View source for General Information/IS naming

====What’s in a name?====
It is clearly important to construct a suitable naming system for biological objects such as transposable elements since it should provide a framework for understanding what they are (e.g. '''IS''' – Insertion Sequence; '''Tn''' – Transposon; '''In''' - integron), where they were initially identified (e.g. IS'''''Ec''''' – ''[[wikipedia:Escherichia_coli|Escherichia coli]]''; IS'''''Sfl''''' – ''[[wikipedia:Shigella_flexneri|Shigella flexneri]]'') and of the particular type (IS''Ec'''1, 2, 3, 4'''''<nowiki/>'''…''') which allows them to be identified when in multiple copies in a large population of different TE in a particular host, strain, species, or genera. Grouping them into families, even though these may change with time and further knowledge (e.g. IS''4'' <ref>{{#pmid:PMC2266710</ref>, also provides information on their relationship with one another. A robust classification system is important since specific properties of one IS in a family are inferred to be shared by other closely related IS in the same family facilitating understanding transposition mechanisms and the way in which closely related IS from different genomes might impact their host genomes. In cases where, for technical reasons, certain experiments cannot be undertaken with one member of a family, its behavior in shaping its host chromosome or plasmid can often be inferred from knowledge of that of other members of the family.  

====TE nomenclature rules defined in 1979====
A committee assembled during the meeting on DNA Insertions at [https://www.cshl.edu/ Cold Spring Harbor] in 1976 proposed a set of rules to be used for the nomenclature of '''T'''ransposable '''E'''lements <ref name=":1">{{#pmid:18778731</ref>. The first attempt to create an concise nomenclature system for '''T'''ransposable '''E'''lements started at [https://www.stanford.edu/ Stanford University] by Campbell and colleagues in 1979 <ref name=":0">{{#pmid:467979</ref>. They classified the prokaryotes elements as simple IS elements to more complex Tn transposons, and self-replicating episomes. In addition, definitions and nomenclature rules for these three classes of prokaryotic TEs were specified <ref name=":0" /> ('''Table 1'''). ISs and TEs were named separately by having IS and Tn as a prefix, respectively, followed by a sequential number in italics such as IS''1'', IS''2'' and Tn''1'', Tn2, etc <ref name=":62">{{#pmid:31624505</ref>.<center>
{| class="wikitable" style="width: 85%;"
|+'''Table 1.''' TE nomenclature rules defined by [https://pubmed.ncbi.nlm.nih.gov/467979/ Campbell et al., 1979]
!Classes
!Definition
!Naming rule
|-
|'''IS elements'''
|IS elements contain no known genes unrelated to insertion functions and are shorter than 2kb.
|IS''1'', IS''2'', IS''3'', IS''4'', IS''5'', etc, with the numbers italicized
|-
|'''Tn elements'''
|Tn are more complex, often containing two copies of an IS element. They are generally larger than 2kb, and contain additional genes unrelated to insertion functions.
|Tn''1'', Tn''2'', Tn''3'', etc, with the numbers italicized
|-
|'''Episomes'''
|Episomes are complex, self-replicating elements, often containing IS and Tn elements. Examples include the phage λ and plasmid F of ''E. coli.''
| -
|}
</center>

====Revised Nomenclature for Insertion Sequences in 2000====
In the late 1990s, several different nomenclature systems were being used. That centralized by [[wikipedia:Esther_Lederberg|Dr Esther Lederberg]] (Stanford University Medical School, CA, USA <ref name=":12">{{#pmid:18778731</ref>) allocated simple numbers to IS and Tn  (e.g. IS1, 2, 3, 4....Tn1,2,3 etc.)  and [https://www-is.biotoul.fr/reserved_blocks.php lists for the registry of these allocations were subsequently published] <ref>{{#pmid:3036649</ref>. These allocations stopped with the retirement of Dr Lederberg and gradually a variety of ways of naming TE appeared in the literature <ref name=":12" />. This included IS names which indicated the bacterial source (e.g. ISRm1 for ''[[wikipedia:Sinorhizobium_meliloti|Rhizhobium meliloti]]'') and other, less clear methods (e.g. RSalpha-9). ISfinder finally assumed the role of administrating the nomenclature and began to systematically use a similar system <ref>Chandler and Mahillon ''Insertion sequence nomenclature.'' In: ''Asm news'', Vol. 66, no. 6, p. 324-324 (2000)</ref> to that used for the numerous restriction modification/ (see '''<ref name=":1" />''') enzymes. A list of [https://www-is.biotoul.fr/nomenclature.php names] proposed for be used for different bacterial and archaeal genera and species and the [https://www-is.biotoul.fr/list_names_attributed.php attributions] are included in ISfinder.

