28
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Is the size of the genome across species roughly the same?
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 ...
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13
votes
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Number of transcription factor genes in the human genome
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 ...
- 1,710
13
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Why reference genome is a reference?
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 ...
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11
votes
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Why do cells vary in shape and function when they have the same genome and the same organelles?
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 ...
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11
votes
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What limits chromosomal length?
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 ...
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10
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Why is it harder to sequence plant genomes than animal genomes?
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 ...
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9
votes
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In percentage, how much is the human genome (DNA) similar to the mouse genome?
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 ...
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8
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Why do some bacteria have most genes on the leading strand of the genome?
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 ...
- 1,761
8
votes
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What causes cells to inactivate one X-chromosome?
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 ...
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7
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Is the size of the genome across species roughly the same?
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 ...
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7
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Do there exist publicly available Genome sequences of a family?
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 ...
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6
votes
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What is the genome size of Saffron (Crocus sativus)?
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 ...
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6
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Is our genome decaying (see "Genetic Entropy"), and, if so, is this evidence for our genome being "young"?
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.
...
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Is our genome decaying (see "Genetic Entropy"), and, if so, is this evidence for our genome being "young"?
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 ...
5
votes
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Importance of knowing GC Content of an organism
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 ...
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5
votes
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What is the strand specificity of a reference genome?
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 ...
5
votes
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Why does polyploidy give an evolutionary advantage?
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 ...
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How Scientists sequence, assemble and annotate plant genomes?
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 ...
- 1,995
5
votes
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Do all chromosomes in one human body contains same genome?
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 ...
- 1,105
5
votes
Are there parts of DNA that do not have genes?
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 ...
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5
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Giga base or Giga byte
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 ...
- 1,105
5
votes
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Difference between NCBI's /genomes and /1000genomes
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, ...
- 431
5
votes
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Protein-coding introns in mitochondrial genomes
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 ...
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5
votes
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Understanding Contig NG50
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 ...
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4
votes
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What is the most genetically complex organism?
Edit: I would define genetic complexity as either genome size or number of genes. Either answer or information would work.
Largest genome: Paris japonica, a rare plant. Its genome is 149,000,000,000 ...
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4
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Where can I find the genome of the L-strain coronavirus and the S-strain coronavirus?
Article links to this publication which has all the information needed:
https://academic.oup.com/nsr/advance-article/doi/10.1093/nsr/nwaa036/5775463
It is mentioned in the paper that:
Although we ...
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votes
Why do microarrays require a priori knowledge of the genome?
If the query genome is unknown, a microarray cannot be made for a target species. Microarrays have DNA fragments of what you want to amplify on them. Those fragments must be known.
From nature:
DNA ...
- 594
4
votes
Has life on Earth explored the entire space of genomes?
The answer to this question is very much no. Genomes are of arbitrary length and structural organisation (i.e. ploidy), so there isn't a fixed number of 'slots' that different base-pairs could inhabit ...
- 2,053
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How to estimate a genome's size?
In the absence of molecular sequencing data the most accurate estimates are based on reassociation kinetics, more commonly known as Cot curves. Here is a classic paper from 1974 that describes the ...
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How to estimate a genome's size?
Gel electrophoresis is a basic lab method to get size info about nucleotide fragments, although one might need to chop up larger DNA to be able to apply this method. The wikipedia page covers the ...
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