Genome

qas: question: In what fields of science is the genome studied?
answers: text: molecular biology and genetics

question: What is the content of the human genome?
answers: text: DNA

question: What constitutes the viral genome?
answers: text: RNA

question: How do scientists classify RNA as?

question: What does a molecule contain?

question: What is one thing that genes have?

question: What is included in virus RNA?

question: What fields study molecule formation?
context: In modern molecular biology and genetics, the genome is the genetic material of an organism. It consists of DNA (or RNA in RNA viruses). The genome includes both the genes and the non-coding sequences of the DNA/RNA.

qas: question: Who coined the word genome?
answers: text: Hans Winkler

question: In what year was the word genome first created?
answers: text: 1920

question: At what university was Hans Winkler employed when he created the word genome?
answers: text: University of Hamburg

question: Which two similar words share etymology with genome?
answers: text: biome, rhizome

question: What word was created to be used in the study of botany in 1920?

question: In what year was Hans Winkler hired in Oxford as professor of botany?

question: How did the University of Hamburg in Germany suggest genome came about?

question: What two other words were used as botany terms frequently at the University of Hamburg?

question: What discussion about botany terms was taking place in 1920?
context: The term was created in 1920 by Hans Winkler, professor of botany at the University of Hamburg, Germany. The Oxford Dictionary suggests the name to be a blend of the words gene and chromosome. However, see omics for a more thorough discussion. A few related -ome words already existed—such as biome, rhizome, forming a vocabulary into which genome fits systematically.

qas: question: A gamate has how many chromosomes relative to a somatic cell?
answers: text: half

question: What process splits the chromosome between gametes?
answers: text: meiosis

question: What are two cellular organelles which contain genetic material?
answers: text: mitochondria and chloroplasts

question: What are examples of terms used to describe a virus type?

question: How many chromosomes do the organelles have compared to the chloroplasts?

question: How is halving genetic material in linear chains of DNA accomplished?

question: What is one thing the term transposable elements can be applied to mean?

question: What three non-chromosomal genetic elements can bacteria comprise?
context: Some organisms have multiple copies of chromosomes: diploid, triploid, tetraploid and so on. In classical genetics, in a sexually reproducing organism (typically eukarya) the gamete has half the number of chromosomes of the somatic cell and the genome is a full set of chromosomes in a diploid cell. The halving of the genetic material in gametes is accomplished by the segregation of homologous chromosomes during meiosis. In haploid organisms, including cells of bacteria, archaea, and in organelles including mitochondria and chloroplasts, or viruses, that similarly contain genes, the single or set of circular or linear chains of DNA (or RNA for some viruses), likewise constitute the genome. The term genome can be applied specifically to mean what is stored on a complete set of nuclear DNA (i.e., the "nuclear genome") but can also be applied to what is stored within organelles that contain their own DNA, as with the "mitochondrial genome" or the "chloroplast genome". Additionally, the genome can comprise non-chromosomal genetic elements such as viruses, plasmids, and transposable elements.

qas: question: What is the science that deals with the common genetic characteristics of related organisms called?
answers: text: genomics

question: In contrast to genomics, genetics usually studies what?
answers: text: single genes or groups of genes

question: What is the catalog of contents of a particular species' genetic makeup?
answers: text: sequenced

question: In both sexes of a species what may a properties of genes be?

question: What term is used to show how the sex chromosomes of a species are found?

question: What is known as the study of autosomes of related organisms?

question: What is known as the study of the properties of single or groups of sex chromosomes?

question: What are people referring to when they say species exist in one sex?
context: When people say that the genome of a sexually reproducing species has been "sequenced", typically they are referring to a determination of the sequences of one set of autosomes and one of each type of sex chromosome, which together represent both of the possible sexes. Even in species that exist in only one sex, what is described as a "genome sequence" may be a composite read from the chromosomes of various individuals. Colloquially, the phrase "genetic makeup" is sometimes used to signify the genome of a particular individual or organism.[citation needed] The study of the global properties of genomes of related organisms is usually referred to as genomics, which distinguishes it from genetics which generally studies the properties of single genes or groups of genes.

qas: question: What is the relation between the number of base pairs and total complement of genes in a species called?
answers: text: C-value paradox

question: Which organism has the most genes?
answers: text: trichomoniasis

question: How many genes is the trichomoniasis estimated to have?
answers: text: 60,000

question: Relative to the human genome, how many more genes does trichomoniasis have?
answers: text: three times

question: What is the highest known number of species?

question: How many genes are in the human genome?

question: What two things vary in the protozoan causing trichomoniasis?

