Suggested Guidelines for Naming Helitrons

 

Hugo K Dooner1, L. Curtis Hannah2, and Shailesh Lal3

1 Waksman Institute, Rutgers University, Piscataway, NJ 08855

2 Horticultural Sciences, University of Florida, Gainesville, FL 32611

3 Dept. of Biological Sciences, Oakland University, Rochester, MI 48039

 

PREAMBLE:  Helitrons are a novel class of transposable elements discovered recently by computational analysis of the complete genome sequences of C. elegans, Arabidopsis, and rice (Kapitonov, V. V. & Jurka, J. 2001. Proc Natl Acad Sci USA 98, 8714-8719).  It has become apparent that, in maize, helitrons are both abundant and highly variable in sequence.  There are currently no guidelines for naming these elements, yet they are highly diverse in size and sequence because they can pick up different gene fragments from the maize genome.  Their diversity in sequence is presently matched by their diversity in names.  For example, they have been named according to the gene where they insert (helitron sh2-7527; helitron ba1-ref) or the names of the locus and ferried gene fragments (helitrons 9002NOPQ and 9008 HI) or identified with a letter (HelA; HelB).  In an attempt to introduce some order into this chaos, we would like to suggest a nomenclature system for maize helitrons at the onset of the maize genome sequencing project.  These guidelines arose from informal discussions at the Maize Genetics Conference in Asilomar in March, 2006.  We will adopt these guidelines in our future publications and hope that other researchers working with helitrons will adopt them, as well.

 

NOMENCLATURE: Although they differ greatly in internal sequences, maize helitrons share substantial sequence homology at their 5Õ and 3Õ ends, the latter being more highly conserved.  By comparing the 3Õ terminal 30 nucleotides of maize helitron sequences currently in the database, it is clear that the elements group into two major clades, Hel1 and Hel2.  The elements in the larger Hel1 clade share at least 70% sequence identity; those in the smaller Hel2 clade are less related, sharing around 50% identity.  We anticipate that many new elements will be identified as helitrons because of conserved sequence features at their 5Õ and 3Õ ends (Kapitonov, V. V. & Jurka, J. 2001).  We propose that new elements be grouped into either Hel1 or Hel2 superfamilies based on the relationship of their 3Õ terminal 30 bp to the respective consensus sequences.  Presently, the consensus sequences for Hel1 and Hel2 correspond to the sequences of HelA and HelB, respectively, in the bz locus of line McC (Lai, J., Li, Y., Messing, J. & Dooner, H. K. 2005. Proc Natl Acad Sci U S A 102, 9068-9073.).  We also propose a criterion of 50% identity as the cutoff to assign helitrons to a particular superfamily.  If, by this criterion, additional helitron superfamilies are identified in the future, they should be named Hel3, Hel4, and so on.

 

Following the symbol designating the superfamily to which a helitron belongs would be a number provided by a clearing house for helitron nomenclature (see below) and an identifier, in parentheses, consisting of the locus or mutation where the element is found, if known, separated by a colon from the name of the maize line.  For simplicity, the entire helitron symbol should be italicized.  Thus, the helitron in sh2-7527 would be Hel1-1(sh2-7527), the first one discovered, and the one in the bz genomic region of McC would be Hel1-3(bz:McC).  The NOPQ element in locus 9002 of B73 would be Hel1-x(9002:B73), where x would stand for a number assigned by the helitron nomenclature clearing house.

 

If a helitron is discovered that is virtually identical to a previously described helitron, but at a different locus, than the letter ÒaÓ is placed after the number assigned to the first helitron and a letter ÒbÓ is placed after the number of the second helitron.  Again, the parenthetical identifier would include the locus and line carrying the new helitron.  For example, B73 has an almost identical copy of Hel1-3(bz:McC) in chromosome 5S, at the same map location as umc1260.  The Hel1 element in the bz locus would become Hel1-3a(bz:McC) and the one in 5S, Hel1-3b(umc1260:B73).  If a helitron is discovered that is virtually identical to a previously described helitron at the same locus, but in a different line, then it should be given the same designation as the first one, specifying in the parenthetical identifier the names of the locus and line where found.  For example, McC and W22 have a copy of Hel1-3 at the same site in the bz genomic region.  The helitron in W22 would then be named Hel1-3a(bz:W22).  Note that this designation does not imply absolute sequence identity of the two helitrons (which is, actually, not the case here).  As with genes, it will be up to the individual investigator to assess sequence relatedness from the sequence database records.  Finally, if a helitron is identified in a BAC sequence not yet associated with any locus, the number of the BAC in the GenBank record can substitute temporarily for the locus name.

 

Dr. Shailesh Lal at Oakland University, MI, has agreed to serve as clearing house for assigning blocks of numbers to investigators, institutions, or multi-institutional projects, such as the maize genome initiative, that have identified new helitrons.

 

AUTONOMOUS HELITRONS.  An autonomous helitron has not been discovered.  Following maize genetics convention, an autonomous helitron can only be defined by a functional test.  Therefore, helitrons should not be designated as ÒautonomousÓ solely on the basis of sequence homology.  If, based on its sequence content, e.g., an intact replicase and helicase, a helitron is considered to be potentially autonomous, it could be called a putative autonomous helitron, yet given a symbol based on the general nomenclature guidelines.  It is suggested that, once confirmed, an autonomous helitron be designated aHel, followed by an identifier as described above.