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34

Since you said plant/animal/anything, I offer the smallest genomes in various categories... (Kb means Kilobases, Mb means Megabases. 1 Kb = 1000 base pairs, 1Mb = 1000Kb) Smallest plant genome: Genlisea margaretae at 63Mb (Greilhuber et al., 2006) Smallest animal genome: Pratylenchus coffeae (nematode worm) at 20Mb (Animal Genome Size DB) Smallest ...


9

The techniques used to do this are ChIP-seq and ChIP-chip. Basically, you let the pathogen bind to the (highly replicated) DNA cut up the DNA into little random pieces by sonication enrich (“pull down”) the pathogen-bound DNA fragments by using a known antibody which binds to the pathogen sequence the thus enriched DNA map the sequenced fragments back to ...


9

Short Answer In a nutshell, DNA sequencing technology has a limit to how long a stretch of DNA it can read in one go. Long Answer So what most commonly occurs is the length of DNA you wish to sequence needs to be (almost randomly) chopped up into given lengths (depending on the technology) and each length or read is sequenced in parallel. But now you ...


9

Here I will assume we are talking about eukaryotic sequence specific transcription factors (ssTFs) and try to answer your first and part of the second question. There is in any case not definitive answer yet. An estimate of ssTFs genes in humans is given in the 2009 Nature Reviews Genetics paper by Vaquerizas, JM et al, A census of human transcription ...


8

I want to say Mycoplasma genitalium with a genome size of 582,970 bp. Turns out the answer is Nanoarchaeum eqitans with a genome of 490,885 bp. http://en.wikipedia.org/wiki/Nanoarchaeum http://www.ncbi.nlm.nih.gov/pubmed/14566062


8

LG stands for "linkage group". It seems the Chicken Genome Sequence group (Hillier et al., 2004) allocated several linkage groups (alleles or genes which tend to be inherited together) to the microchromosomes (tiny chromosomes typical of birds and reptiles), in this case called "linkage group E64" and "linkage group E22....". There are a load more ...


7

You're asking about the C-value enigma, in particular this kind of diagram:1 The quick answer is that there is no "why" in evolution; things happen and if they're beneficial they tend to stick around more than the deleterious things. The longer, (slightly) more satisfying answer is non-coding DNA. Thanks to non-coding DNA the size of a genome doesn't ...


7

I need to point out one thing, natural selection does not bring species to perfection. The best mutant may not be selected for many reasons. When you have no selection pressure then you have neutral evolution concurring and what takes over instead of natural selection is genetic drift. Genetic drift is just sample error. Say you have 1,000 individuals in ...


6

Yes, we can say the number of species is limited as you conjecture. However, quick estimation shows that the limitation has no apparent usefulness: A reasonable estimate of the largest known genome is 150 GB (150,000,000,000 or 1.5e11 nucleobases). The limit would be 4 raised to that power. That limit is so high that it is too large for most calculators ...


6

That's an interesting conjecture about the total amount of genetic variation that is possible. I would modify a few things. First, since the size of genomes varies greatly among organisms (from 0.5 Mb to 15 Mb just for prokaryotes), there should be a fifth character in your set, representing the absence of a nucleotide. There are also issues of whether ...


6

Genome size is a poor indicator of an organism's complexity (already an ill-defined term). We cannot assume by any means that a larger genome corresponds to a more "complex" organism. There are some plants whose genomes are larger than most mammals, and indeed the largest eukaryotic genome (at least as of 2010) is the plant Paris japonica, weighing in at 1C ...


5

See here for an ENCODE author's reflections on their use of the word "functional". (I don't think anyone is using the word "essential".) It is clear from this that, for them, one class of functional DNA is intronic DNA: i.e. introns are defined by ENCODE as functional DNA. It is well known that puffer fish have reduced genomes and that this is largely due ...


5

That was surprisingly buried. I found this in a paper describing genome build 3 - See "Materials and Methods". I imagine that this is consistent through to the current build. In any case it should get you started. "Sequencing templates were made from P1, BAC and WGS DNA libraries using the D. melanogaster strain yellow (y1); cinnabar (cn1) brown (bw1) ...


5

I know that 1000 Genomes has sequenced Mother-Father-Child genomes from populations around the world (I think at least some of these samples were obtained from HapMap) and their data is publicly available by following the links in their website.


