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| Content | |
| Description | Long terminal repeat-retrotransposons |
| Organisms | Rice |
| Contact | |
| Primary citation | Chaparro & al. (2007) [1] |
| Release date | 2006 |
| Access | |
| Website | http://retroryza.fr/ |
RetrOryza is a database of Long terminal repeat-retrotransposons for the rice genome. [1]
In the fields of molecular biology and genetics, a genome is all genetic information of an organism. It consists of nucleotide sequences of DNA. The genome includes both the genes and the noncoding DNA, as well as mitochondrial DNA and chloroplast DNA. The study of the genome is called genomics. The genome for several organisms have been sequenced and genes analyzed, the human genome project which sequenced the entire genome for Homo sapiens was successfully completed in April 2003.
Retroposons are repetitive DNA fragments which are inserted into chromosomes after they had been reverse transcribed from any RNA molecule.
A transposable element is a DNA sequence that can change its position within a genome, sometimes creating or reversing mutations and altering the cell's genetic identity and genome size. Transposition often results in duplication of the same genetic material. Barbara McClintock's discovery of them earned her a Nobel Prize in 1983.
Oryza is a genus of plants in the grass family. It includes the major food crop rice. Members of the genus grow as tall, wetland grasses, growing to 1–2 m tall; the genus includes both annual and perennial species.
Retrotransposons are a type of genetic component that copy and paste themselves into different genomic locations (transposon) by converting RNA back into DNA through the process reverse transcription using an RNA transposition intermediate.
Oryza sativa, commonly known as Asian rice, is the plant species most commonly referred to in English as rice. It is the type of farmed rice whose cultivars are most common globally, and was first domesticated in the Yangtze River basin in China 13,500 to 8,200 years ago.
Retrotransposon markers are components of DNA which are used as cladistic markers. They assist in determining the common ancestry, or not, of related taxa. The "presence" of a given retrotransposon in related taxa suggests their orthologous integration, a derived condition acquired via a common ancestry, while the "absence" of particular elements indicates the plesiomorphic condition prior to integration in more distant taxa. The use of presence/absence analyses to reconstruct the systematic biology of mammals depends on the availability of retrotransposons that were actively integrating before the divergence of a particular species.
LTR or ltr may refer to:
A long terminal repeat (LTR) is a pair of identical sequences of DNA, several hundred base pairs long, which occur in eukaryotic genomes on either end of a series of genes or pseudogenes that form a retrotransposon or an endogenous retrovirus or a retroviral provirus. All retroviral genomes are flanked by LTRs, while there are some retrotransposons without LTRs. Typically, an element flanked by a pair of LTRs will encode a reverse transcriptase and an integrase, allowing the element to be copied and inserted at a different location of the genome. Copies of such an LTR-flanked element can often be found hundreds or thousands of times in a genome. LTR retrotransposons comprise about 8% of the human genome.
The R2 RNA element is a non-long terminal repeat (non-LTR) retrotransposable element that inserts at a specific site in the 28S ribosomal RNA (rRNA) genes of most insect genomes. In order to insert itself into the genome, retrotransposon encoded protein (R2) protein makes a specific nick in one of the DNA strands at the insertion site and uses the 3′ hydroxyl group exposed by this nick to prime the reverse transcription process termed target primed reverse transcription (TPRT), where the RNA genome is transcribed into DNA.
Magnaporthe salvinii is a fungus known to attack a variety of grass and rice species, including Oryza sativa and Zizania aquatica. Symptoms of fungal infection in plants include small, black, lesions on the leaves that develop into more widespread leaf rot, which then spreads to the stem and causes breakage. As part of its life cycle, the fungus produces sclerotia that persist in dead plant tissue and the soil. Management of the fungus may be effected by tilling the soil, reducing its nitrogen content, or by open field burning, all of which reduce the number of sclerotia, or by the application of a fungicide.
Broken rice is fragments of rice grains, broken in the field, during drying, during transport, or during milling. Mechanical separators are used to separate the broken grains from the whole grains and sort them by size.
Oryza barthii, also called Barth's rice, wild rice, or African wild rice, is a grass in the rice genus Oryza. It is an annual, erect to semierect grass. It has leaves with a short ligule (<13 mm), and panicles that are compact to open, rarely having secondary branching. The inflorescence structure are large spikelets, 7.7-12.3 mm long and 2.3-3.5 mm wide, with strong awns, usually red. The inflorescences have anthers 1.5–3 mm long.
Oryza rufipogon, known as brownbeard rice, wild rice, and red rice, is a member of the genus Oryza.
Oryza longistaminata is a perennial species of grass from the same genus as cultivated rice. It is native to most of sub-Saharan Africa and Madagascar. It has been introduced into the United States, where it is often regarded as a noxious weed. Its common names are longstamen rice and red rice.
Oryza glaberrima, commonly known as African rice, is one of the two domesticated rice species. It was first domesticated and grown in West Africa around 3,000 years ago. In agriculture, it has largely been replaced by higher-yielding Asian rice, and the number of varieties grown is declining. It still persists, making up an estimated 20% of rice grown in West Africa. It is now rarely sold in West African markets, having been replaced by Asian strains.
Japonica rice, sometimes called sinica rice, is one of the two major domestic types of Asian rice varieties. Japonica rice is extensively cultivated and consumed in East Asia, whereas in most other regions indica rice is the dominant type of rice. Japonica rice originated from Central China, where it was first domesticated along the Yangtze River basin approximately 9,500 to 6,000 years ago.
LTR retrotransposons are class I transposable element characterized by the presence of long terminal repeats (LTRs) directly flanking an internal coding region. As retrotransposons, they mobilize through reverse transcription of their mRNA and integration of the newly created cDNA into another location. Their mechanism of retrotransposition is shared with retroviruses, with the difference that most LTR-retrotransposons do not form infectious particles that leave the cells and therefore only replicate inside their genome of origin. Those that do (occasionally) form virus-like particles are classified under Ortervirales.
Long interspersed nuclear elements (LINEs) are a group of non-LTR retrotransposons that are widespread in the genome of many eukaryotes. They make up around 21.1% of the human genome. LINEs make up a family of transposons, where each LINE is about 7,000 base pairs long. LINEs are transcribed into mRNA and translated into protein that acts as a reverse transcriptase. The reverse transcriptase makes a DNA copy of the LINE RNA that can be integrated into the genome at a new site.
A plant genome assembly represents the complete genomic sequence of a plant species, which is assembled into chromosomes and other organelles by using DNA fragments that are obtained from different types of sequencing technology.
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