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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 an ...
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
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
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 ...
8
Even a male cell can count the number of X chromosomes. (Lee et al. 1996; Cell 86: 83-84)
When X inactivation is getting started the two chromosomes "kiss" - a process that lasts for a couple of hours (first shown by Jeannie Lee in 1996). The physical contact between two X chromosomes is over a small fraction of the chromosome but it's essential for ...
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
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
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.
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
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
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
First of all I am not sure if your examples are per se correct. But they might also be an additional bonus. Secondly, I would like to refer to two articles: "Polyploidy" and "The advantages and disadvantages of being polyploid".
One of the main benefits could be allowing organisms long-term evolutionary flexibility. Often adapted polyploids can undergo a ...
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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Most the genome is not coding for proteins. Here is a pie chart of what the human genome is made of
As you can see, only 1.5% of the human genome codes for proteins. The term gene is often a bit vaguely defined but if we assume that a gene is all the exons, all the introns and all the regulatory sequences, then 25.5% of the human genome are genes. So, yes ...
5
This refers to base pairs.
File size has no particular meaning beyond practical considerations, given that it depends on the format. (For example, 2bit files use 2 bits per base, as the name indicates, compared to the 8 bits necessary for each letter in a plain text format like FASTA & derivatives.)
For your additional question, (number of reads * ...
5
The simplest difference is the scale and range. The aim of 1000 genome project was to provide comprehensive library of human genetic variation. DNA of individuals coming from different ethnic groups, geographic locations were sequenced and the results of the study were published here.
Genomes from NCBI come from different organisms and the number of ...
5
Mitochondrial genomes differ greatly in size, coding potential and even whether they are circular or linear. Mammalian mitochondrial DNA is small (11–28 kbp) and intronless. However the mitochondria of certain other organisms range up to 1000 kbp in size.
Certain sponges (demosponges) with large mitochondrial genomes contain type I introns and type II ...
5
If you arrange your contigs from longest to shortest, what is the shortest contig in the smallest subset of contigs that covers at least half the expected genome length?
An example with arbitrary units...
You have a set of contigs of lengths 30, 20, 20, 10, 5, 5, 1, 1, 1, and many contigs < 1. Your expected genome length is 150. The smallest subset of ...
4
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 ...
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