4

As Armatus pointed out above, all viruses are obligately intracellular, and their medical and economic importance cannot be overstated. Many bacterial species live intracellularly. The arthropod specific Wolbachia has a wide variety of consequences for its host, including alteration of reproduction and sex ratios, induction of reproductive isolation ...


4

You can package linear genomes much more efficiently than circular genomes, and bacteria simply don't require the information density to be prosperous. To be a bit more specific, it's the torque strain put on the double-helix while it's being wound that makes the difference. Linear genomes can be wound around Histones, and these Histones can be further ...


4

In GWA studies you tend to analyze your "lead" SNPs in regions where genotypes are correlated (known as linkage disequilibrium). If you find an association between another SNP with the outcome, and this SNP is correlated with the original variant, you can perform a conditional analysis where you adjust for the original SNP in the model. This is to test if ...


3

I have written a script that will get you started. It downloads all protein coding transcripts of the species of interest from Ensembl and prints the codon use for each codon on each transcript. You will need to install the Bio::EnsEMBL::Registry Perl module, see here for instructions. The script also uses the Math::Round module, everything else should be ...


3

The GOLD database (Genomes Online DB) contains data on the sequencing status, and also some stats (number of chromosomes, genome size) -- but this extra data is not available for all species.


3

This question appears to start from the premise that different species of yeast are closely related, but they aren't. Saccharomyces cerevisae and Schizosaccharomyces pombe, both Ascomycetes, are thought to have diverged at least 300 million years ago (c.f. the mammalian divergence from other vertebrates was about 200 million years ago). S. cerevisiae has a ...


3

The seedbank terdon mentions is the Norwegian Svalbard Global Seed Vault located at Spitsbergen island: http://en.wikipedia.org/wiki/Svalbard_Global_Seed_Vault However, the closest thing to a concerted initiative for sequencing animals I know of is the Genome 10K project: http://genome10k.soe.ucsc.edu/ Their list of first 101 vertebrata proposed for ...


3

As @dd3 points out, average GC% indicates a need for stability and coding regions or structural regions of the genome may need to be more stable. But the largest %GC in genomes are found in thermophiles - organisms which live in high temperature water - in hotsprings and undersea geothermal vents. This review mentions how some thermophiles can be found with ...


3

I'm going to define a species according to the biological species concept, probably the most widely "accepted" species concept where a species is a group of individuals that reproduce, or have the potential to do so. Using a simplified example I will show you that gene*environment interactions affecting phenotype can allow separate species to occur despite ...


3

Deep sequencing is naturally error prone. Sequencing will never be perfect, because no enzyme will ever perform 100.00000% perfectly. In Illumina sequencing, you put your starting molecule down on the flowcell, then the polymerase makes a cluster of copies around it. But at each step of building each copy, there's a chance the polymerase will make a ...


3

Assuming that you are looking at data used to describe the differences for a new individual, as opposed to a human reference genome build: A fastq file is the typical format of data from a sequencer. It would require a text field of some sort as they can be quite large, even for single reads. If you had a specific sequencer in mind with very short read ...


3

Because cells are not only characterized by by their genetic material and other interior components, but also by the genes they express. Cells have to fulfill multiple different functions to be able to build complex multicellular organisms. Differently expressed genes lead to different proteins made in the cell, which leads to different morphology, shape or ...


3

Interesting question. The GC-content seems to evolve over time and it also seems that the GC-content of coding regions is higher than for the surrounding non-coding regions (see reference 1). If there is a specific function for this higher GC-content or not is (if I understand this right) debated among the groups which do research in this field. Have a look ...


2

For DNA extraction, you would need only a few eggs. PCR would then give you all the copies of your target gene(s). A quick Google Scholar search on Takifugu fecundity revealed a paper by Yang and Chen (2008). They found that T. obscurus produced an average of 320.8 oocytes mg$^{-1}$ ovary wet weight. In comparison, T. ocellatus produced 125.2 oocytes ...


2

A colleague of mine discovered the cipher that determines TAL effector DNA specificities, which is described in this short paper. These specificities were determined by observing TAL effectors bound to DNA and recording how often a given repeat-variable diresidue (RVD) would correspond to a given nucleotide (using a weight matrix). Now that the ...


2

There is significant variation in genomic GC content, both between species and within an individual genome. An average GC content in the range of 35%-45% is common, although there are definitely organisms that fall outside this range. The plasmodium species you link to above is an example of extreme AT richness (low GC content), whereas some bacterial ...



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