question: What is the relationship between base pairs and trichomoniasis?

question: What is the relation between base pairs and the human genome called?
context: Both the number of base pairs and the number of genes vary widely from one species to another, and there is only a rough correlation between the two (an observation known as the C-value paradox). At present, the highest known number of genes is around 60,000, for the protozoan causing trichomoniasis (see List of sequenced eukaryotic genomes), almost three times as many as in the human genome.

qas: question: Who was the first person to sequence a viral genome?
answers: text: Walter Fiers

question: Which viral genome did Fiers sequence?
answers: text: Bacteriophage MS2

question: Who was first to sequence a DNA-based genome?
answers: text: Fred Sanger

question: What organization first sequenced a bacterial genome?
answers: text: Institute for Genomic Research

question: In what year was the archaeon genome sequenced?
answers: text: 1996

question: In what year did Fred Sanger first establish the complete nucleotide sequence of  a viral RNA genome?

question: When was The Institute for Genome Research founded?

question: What did Walter Fiers complete in 1996?

question: What did Fred Sanger complete when part of a team in 1995?

question: What was the name of the first bacterial genome sequenced by Fred Sanger in 1995?
context: In 1976, Walter Fiers at the University of Ghent (Belgium) was the first to establish the complete nucleotide sequence of a viral RNA-genome (Bacteriophage MS2). The next year Fred Sanger completed the first DNA-genome sequence: Phage Φ-X174, of 5386 base pairs. The first complete genome sequences among all three domains of life were released within a short period during the mid-1990s: The first bacterial genome to be sequenced was that of Haemophilus influenzae, completed by a team at The Institute for Genomic Research in 1995. A few months later, the first eukaryotic genome was completed, with sequences of the 16 chromosomes of budding yeast Saccharomyces cerevisiae published as the result of a European-led effort begun in the mid-1980s. The first genome sequence for an archaeon, Methanococcus jannaschii, was completed in 1996, again by The Institute for Genomic Research.

qas: question: Which U.S. government agency keeps a large amount of information on genomes?
answers: text: US National Institutes of Health

question: What is a mammal whose genome has been sequenced?
answers: text: mouse

question: What is a fish whose genome has been sequenced?
answers: text: puffer fish

question: When was the Neanderthal's genome sequenced?
answers: text: December 2013

question: How old in years was the material that was used to sequence the Neanderthal genome?
answers: text: 130,000

question: What has extracting genes from a Neanderthal made it easier for scientists to do?

question: What is happening with the knowledge gained from sequencing a mouse?

question: What have scientists been maintaining since 2013?

question: Where has the bacteria E. coli been found to be sequenced?

question: How old was the material used to sequence the Arabidopsis thaliana genome?
context: The development of new technologies has made it dramatically easier and cheaper to do sequencing, and the number of complete genome sequences is growing rapidly. The US National Institutes of Health maintains one of several comprehensive databases of genomic information. Among the thousands of completed genome sequencing projects include those for rice, a mouse, the plant Arabidopsis thaliana, the puffer fish, and the bacteria E. coli. In December 2013, scientists first sequenced the entire genome of a Neanderthal, an extinct species of humans. The genome was extracted from the toe bone of a 130,000-year-old Neanderthal found in a Siberian cave.

qas: question: What is a recent development in sequencing methods?
answers: text: massive parallel sequencing

question: Which company has led the way in sequencing of individual genetic makeup?
answers: text: Manteia Predictive Medicine

question: Whose complete genetic information was recorded in 2007?
answers: text: James D. Watson

question: What is Watson famous for helping discover?
answers: text: the structure of DNA

question: What is Manteia Predictive Medicine famous for discovering?

question: What technology did James D. Watson develop to sequence individual DNA?

question: What has James D. Watson recently develop that may lead to personal genome sequencing?

question: What did Manteia Predictive Medicine help discover the structure of in 2007?

question: Who pioneered using the DNA structure as a diagnostic tool?
context: New sequencing technologies, such as massive parallel sequencing have also opened up the prospect of personal genome sequencing as a diagnostic tool, as pioneered by Manteia Predictive Medicine. A major step toward that goal was the completion in 2007 of the full genome of James D. Watson, one of the co-discoverers of the structure of DNA.

qas: question: What is the term for something that lists the important and notable parts of a genome?
answers: text: genome map

question: Which group was created to generate a genome map of human genetic material?
answers: text: The Human Genome Project

question: Whose genome map greatly aided the Human Genome Project?
answers: text: Jean Weissenbach

question: Where did Weissenbach and his colleagues work?
answers: text: Genoscope

question: What does a genome map list the order of?

