Glires (/ˈɡlaɪəriːz, -aɪərz/; from Latin glīrēs 'dormice') is a clade (sometimes ranked as a grandorder) consisting of rodents and lagomorphs (rabbits, hares, and pikas). The hypothesis that these form a monophyletic group has been long debated based on morphological evidence. Two morphological studies, published in 2001 and 2003, strongly support the monophyly of Glires. In particular, the 2003 study reported the discovery of fossil material of basal members of Glires, particularly the genera Mimotona, Gomphos, Heomys, Matutinia, Rhombomylus, and Sinomylus. Their description, in 2005, helped to bridge the gap between more typical rodents and lagomorphs. Data published in 2001, based on nuclear DNA, supported Glires as a sister of Euarchonta to form Euarchontoglires, but some genetic data from both nuclear and mitochondrial DNA have been less supportive. A study, published in 2007, investigating retrotransposon presence/absence data unambiguously supports the Glires hypothesis. Studies published in 2011 and 2015 place Scandentia as a sister clade of the Glires, invalidating Euarchonta as a clade.
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Retrotransposon in the context of Fowl
Fowl are birds belonging to one of two biological orders, namely the gamefowl or landfowl (Galliformes) and the waterfowl (Anseriformes). Anatomical and molecular similarities suggest these two groups are close evolutionary relatives; together, they form the fowl clade which is scientifically known as Galloanserae or Galloanseres (initially termed Galloanseri) (Latin gallus ("rooster") + ānser ("goose")). This clade is also supported by morphological and DNA sequence data as well as retrotransposon presence/absence data.
Retrotransposon in the context of Telomerase
Telomerase, also called terminal transferase, is a ribonucleoprotein that adds a species-dependent telomere repeat sequence to the 3' end of telomeres. A telomere is a region of repetitive sequences at each end of the chromosomes of most eukaryotes. Telomeres protect the end of the chromosome from DNA damage or from fusion with neighbouring chromosomes. The fruit fly Drosophila melanogaster lacks telomerase, but instead uses retrotransposons to maintain telomeres.
Telomerase is a reverse transcriptase enzyme that carries its own RNA molecule (e.g., with the sequence 3′-CCCAAUCCC-5′ in Trypanosoma brucei) which is used as a template when it elongates telomeres. Telomerase is active in gametes and most cancer cells, but is normally absent in most somatic cells.
Retrotransposon in the context of Gene duplication
Gene duplication (or chromosomal duplication or gene amplification) is a mechanism through which new genetic material is generated during molecular evolution. It can be defined as any duplication of a region of DNA that contains a gene. Gene duplications can arise as products of several types of errors in DNA replication and repair machinery as well as through fortuitous capture by selfish genetic elements. Common sources of gene duplications include ectopic recombination, retrotransposition event, aneuploidy, polyploidy, and replication slippage.
Retrotransposon in the context of Laurasiatheria
Laurasiatheria (/lɔːrˌeɪʒəˈθɪəriə, -θɛriə/; "Laurasian beasts") is a superorder of placental mammals that groups together true insectivores (eulipotyphlans), bats (chiropterans), carnivorans, pangolins (pholidotes), even-toed ungulates (artiodactyls), odd-toed ungulates (perissodactyls), and all their extinct relatives (pan-euungulates). From systematics and phylogenetic perspectives, it is subdivided into order Eulipotyphla and clade Scrotifera. It is a sister group to Euarchontoglires with which it forms the magnorder Boreoeutheria. Laurasiatheria was discovered on the basis of the similar gene sequences shared by the mammals belonging to it; no anatomical features have yet been found that unite the group, although a few have been suggested such as a small coracoid process, a simplified hindgut (reversed in artiodactyls), high intelligence, lack of grasping hands (though mimicry of grasping is observed in felines) and allantoic vessels that are large to moderate in size. The Laurasiatheria clade is based on DNA sequence analyses and retrotransposon presence/absence data. The superorder originated on the northern supercontinent of Laurasia, after it split from Gondwana when Pangaea broke up. Its last common ancestor is supposed to have lived between ca. 76 to 90 million years ago.
Retrotransposon in the context of Reverse transcription
A reverse transcriptase (RT) is an enzyme used to convert RNA to DNA, a process termed reverse transcription. Reverse transcriptases are used by viruses such as HIV and hepatitis B to replicate their genomes, by retrotransposon mobile genetic elements to proliferate within the host genome, and by eukaryotic cells to extend the telomeres at the ends of their linear chromosomes. The process does not violate the flows of genetic information as described by the classical central dogma, but rather expands it to include transfers of information from RNA to DNA.
Retroviral RT has three sequential biochemical activities: RNA-dependent DNA polymerase activity, ribonuclease H (RNase H), and DNA-dependent DNA polymerase activity. Collectively, these activities enable the enzyme to convert single-stranded RNA into double-stranded cDNA. In retroviruses and retrotransposons, this cDNA can then integrate into the host genome, from which new RNA copies can be made via host-cell transcription. The same sequence of reactions is widely used in the laboratory to convert RNA to DNA for use in molecular cloning, RNA sequencing, polymerase chain reaction (PCR), or genome analysis.