MicroRNAs: Genomics, Biogenesis, Mechanism, and Function

Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

So far in this course we have dealt entirely with the evolution of characters that are controlled by simple Mendelian inheritance at a single locus. There are notes on the course website about gametic disequilibrium and how allele frequencies change at two loci simultaneously, but we didn’t discuss them. In every example we’ve considered we’ve imagined that we could understand something about evolution by examining the evolution of a single gene. That’s the domain of classical population genetics. For the next few weeks we’re going to be exploring a field that’s actually older than classical population genetics, although the approach we’ll be taking to it involves the use of population genetic machinery. If you know a little about the history of evolutionary biology, you may know that after the rediscovery of Mendel’s work in 1900 there was a heated debate between the “biometricians” (e.g., Galton and Pearson) and the “Mendelians” (e.g., de Vries, Correns, Bateson, and Morgan). Biometricians asserted that the really important variation in evolution didn’t follow Mendelian rules. Height, weight, skin color, and similar traits seemed to

Human biochemical genetics

The flowering plant Arabidopsis thaliana is an important model system for identifying genes and determining their functions. Here we report the analysis of the genomic sequence of Arabidopsis. The sequenced regions cover 115.4 megabases of the 125-megabase genome and extend into centromeric regions. The evolution of Arabidopsis involved a whole-genome duplication, followed by subsequent gene loss and extensive local gene duplications, giving rise to a dynamic genome enriched by lateral gene transfer from a cyanobacterial-like ancestor of the plastid. The genome contains 25,498 genes encoding proteins from 11,000 families, similar to the functional diversity of Drosophila and Caenorhabditis elegans--the other sequenced multicellular eukaryotes. Arabidopsis has many families of new proteins but also lacks several common protein families, indicating that the sets of common proteins have undergone differential expansion and contraction in the three multicellular eukaryotes. This is the first complete genome sequence of a plant and provides the foundations for more comprehensive comparison of conserved processes in all eukaryotes, identifying a wide range of plant-specific gene functions and establishing rapid systematic ways to identify genes for crop improvement.

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Analysis of the genome sequence of the flowering plant Arabidopsis thaliana.

INTRODUCTIONOne of the most commonly used markers for the selection of transgenic Arabidopsis is resistance to glufosinate ammonium, an herbicide that is sold under a variety of trade names including Basta and Finale. Resistance to glufosinate ammonium is conferred by the bacterial bialophos resistance gene (BAR) encoding the enzyme phosphinotricin acetyl transferase (PAT). This protocol describes the use of glufosinate ammonium to select transformed Arabidopsis plants. The major advantage of glufosinate ammonium selection is that it can be performed on plants growing in soil and does not require the use of sterile techniques.

Glufosinate ammonium selection of transformed Arabidopsis.

The quantitative resistance gene ACCELERATED CELL DEATH 6 (ACD6), which encodes a transmembrane protein with intracellular ankyrin repeats, has been implicated in a trade-off between growth and defense among wild strains of Arabidopsis thaliana. Naturally hyperactive alleles of the ACD6-Est-1 type can lead to spontaneous activation of immune responses, although the extent of visible hyperimmunity in strains with this allele varies substantially. We have identified a natural suppressor locus, MODULATOR OF HYPERACTIVE ACD6 1 (MHA1), which codes for a small protein of ~7 kDa that attenuates activity of the ACD6-Est-1 allele. MHA1 and its paralog MHA1-LIKE (MHAL) differentially interact with specific ACD6 variants, and both MHA1 and MHAL peptides can bind to the ACD6 ankyrin repeats. MHAL also enhances accumulation of an ACD6 complex, thereby increasing activity of the ACD6 standard allele. The ACD6 ankyrin repeats are similar to those of transient receptor potential (TRP) ion channels, and several lines of evidence support that increased ACD6 activity is linked to enhanced calcium signaling. Our work highlights how the study of natural variation reveals new aspects of plant immunity.

Small peptides modulate the immune function of the ion channel-like protein ACD6 in Arabidopsis thaliana

Improving the peer review process, overcoming the limitations of print journals and providing open access to the very best work in the life and biomedical sciences are three highlights of our first year.

/pdf/a-year-in-the-life-of-elife-29q6gl9x5x.pdf

A year in the life of eLife.

New combinations of genetic material brought together through hybridization can lead to unfit offspring as a result of outbreeding or inbreeding depression. In selfing plants such as Arabidopsis thaliana, outbreeding depression is typically the result of pairwise deleterious epistatic interactions between two alleles that can geographically co-occur. What remains elusive is how often alleles resulting in genetic incompatibilities co-occur in natural populations of outcrossing plant species. To address this question, we screened over two thousand five hundred wild Arabidopsis arenosa hybrid plants in search for potential genetic mismatches. We show that although abnormal deleterious phenotypes are common, the transcriptional profiles of these abnormal A. arenosa plants differ substantially from those seen in incompatible A. thaliana hybrids. The abnormal hybrid phenotypes in A. arenosa had different underlying genetic architectures, yet a repeated theme was increased homozygosity, indicating that inbreeding rather than outbreeding depression gives rise to some of the deleterious phenotypes segregating in wild A. arenosa populations.

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Homozygosity at its Limit: Inbreeding Depression in Wild Arabidopsis arenosa Populations

The most commonly used bacterial pathogen of Arabidopsis is Pseudomonas syringae, pathovar tomato strain DC3000 or pathovar maculicola strain ES4326. Plants used for infection with P. syringae should be grown on a short-day light cycle, so that they develop large leaves. For consistent results, it is important that the plants are watered well and do not experience any abiotic stresses. The plants should be grown and tested in a temperature- and humidity-controlled growth chamber, because the extent of bacterial growth is highly dependent on both factors. Gene-for-gene resistance to P. syringae is usually accompanied by the hypersensitive response (HR), a form of localized cell death that occurs in response to pathogen challenge. P. syringae strains carrying one of the avirulence genes avrRpt2, avrRpm1, avrB, avrPphB, and avrRps4 trigger the HR in wild-type Columbia. Other ecotypes may lack one or more of the R genes needed for recognition of these avirulence genes. Bacterial growth can be monitored by grinding up infected tissue, plating serial dilutions on King's B medium, and counting colonies. This protocol describes methods for preparing bacterial cultures, inoculating plants, testing the HR, and assessing bacterial growth.

Detlef Weigel

Papers

Glufosinate ammonium selection of transformed Arabidopsis.

Small peptides modulate the immune function of the ion channel-like protein ACD6 in Arabidopsis thaliana

A year in the life of eLife.

Homozygosity at its Limit: Inbreeding Depression in Wild Arabidopsis arenosa Populations

Phenotypic analysis of Arabidopsis mutants: Bacterial pathogens