====Revised Nomenclature for Transposable Genetic Elements proposed in 2008====

Over this period, new types of transposable elements, such as the mobilizable and conjugative transposons, were being discovered <ref>{{#pmid:26104437</ref><ref>{{#pmid:26104696</ref><ref>{{#pmid:11018140</ref>. Additionally, interactions between different elements including transposition and/or recombination events led to novel chimeric transposons. These exacerbated the nomenclature problem <ref name=":12" />. Subsequent nomenclature systems have become complicated, with different systems being adopted for related elements by different research groups <ref name=":12" />. Therefore, Roberts and colleagues in 2008 proposed a new version of the early nomenclature system, but not including non-autonomous elements (such as integron cassettes and MITEs) <ref name=":12" /> ('''Table 2''').<center>
{| class="wikitable" style="width: 85%;"
|+Table 2. Revised Nomenclature for Transposable Genetic Elements proposed by Roberts et al., 2008.
!Type of transposable element <sup>a</sup>
!Definition
|-
|'''Composite transposons'''
|Flanked by IS elements. The transposase of the IS element is responsible for the catalysis of insertion and excision.
|-
|'''Unit transposons'''
|Typical unit elements encode an enzyme involved in excision and integration (DD(35)E or tyrosine) often a site-specific recombinase or resolvase and one or several accessory (e.g. resistance) genes in one genetic unit.
|-
|'''Conjugative transposons (CTns) / Integrative conjugative elements (ICEs)'''
|The conjugative transposons (CTns), also known as integrative conjugative elements (ICEs), carry genes for excision, conjugative transfer, and for integration within the new host genome. They carry a wide range of accessory genes, including antibiotic resistance
|-
|'''Mobilisable transposons (MTns) / Integrative mobilisable elements (IMEs)'''
|The mobilizable transposons (MTns), also known as integrative mobilizable elements (IMEs), can be mobilized between bacterial cells by other “helper” elements that encode proteins involved in the formation of the conjugation pore or mating bridge. The MTns exploit these conjugation pores and generally provide their own DNA processing functions for intercellular transfer and subsequent transposition.
|-
|'''Mobile genomic islands'''
|Some chromosomally integrated genomic islands encode tyrosine or serine site-specific recombinases that catalyze their own excision and integration but do not harbor genes involved in the transfer. They carry genes encoding for a range of phenotypes. The name of a genomic island reflects the phenotype it confers, e.g. pathogenicity islands encode virulence determinants (toxins, adhesins etc).
|-
|'''Integrated or transposable prophage'''
|An integrated or transposable prophage is a phage genome inserted as part of the linear structure of the chromosome of a bacterium which is able to excise and insert from and into the genome.
|-
|'''Integrated satellite prophage'''
|Bacteriophage genome inserted into that of the host which requires gene products from “helper” phages to complete its replication cycle
|-
|'''Group I intron'''
|Small post-transcriptionally splicing (splicing occurs in the pre-mRNA), endonuclease encoding element. Will home to the allelic site
|-
|'''Group II intron'''
|Small post-transcriptionally splicing (splicing occurs in the pre-mRNA), restriction endonuclease encoding element
|-
|'''IStron intein'''
|Chimeric ribozyme consisting of a group I intron linked to an IS''605'' like transposase Small post-translational splicing (splicing occurs in the polypeptide), endonuclease encoding element. Will home to allelic site.
|}
<sup>a</sup>; not all reported elements have been shown to be mobile
</center>

