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.

/pdf/analysis-of-the-genome-sequence-of-the-flowering-plant-3vizsb52m2.pdf

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

Genome resequencing with short reads generally relies on alignments against a single reference. GenomeMapper supports simultaneous mapping of short reads against multiple genomes by integrating related genomes (e.g., individuals of the same species) into a single graph structure. It constitutes the first approach for handling multiple references and introduces representations for alignments against complex structures. Demonstrated benefits include access to polymorphisms that cannot be identified by alignments against the reference alone. Download GenomeMapper at http://1001genomes.org.

/pdf/simultaneous-alignment-of-short-reads-against-multiple-q5xetdb9pi.pdf

Simultaneous alignment of short reads against multiple genomes

The identity of floral organs in Arabidopsis thaliana is determined by homeotic genes, which are expressed in specific regions of the developing flower. The initial activation of homeotic genes is accomplished at least in part by the products of two earlier acting genes with overlapping functions. These are the floral meristem—identity genes LEAFY and APETALA1. The requirements of LEAFY and APETALA1 activity vary for different homeotic genes.

Activation of floral homeotic genes in Arabidopsis.

Position-dependent regulation of growth is important for shaping organs in
multicellular organisms. We have characterized the role of JAGGED, a
gene that encodes a protein with a single C2H2
zinc-finger domain, in controlling the morphogenesis of lateral organs in
Arabidopsis thaliana. Loss of JAGGED function causes organs
to have serrated margins. In leaves, the blade region is most severely
affected. In sepals, petals and stamens, the strongest defects are seen in the
distal regions. By monitoring cell-cycle activity in developing petals with
the expression of HISTONE 4, we show that JAGGED suppresses
the premature differentiation of tissues, which is necessary for the formation
of the distal region. The localization of defects overlaps with the expression
domain of JAGGED, which is restricted to the growing regions of
lateral organs. JAGGED expression is notably absent from the cryptic
bract, the remnant of a leaf-like organ that subtends the flower in many
species but does not normally develop in wild-type Arabidopsis. If
misexpressed, JAGGED can induce the formation of bracts, suggesting
that the exclusion of JAGGED from the cryptic bract is a cause of
bractless flowers in Arabidopsis.

/pdf/the-role-of-jagged-in-shaping-lateral-organs-4gm6tgnytn.pdf

The role of JAGGED in shaping lateral organs

Plant stem cells, contained in specialized structures called meristems, have amazing regenerative powers. They enable plants to grow and produce new organs throughout lifetimes that can span hundreds of years.

Detlef Weigel

Papers

Simultaneous alignment of short reads against multiple genomes

Activation of floral homeotic genes in Arabidopsis.

The role of JAGGED in shaping lateral organs

Stem cells that make stems

A LEAFY co-regulator encoded by UNUSUAL FLORAL ORGANS.