question: What does a genome sequence identify?

question: What is a Genoscope less detailed than?

question: What does a Genoscope help a scientist do?

question: Why was the Genoscope created?
context: Whereas a genome sequence lists the order of every DNA base in a genome, a genome map identifies the landmarks. A genome map is less detailed than a genome sequence and aids in navigating around the genome. The Human Genome Project was organized to map and to sequence the human genome. A fundamental step in the project was the release of a detailed genomic map by Jean Weissenbach and his team at the Genoscope in Paris.

qas: question: What is the term that accounts for the constituents of the haploid genome?
answers: text: Genome composition

question: What aspect of a genome can genome compositions help researchers in learning about?
answers: text: evolutionary history

question: What is the history of a genome used for?

question: What should be included in the history of a genome?

question: What can scientists learn by comparing repetitive DNA and genome size?

question: What term is used to describe the history of DNA?

question: By comparing repetitive DNA, what can scientists understand the history of?
context: Genome composition is used to describe the make up of contents of a haploid genome, which should include genome size, proportions of non-repetitive DNA and repetitive DNA in details. By comparing the genome compositions between genomes, scientists can better understand the evolutionary history of a given genome.

qas: question: What two types of organisms have remarkable differences in their genomic composition?
answers: text: prokaryotes and eukaryotes

question: What type of organizing can be observed in eukaryote genomes?
answers: text: exon-intron

question: In what types of eukaryotes is there a large amount of non-coding DNA?
answers: text: mammals and plants

question: What should you distinguish between when talking about gene coding?

question: How much of the genome is non-repetitive DNA in eukaryotes?

question: What is a major part of contents structure made of in non-coding regions?

question: What organization feature do prokaryotes have?

question: What area do mammals and plants have differences in?
context: When talking about genome composition, one should distinguish between prokaryotes and eukaryotes as the big differences on contents structure they have. In prokaryotes, most of the genome (85–90%) is non-repetitive DNA, which means coding DNA mainly forms it, while non-coding regions only take a small part. On the contrary, eukaryotes have the feature of exon-intron organization of protein coding genes; the variation of repetitive DNA content in eukaryotes is also extremely high. In mammals and plants, the major part of the genome is composed of repetitive DNA.

qas: question: What is an example of an organism that has a portion of its genetic material outside of its chromosomes?
answers: text: pathogenic microbe

question: What is an example of an organism whose full complement of genetic material resides in its chromosomes?
answers: text: virus

question: Where is additional genetic material found in pathogenic microbes?
answers: text: plasmids

question: What do viruses always carry within their structure?

question: Where is additional genetic material found in a virus?

question: What is another word used for genome?

question: What organism has part of its genetic material inside a virus?

question: What do most viruses more complex than plasmids carry?
context: Most biological entities that are more complex than a virus sometimes or always carry additional genetic material besides that which resides in their chromosomes. In some contexts, such as sequencing the genome of a pathogenic microbe, "genome" is meant to include information stored on this auxiliary material, which is carried in plasmids. In such circumstances then, "genome" describes all of the genes and information on non-coding DNA that have the potential to be present.

qas: question: What are examples of classes of eukaryotes where genome only refers to the information found in chromosomes?
answers: text: plants, protozoa and animals

question: What is a name for the genetic material found within chloroplasts?
answers: text: plastome

question: What is a name for the genetic makeup of mitochondria?
answers: text: mitochondrial genome

question: What are the eukaryotes found in the mitochondria called?

question: What are examples of chloroplasts?

question: What does genome mean when referring to eukaryotes such as mitochondria?

question: What is not considered as part of the plastome?

question: What do chloroplasts have that is referred to as the mitochondrial genome?
context: In eukaryotes such as plants, protozoa and animals, however, "genome" carries the typical connotation of only information on chromosomal DNA. So although these organisms contain chloroplasts or mitochondria that have their own DNA, the genetic information contained by DNA within these organelles is not considered part of the genome. In fact, mitochondria are sometimes said to have their own genome often referred to as the "mitochondrial genome". The DNA found within the chloroplast may be referred to as the "plastome".

qas: question: What is the name for the count of all DNA base pairs in a single haploid genome?
answers: text: Genome size

question: What does genome size have a direct relationship with in prokaryotes and lower eukaryotes?
answers: text: morphological complexity

question: What accounts for the breakdown of the relation between genome size and morphological complexity in higher eukaryotes?
answers: text: repetitive DNA

question: What is the term for the total DNA base pairs in one lower eukaryote?

