mice as well as in guinea pigs by comparison with the efficacy and toxicity induced by the naked DNA preparation or BCG. The single-shot prime-boost formulation clearly presented good efficacy and diminished lung pathology in both mice and guinea pigs.     

Pathways of introduction of the invasive aquatic plant Cabomba caroliniana

The pathway and frequency of species' introductions can affect the extent, impact, and management of biological invasions. Here, we examine the pathway of introduction of the aquatic plant Cabomba caroliniana (fanwort) into Canada and the northern United States using plastid DNA sequence (intergenic spacers atpF‐atpH, trnH‐psbA, and trnL‐trnF) and DNA content analyses. We test the hypothesis that the spread of fanwort is a result of commercial trade by comparing a Canadian population (Kasshabog Lake, ON) to native populations from southern U.S., introduced populations in northern U.S., and plants from commercial retailers. Thirteen plastid haplotypes were identified throughout North America, including one dominant haplotype, which was present in all C. caroliniana populations. Several rare haplotypes were used to infer shared colonization history. In particular, the Canadian population shared two rare alleles with a population from Massachusetts, suggesting range expansion of C. caroliniana from the northern U.S. However, the possibility of a commercial introduction cannot be excluded, as common alleles were shared between the Canadian population and both commercial and southern U.S. sources. Variation in C. caroliniana genome size was bimodal and populations were classified into “high” and “low” categories. The Canadian population had DNA contents similar to several northern U.S. populations (low DNA content). This may provide additional support for range expansion from these introduced populations rather than from commercial sources or populations in the southern U.S., which had high DNA content.     

Long-term effects of nitrogen and phosphorus fertilization on soil microbial community structure and function under continuous wheat production

Soil microorganisms play a critical role in the biosphere, and the influence of cropland fertilization on the evolution of soil as a living entity is being actively documented. In this study, we used a shotgun metagenomics approach to globally expose the effects of 50-year N and P fertilization of wheat on soil microbial community structure and function, and their potential involvement in overall N cycling. Nitrogen (N) fertilization increased alpha diversity in archaea and fungi while reducing it in bacteria. Beta diversity of archaea, bacteria and fungi, as well as soil function, were also mainly driven by N fertilization. The abundance of archaea was negatively impacted by N fertilization while bacterial and fungal abundance was increased. The responses of N metabolism-related genes to fertilization differed in archaea, bacteria and fungi. All archaeal N metabolic processes were decreased by N fertilization, while denitrification, assimilatory nitrate reduction and organic-N metabolism were highly increased by N fertilization in bacteria. Nitrate assimilation was the main contribution of fungi to N cycling. Thaumarchaeota and Halobacteria in archaea; Actinobacteria, Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria and Deltaproteobacteria in bacteria; and Sordariomycetes in fungi participated dominantly and widely in soil N metabolic processes.     

Composition and preservation of the Chengjiang fauna –a Lower Cambrian soft-bodied biota

The Lower Cambrian Chengjiang fauna is reviewed and shown to be closely comparable with the younger Burgess Shale fauna. but with various differences in detail. A diverse group of more or less annulated lobopod animals including 'armoured lobopods' are regarded as representatives of the phylum Onychophora. 'Trilobitomorphs' include several new types. Probable protaspides of the trilobitomorph Naraoia are described. No molluses or deuterostomes have been identified. The preservational orientations of the various taxa are reviewed and compared with orientations of the Burgess Shale taxa. Orientation in the sediment is found to be closely correlated to the original shape of individuals. Several new genera and species are described: the segmented. worm-shaped Yunnanozoon lividum gen. et sp.n., the 'armoured lobopods' Onychodictyon ferox gen. et sp.n. and Cardiodictyon catenulum gen. et sp.n. and the arthropods Saperion glumaceum gen. et sp.n., Sinoburius Iunaris gen. et sp.n., and Xandarella spectaculum gen. et sp.n.     

Growth response of crops to soil microbial communities from conventional monocropping and tree-based intercropping systems

Background and aims

Recent studies have shown that tree-based intercropping (TBI) systems support a more diverse soil microbial community compared to conventional agricultural systems. However, it is unclear whether differences in soil microbial diversity between these two agricultural systems have a functional effect on crop growth.

Methods

In this study, we used a series of greenhouse experiments to test whether crops respond differently to the total soil microbial community (Experiment 1) and to arbuscular mycorrhizal (AM) fungal communities alone (Experiment 2) from conventionally monocropped (CM) and TBI systems.

Results

The crops had a similar growth response to the total soil microbial communities from both cropping systems. However, when compared to sterilized controls, barley (Hordeum vulgare) and canola (Brassica napus) exhibited a negative growth response to the total soil microbial communities, while soybean (Glycine max) was unaffected. During the AM fungal establishment phase of the second experiment, ‘nurse’ plants had a strong positive growth response to AM fungal inoculation, and significantly higher biomass when inoculated with AM fungi from the CM system compared to the TBI system. Soybean was the only crop species to exhibit a significant positive growth response to AM fungal inoculation. Similar to the total soil microbial communities, AM fungi from the two cropping systems did not differ in their effect on crop growth.

Conclusion

Overall, AM fungi from both cropping systems had a positive effect on the growth of plants that formed a functional symbiosis. However, the results from these experiments suggest that negative effects of non-AM fungal microbes are stronger than the beneficial effects of AM fungi from these cropping systems.     

Organellar genome,nuclear ribosomal DNA repeat unit,and microsatellites isolated from a small-scale of 454 GS FLX sequencing on two mosses

Recent innovations in high-throughput DNA sequencing methodology (next generation sequencing technologies [NGS]) allow for the generation of large amounts of high quality data that may be particularly critical for resolving ambiguous relationships such as those resulting from rapid radiations. Application of NGS technology to bryology is limited to assembling entire nuclear or organellar genomes of selected exemplars of major lineages (e.g., classes). Here we outline how organellar genomes and the entire nuclear ribosomal DNA repeat can be obtained from minimal amounts of moss tissue via small-scale 454 GS FLX sequencing. We sampled two Funariaceae species, Funaria hygrometrica and Entosthodon obtusus, and assembled nearly complete organellar genomes and the whole nuclear ribosomal DNA repeat unit (18S-ITS1-5.8S-ITS2-26S-IGS1-5S-IGS2) for both taxa. Sequence data from these species were compared to sequences from another Funariaceae species, Physcomitrella patens, revealing low overall degrees of divergence of the organellar genomes and nrDNA genes with substitutions spread rather evenly across their length, and high divergence within the external spacers of the nrDNA repeat. Furthermore, we detected numerous microsatellites among the 454 assemblies. This study demonstrates that NGS methodology can be applied to mosses to target large genomic regions and identify microsatellites.