44
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 ...
28
Chart of C-values (the mass of DNA in a single haploid cell); there is no logical order to the groups:
[source]
Base pairs in haploid genome (some examples):
Escherichia coli (bacterium): ~4.5 million
Caenorhabditis elegans (nematode worm): ~100 million
Homo sapiens (we all know what these are): ~3 billion
Pinus taeda (coniferous tree): ~22 billion
...
13
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 ...
13
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 ...
11
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 ...
11
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 ...
10
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
10
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
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 even ...
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 don'...
9
This question cannot be answered as simply as you put it, but it's not too much to elaborate on.
The order of the base pairs will be drastically different, but the same proteins and amino acids will be coded for in genes, just at different points along the DNA. For example, you may find the same sequence to code for a protein in a mouse as in a human, but ...
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 ...
8
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 ...
8
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 ...
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
It is already mentioned by canadianer that genome size differs between organisms. But what about complexity?
First we should define what complexity is: complexity can be defined as number of different cell types that a multicellular organism can produce, with the same genome. Yes complexity does not correlate with genome size. However, it seems to correlate ...
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 =...
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
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.
...
6
If I understand the question correctly, you are asking why random mutations (most of the non-silent ones are deleterious) cannot create information and improve the overall fitness of the organism.
This is a common creationist statement, and has been shown to be incorrect in many different ways. The best way this can be shown to be false is by simply ...
6
Regarding the reference to Lynch, actually reading this paper is illuminating (http://www.pnas.org/content/107/3/961.full). What Lynch is saying with regards to degeneration is that he and others feel that modern technological advances may relax selection pressures, thus allowing the survival and reproduction of many who would otherwise be selected against, ...
5
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 ...
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
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 ...
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 ...
5
First of all, the reference genome strand specificity is referred to as sense (positive strand) or antisense (negative strand). Now let's consider to sequencing data or FASTQ files. When we align reads, a resulting SAM or BAM file has a column specifying strand information, we usually see a + or - strand.
For more background on the strand names here's a ...
5
Yes, all cells contains the same genome. This is because, for a given individual, all of its cells comes from the zygote, a singular cell formed after fecondation of the maternal ovum and paternal spermatozoa, through repeated cell division (mitosis). This is a process which replicates quite exactly the genome that will be passed to the newly formed cells.
...
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