====IS classification system proposed in 2008====
Likewise, a number of different types of IS derivatives also began to be identified and the ISfinder nomenclature scheme was extended to these distinct forms <ref>Michael Chandler, Patricia Siguier, Jacques Mahillon. Nomenclature for insertion sequences and other forms. Microbe. 10 (45) 2008.</ref> and now including terms and definitions for MICs ('''M'''obile '''I'''nsertion '''C'''assette), composed of passenger genes but no transposase, MITES ('''M'''iniature '''I'''nverted repeat '''T'''ransposable '''E'''lement), which are short IS-related elements with no internal open reading frame but which, like most ISs, transposons and MICs, include IS-like extremities and tIS which are IS into which passenger genes have been incorporated. It is important to note that a single IS might in principle be represented in all four forms ('''Table 3''')
<center>
{| class="wikitable"
|+'''Table 3. IS classification system proposed by Siguier et al., 2008'''
!
!'''Extremities'''
!Transposase
!'''Passenger genes'''
|-
|'''MITE'''
|yes
|no
|no
|-
|'''IS'''
|yes
|yes
|no
|-
|'''tIS'''
|yes
|yes
|yes
|-
|'''MIC'''
|yes
|no
|yes<br />
|} 
</center>
====IS identification====
[[Image:1.5.1.png|thumb|640x640px|'''Fig.5.1.''' '''Results of Markov Cluster (MCL) Analysis.''' Each circle represents an individual IS transposase amino acid sequence. a) Inflation factor of 1.2, score >30 (links with scores of less than 30 were removed).  IS<i>1</i> family: blue circles. IS<i>1595</i> family: green circles. b) The inflation factor of 2 increases stringency and separates each major group into groups. The IS<i>1</i> family generated the IS<i>Mhu11</i> group (magenta). The IS<i>1595</i> family separated into four groups: IS<i>1595</i> <span style="color:#FFFFFF; background:#008000">(green)</span>, IS<i>1016</i> <span style="color:#000000; background:#ffff00">(yellow)</span>, IS<i>Pna2</i> <span style="color:#FFFFFF; background:#0000ff">(blue</span>-<span style="color:#FFFFFF; background:#008000">green)</span>, and IS<i>H4</i> <span style="color:#000000; background:#00ffff">(light blue)</span>. c) Gradually reducing the weakest links between groups (Inflation factor 2, score >140) further divided the IS<i>1595</i> family into 4 additional groups (IS<i>1595</i>, IS<i>Sod1</i>, IS<i>Nwi1</i>, and IS<i>Nha5</i>).|alt=|border]]

'''<big>T</big>'''he families in ISfinder are defined using an initial manual [https://blast.ncbi.nlm.nih.gov/Blast.cgi BLAST] analysis often followed by reiterative [https://blast.ncbi.nlm.nih.gov/Blast.cgi BLAST] analyses with the primary transposase sequence of representative elements used as a query in a BLASTP<ref>{{#pmid:2231712</ref> search of microbial genomes. Potential full-length Tpases are retained and that with the lowest score then used as a query in a second BLASTP search. This is continued until no new potential candidates are detected. The [http://www.clustal.org/ ClustalW] multiple alignment algorithm<ref>{{#pmid:7984417</ref> is then used and the results displayed using the [https://www.jalview.org/ Jalview] alignment editor<ref>{{#pmid:14960472</ref> for assessment. 

The corresponding DNA together with 1000 base pairs up- and down-stream is then extracted and examined manually for the IRs or other typical features such as secondary structures and flanking '''D'''irect '''R'''epeats (DRs). This, together with a comparison of the DNA extremities of various elements, allows identification of both ends of the collected elements. In cases where more than a single IS copy is identified, BLASTN can be used to define the IS ends. Where only a single copy is found, the ends can often be defined by identifying and comparing it with empty sites.

In a second step, we use the Markov Cluster Algorithm (MCL) (http://micans.org/mcl/)<ref>Van Dongen S. A cluster algorithm for graphs. Technical Report INS-R0010, National Research Institute for Mathematics and Computer Science in the Netherlands Amsterdam. 2000; </ref><ref>{{#pmid:11917018</ref> to weigh the relationships between clusters of ISs and to validate prior ISfinder classification of ISs into families and subgroups. This is explained in detail in <ref>{{#pmid:19286454</ref> and is based on the parameters used in the MCL [[:Image:1.5.1.png|(Fig.5.1)]] in addition to characteristics such as the specificity of target site duplications, the detailed sequence of the ends, genetic organization. 

It should be understood that the distinction between families and subgroups can evolve as the number of ISs in the database increases.
Several semi-automatic IS annotation pipelines are now available. The interested reader is directed to three of these: [http://issaga.biotoul.fr/issaga_index.php ISsaga]<ref>{{#pmid:21443786</ref> which is now integrated into the ISfinder platform<ref>{{#pmid:16381877</ref>, ISScan<ref>{{#pmid:17686783</ref> and Oasis<ref>{{#pmid:22904081</ref>. At present, ''de novo'' prediction of ISs is not efficient and these pipelines all employ the ISfinder database to function. While all three pipelines permit identification of IS fragments as well as full length ISs, a certain level of manual assessment is essential.