question: What kind of relationship do copies of a haploid genome have with mollusks that isn't effective?

question: What has a strong influence on DNA base pairs?

question: What does a haploid genome have strong influence on?

question: How many base pairs are in mollusks?
context: Genome size is the total number of DNA base pairs in one copy of a haploid genome. The genome size is positively correlated with the morphological complexity among prokaryotes and lower eukaryotes; however, after mollusks and all the other higher eukaryotes above, this correlation is no longer effective. This phenomenon also indicates the mighty influence coming from repetitive DNA act on the genomes.

qas: question: What is a name for the reduced complement of genetic material necessary for an organism to live?
answers: text: minimal genomes

question: In what experimental contexts are experiments being carried out on minimal genomes?
answers: text: in vivo and in silico

question: What is a research strategy to understand silico?

question: What is being done on single cell silico?

question: In what two ways are experiments being carried out to understand how genes survive?

question: What do scientists want a silico to do in the experiment?

question: What are scientists studying to understand how they survive a reduction in silico?
context: Since genomes are very complex, one research strategy is to reduce the number of genes in a genome to the bare minimum and still have the organism in question survive. There is experimental work being done on minimal genomes for single cell organisms as well as minimal genomes for multi-cellular organisms (see Developmental biology). The work is both in vivo and in silico.

qas: question: What are two types of non-repetitive DNA?
answers: text: Protein-coding genes and RNA-coding genes

question: In higher eukaryotes, what has an inverse relationship with genome size?
answers: text: proportion of non-repetitive DNA

question: What is the size of non-repetitive DNA divided by to get the proportion of non-repetitive DNA?
answers: text: genome size

question: How is protein coding calculated?

question: What are two examples of higher eukaryotes?

question: What does having more protein coding genes not mean?

question: What decreases if RNA coding genes are increased?

question: What is the number of protein-coding genes divided by to get the proportion of non-repetitive DNA?
context: The proportion of non-repetitive DNA is calculated by using the length of non-repetitive DNA divided by genome size. Protein-coding genes and RNA-coding genes are generally non-repetitive DNA. A bigger genome does not mean more genes, and the proportion of non-repetitive DNA decreases along with increasing genome size in higher eukaryotes.

qas: question: What is an example of an organism which does not contain any repetitive DNA?
answers: text: E. coli

question: What are two organisms that have more non-repetitive than repetitive DNA?
answers: text: C. elegans and fruit fly

question: What is the percentage of non-repetitive DNA in some plant and amphibian genomes?
answers: text: 20%

question: What is the percentage of non-repetitive DNA in E. coli? 

question: What one kind of DNA do fruit flies only have?

question: What does E. coli tend to have more of than non-repetitive DNA?

question: What is a minority component in E. coli?

question: What do some plants and amphibians only have?
context: It had been found that the proportion of non-repetitive DNA can vary a lot between species. Some E. coli as prokaryotes only have non-repetitive DNA, lower eukaryotes such as C. elegans and fruit fly, still possess more non-repetitive DNA than repetitive DNA. Higher eukaryotes tend to have more repetitive DNA than non-repetitive ones. In some plants and amphibians, the proportion of non-repetitive DNA is no more than 20%, becoming a minority component.

qas: question: What are two types of repetitive DNA found in genomes?
answers: text: tandem repeats and interspersed repeats

question: What is found by dividing size of repetitive DNA by length of total genome?
answers: text: proportion of repetitive DNA

question: What are two examples of genome size?

question: What do you use to calculate genome size?

question: How do you calculate tandem repeats?

question: What are interspersed repeats divided by to get the proportion of repetitive DNA?

question: What do you get when dividing tandem repeats by interspersed repeats?
context: The proportion of repetitive DNA is calculated by using length of repetitive DNA divide by genome size. There are two categories of repetitive DNA in genome: tandem repeats and interspersed repeats.

qas: question: Unequal crossing over can create what type of repetitive DNA?
answers: text: Tandem repeats

question: What are two examples of tandem repeats in DNA?
answers: text: satellite DNA and microsatellites

question: What is the most common type of repetitive DNA in mammals?
answers: text: interspersed repeats.

question: In what group are tandem repeats in the largest number?

question: What causes interspersed repeats?

question: What are two examples of interspersed repeats?

question: How much satellite DNA is found in the genome?

question: What is gene conversion caused by?
context: Tandem repeats are usually caused by slippage during replication, unequal crossing-over and gene conversion, satellite DNA and microsatellites are forms of tandem repeats in the genome. Although tandem repeats count for a significant proportion in genome, the largest proportion in mammalian is the other type, interspersed repeats.

