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38

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 ...


12

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 ...


12

The main reason is because the genetic differences between individuals of the same species are tiny. For the vast majority of studies, they can simply be ignored. Differences between individuals are usually (not always, but mostly) differences in SNP genotypes. These are single nucleotide differences which, while they can have phenotypic effect, don't ...


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

The authors of this 2012 review article summarize the problem well in their introduction: In contrast to the tremendous advances in throughput, assembling sequencing reads remains a substantial endeavor, much greater than the sequencing efforts alone would suggest [22-24]. Large complex plant genomes remain a particularly difficult challenge for de novo ...


9

There is both an upper and lower limit which are species specific. The upper limit is caused by incomplete segregation of sister chromatids and subsequent trimming of the long arm(s). The reason for the lower limit is, as far as I can tell, unknown. Upper Limit Schubert I, Oud JL. 1997. There is an Upper Limit of Chromosome Size for Normal Development of ...


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 ...


7

The pattern we see in B. subtilis is quite common in prokaryotes. The origin of replication is shown at the top of the genome diagram. DNA replication proceeds bidirectionally from this point. In the B. subtilis diagram, most genes are located along the leading strand in each direction. Even in E. coli, by the way, important genes, including all rRNAs, tend ...


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.


5

Neither NCBI nor Ensembl have a genome project listed for any crocus species, although individual ethidium bromide stained nuclei have been analyzed by flow cytometry, revealing approximately 11.4 pg of DNA per nucleus (warning, pay wall). C. sativus is triploid, giving it a C-value of 3.8 pg which works out to a haploid genetic content of about 3.45 Gbp. ...


5

Let's try and answer all three parts of your question. Sequencing The general method is the same. Sequencing is just sequencing. But as for every single sequencing, there are factors to consider and protocols to be selected. One important thing is, that you might want comparably long reads to cope with the repeats and the general large size of plant ...


4

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 ...


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

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 ...



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