=====Insertion Sequences nomenclature and naming attribution=====
Nowadays the IS nomenclature and naming attribution is controlled by [https://www-is.biotoul.fr/index.php ISfinder database] team <ref name=":5">{{#pmid:16381877</ref>. They adopted a nomenclature similar to that of restriction enzymes <ref name=":5" />. Although this is not perfect, since some ISs are found in different species or even in different genera, the system is viable and has the advantage of indicating the host species rather than being confronted with a long series of numbers in the names as in the original nomenclature system <ref name=":02">{{#pmid:467979</ref><ref name=":5" />. The original Campbell classification system assign blocks of IS numbers to individual scientists, groups or institutions<ref name=":02" />. The ISfinder database includes a listing of these original ISs numbers together with the last known address of the attribution <ref name=":5" /> (See [https://isfinder.biotoul.fr/reserved_blocks.php ISfinder page]). Moreover, ISfinder includes an online form for registering (requesting a name for) new ISs <ref name=":5" /> (See [https://isfinder.biotoul.fr/request_name_form.php ISfinder form]). Several journals now suggest that authors register their new IS elements with ISfinder before publication<ref name=":5" />. Since a unique name can be attributed, this avoids some of the confusion in the literature<ref name=":5" />.
=====Tn nomenclature and naming attribution=====
The Tn nomenclature and naming attribution is controlled by "[https://transposon.lstmed.ac.uk/ The Transposon Registry]" database <ref name=":4">{{#pmid:31624505</ref>. The Transposon Registry is a nomenclature system for the assignment of Tn numbers for bacterial and archaeal autonomous TEs, including unit transposons, composite transposons, conjugative transposons (CTns)/Integrative Conjugative Elements (ICEs), Mobilisable transposons (MTns)/Integrative mobilizable elements (IMEs) and mobile genomic islands<ref name=":4" />. It excludes ISs, which are managed by ISfinder database and other TEs such as introns and inteins for which other databases already exist, and non-autonomous TEs such as integron cassettes and MITES<ref name=":4" />.
====Bioinformatics approaches for TE identification and annotation in prokaryotes genomes====
Most genome annotation pipelines developed to date are dedicated to the prediction and characterization of coding regions and their putative products, signal peptides, pseudogenes, and noncoding RNAs. Surprisingly, annotation of ubiquitous genomic features such as Mobile Genetic Elements (MGEs) is generally not fully addressed and/or is neglected in most of these pipelines, and thus MGEs are seldom well-characterized and annotated <ref name=":7">{{#pmid:29277867</ref>.

To begin an analysis of the MGE content of a given genome, it is first necessary to identify and annotate ordinary genome features such as coding sequences (CDSs), rRNAs, and tRNAs <ref name=":7" /> . For MGE detection and annotation, it is essential to use a variety of approaches including additional specialized pipelines and software which are normally not implemented in a regular annotation pipeline <ref name=":7" />. Therefore, it is not a simple task and requires different approaches depending on the level of analysis (reviewed in<ref name=":7" />).
====Eukaryotic TE nomenclature and naming attribution====
TEs have been found in virtually all eukaryotic species investigated so far, displaying an extreme diversity, revealed by thousands or even tens of thousands of different TE families<ref name=":2">{{#pmid: 2543105</ref>. Finnegan and colleagues in 1989,  proposed the first TE classification system, which distinguished two classes by their transposition intermediate: RNA ('''Class I or retrotransposons''') or DNA ('''Class II or DNA transposons''')<ref name=":2" /><ref name=":3">{{#pmid:2543105</ref>. The transposition mechanism of '''Class I''' is commonly called ‘'''copy-and-paste'''’, and that of '''Class II''', ‘'''cut-and-paste'''’ <ref name=":3" />. Later, in 2007, Wicker and colleagues proposed a common TE classification system that can be easily handled by non-specialists during genome and TEs annotation procedures<ref name=":8">{{#pmid:17984973</ref>. This system provided a consensus between the various conflicting classification and naming systems that are currently in use<ref name=":2" />. A key component of this system is a naming convention: a three-letter code with each letter respectively denoting '''class''', '''order''' and '''superfamily'''; the '''family''' (or '''subfamily''') name; the sequence (database accession number) on which the element was found; and the ‘running number’, which defines the individual insertion in the accession. The unified system is also intended to facilitate comparative and evolutionary studies on TEs from different species <ref name=":8" /> .

Nowadays, the Wicker TE classification system is well-recognized by the scientific community and is currently in use by Eukaryotic TE annotation pipelines, such as REPET<ref>{{#pmid:21304975</ref><ref>{{#pmid:16110336</ref>, PASTEC<ref>{{#pmid:24786468</ref> and RepeatExplorer <ref>{{#pmid:23376349</ref>, and many others.
<br />
==Bibliography==
<references />