qas: question: What is the main source of interspersed repeats?
answers: text: Transposable elements

question: What do researchers think transposable elements are key factors in when considering higher eukaryotes?
answers: text: genome evolution

question: What are the constituents of Class 1 transposable elements?
answers: text: retrotransposons

question: What are the constituents of Class 2 transposable elements?
answers: text: DNA transposons

question: How are pseudogenes classified?

question: What two categories are pseudogenes classified into?

question: Where do cells mainly come from?

question: What do cells also include?

question: What are pseudogenes able to do within the cell?
context: Interspersed repeats mainly come from transposable elements (TEs), but they also include some protein coding gene families and pseudogenes. Transposable elements are able to integrate into the genome at another site within the cell. It is believed that TEs are an important driving force on genome evolution of higher eukaryotes. TEs can be classified into two categories, Class 1 (retrotransposons) and Class 2 (DNA transposons).

qas: question: What kind of genetic material can be produced from retrotransposons?
answers: text: RNA

question: What can long terminal repeats produce?

question: What happens when long terminal repeats are transcribed into RNA?

question: What is one thing RNA can be divided into?

question: What can the genome also be divided into?

question: Where are Long terminal repeats duplicated?
context: Retrotransposons can be transcribed into RNA, which are then duplicated at another site into the genome. Retrotransposons can be divided into Long terminal repeats (LTRs) and Non-Long Terminal Repeats (Non-LTR).

qas: question: What is a term that can describe how DNA transposons move?
answers: text: cut and paste

question: DNA transposons do not use which genetic material used by Class 1 TEs?
answers: text: RNA

question: What term describes how duplication happens in the genome?

question: What do genome not use as intermediate?

question: What helps metozoan move?

question: In what organism is duplication popular?

question: What does cut and paste help metazoan do?
context: DNA transposons generally move by "cut and paste" in the genome, but duplication has also been observed. Class 2 TEs do not use RNA as intermediate and are popular in bacteria, in metazoan it has also been found.

qas: question: What is another word for the total count of chromosomes?
answers: text: karyotype

question: Aside from karyotype, what are other genomic traits studied by scientists?
answers: text: genome size, gene order, codon usage bias, and GC-content

question: What were other traits besides karyotype studied by Brown in 2002?

question: What is another word for gene order?

question: What does GC-content have that can be measured?

question: Why do researchers calculate the sum of an organisms genes?

question: What are two things that Reese studied about karyotype in 2004?
context: Genomes are more than the sum of an organism's genes and have traits that may be measured and studied without reference to the details of any particular genes and their products. Researchers compare traits such as chromosome number (karyotype), genome size, gene order, codon usage bias, and GC-content to determine what mechanisms could have produced the great variety of genomes that exist today (for recent overviews, see Brown 2002; Saccone and Pesole 2003; Benfey and Protopapas 2004; Gibson and Muse 2004; Reese 2004; Gregory 2005).

qas: question: What type of generation of genetic material has a big part in making the genome what it is?
answers: text: Duplications

question: What is a possible product of duplications?
answers: text: genetic novelty

question: What role does genetic novelty play in the genome?

question: What is the first range of genetic novelty?

question: What are gene clusters a large part of?

question: How far can genetic novelty go?

question: What is the first example of genetic novelty?
context: Duplications play a major role in shaping the genome. Duplication may range from extension of short tandem repeats, to duplication of a cluster of genes, and all the way to duplication of entire chromosomes or even entire genomes. Such duplications are probably fundamental to the creation of genetic novelty.

qas: question: What is an explanation for the resemblance between disparate parts of the genome?
answers: text: Horizontal gene transfer

question: In which organisms does horizontal gene transfer appear to occur commonly?
answers: text: microbes

question: Parts of which organelle genomes are thought to have ended up in the nucleus of eukaryotic cells via transfer?
answers: text: chloroplast and mitochondrial genomes

question: What helps explain why different parts of chloroplasts are similar?

question: In what organism are eukaryotic cells common?

question: What does horizontal gene transfer explain about nuclear chromosomes?

question: Where do microbes transfer material from their chloroplast and mitochondrial genomes?

question: What do microbes transfer to chloroplasts?
context: Horizontal gene transfer is invoked to explain how there is often extreme similarity between small portions of the genomes of two organisms that are otherwise very distantly related. Horizontal gene transfer seems to be common among many microbes. Also, eukaryotic cells seem to have experienced a transfer of some genetic material from their chloroplast and mitochondrial genomes to their nuclear chromosomes.