About
In
plants, ploidy levels and
repetitive sequences contribute significantly to genome size. A number
of
different repetitive sequences have been reported in the plant genome
and these
can be classified into super-classes, classes, and subclasses based on
structure
and sequence composition. The transposable element (TEs) super-class
includes
retrotransposons, transposons, and miniature inverted-repeat
transposable
elements (MITEs). Other repetitive sequences are associated the
centromere and
telomere. Another super-class of repetitive sequences are rDNAs which
encode
the structural RNA components of ribosomes.
Methods
Repetitive
DNA sequences of selected
plant genera were queried from GenBank and other published records.
After
eliminating the duplicated sequences and vector sequences, the repeats
were coded into five
superclasses: Transposable
elements, Centromere-related, Telomere-related, rDNA and Unclassified.
The
superclasses were then broken down into major classes of repeats. The
collected
repetitive sequences within the same plant family were combined into a
repeat
database for the plant family.
The extracted
repeats for a
genus (e.g. Oryza), if available, were generated by
searching available
genomic sequences from the HTGS and PLN divisions of GenBank with the
family
repeat database (e.g. Gramineae Repeat Database) using FLAST.
Genomic
sequences that matched a repetitive DNA sequence in the family repeat
database
with ~75% identity and ~95% in overall length were selected, and coded
accordingly. The sequences were combined with repetitive sequences
obtained
previously from public databases, to create the repeat database
for that
genus. Please click here
to get the
composition of each repeat
database.
Codes for Plant Repetitive Sequences
Super-class
|
Class
|
Sub-class
|
Code
|
|
|
Transposable
Elements |
Retrotransposons |
Ty1-copia |
TERT001 |
|
|
Ty3-gypsy |
TERT002 |
|||
|
LINE |
TERT003 |
|||
|
SINE |
TERT004 |
|||
|
Unclassified
Retrotransposons |
TERTOOT |
|||
|
|
||||
|
Transposons |
Ac/Ds |
TETN001 |
||
|
CACTA,
En/Spm |
TETN002 |
|||
|
Mutator
(MULE) |
TETN003 |
|||
|
Mariner
(MLE) |
TETN004 |
|||
|
ping/pong/SNOOPY |
TETN005 |
|||
|
Unclassified
Transposons |
TETNOOT |
|||
|
|
||||
|
Miniature
inverted-repeat transposable elements (MITEs) |
Tourist |
TEMT001 |
||
|
Stowaway |
TEMT002 |
|||
|
Crackle |
TEMT003 |
|||
|
Explorer |
TEMT004 |
|||
|
Gaijin/Gaigin |
TEMT005 |
|||
|
Castaway |
TEMT006 |
|||
|
Snap |
TEMT007 |
|||
|
Amy/LTP |
TEMT008 |
|||
|
Ditto |
TEMT009 |
|||
|
Wanderer |
TEMT010 |
|||
|
p-SINE1 |
TEMT011 |
|||
|
Pop |
TEMT012 |
|||
|
Krispie |
TEMT013 |
|||
|
Snabo |
TEMT014 |
|||
|
MITE-adh, type Aa |
TEMT015 |
|||
|
MITE-adh, type B |
TEMT016 |
|||
|
MITE-adh, type D |
TEMT017 |
|||
|
MITE-adh, type G |
TEMT018 |
|||
|
MITE-adh, type H |
TEMT019 |
|||
|
MITE-adh, type I |
TEMT020 |
|||
|
MITE-adh, type J |
TEMT021 |
|||
|
MITE-adh, type K |
TEMT022 |
|||
|
|
TEMT023 |
|||
|
MITE-adh, type M |
TEMT024 |
|||
|
MITE-adh, type N |
TEMT025 |
|||
|
MITE-adh-1 |
TEMT026 |
|||
|
MITE-adh-2 |
TEMT027 |
|||
|
MITE-adh-3 |
TEMT028 |
|||
|
MITE-adh-4 |
TEMT029 |
|||
|
MITE-adh-5 |
TEMT030 |
|||
|
MITE-adh-6 |
TEMT031 |
|||
|
MITE-adh-7 |
TEMT032 |
|||
|
MITE-adh-8 |
TEMT033 |
|||
|
MITE-adh-9 |
TEMT034 |
|||
|
MITE-adh-10 |
TEMT035 |
|||
|
MITE-adh-11 |
TEMT036 |
|||
|
MITE-adh-12 |
TEMT037 |
|||
|
Buhuib |
TEMT038 |
|||
|
Casin |
TEMT039 |
|||
|
Centre |
TEMT040 |
|||
|
Delay |
TEMT041 |
|||
|
ECR |
TEMT042 |
|||
|
Helia |
TEMT043 |
|||
|
ID-2 |
TEMT044 |
|||
|
ID-3 |
TEMT045 |
|||
|
ID-4 |
TEMT046 |
|||
|
Lier |
TEMT047 |
|||
|
Stola |
TEMT048 |
|||
|
Stone |
TEMT049 |
|||
|
Susu |
TEMT050 |
|||
|
Wuji |
TEMT051 |
|||
|
Youren |
TEMT052 |
|||
|
Micron |
TEMT053 |
|||
|
Truncator |
TEMT054 |
|||
|
Heart
breaker |
TEMT055 |
|||
|
Frequent
Flyer |
TEMT056 |
|||
|
Heart Healer |
TEMT057 |
|||
|
Acrobat |
TEMT058 |
|||
|
mPIF |
TEMT059 |
|||
|
Pangrangja |
TEMT060 |
|||
|
Kiddo |
TEMT061 |
|||
|
mPing/miniSNOOPY |
TEMT062 |
|||
|
MDM |
TEMT063 |
|||
|
Unclassified
MITEs |
TEMTOOT |
|||
|
|
||||
|
Centromere-related
sequences |
Centromere-specific
Retrotransposons |
|
CMCM001 |
|
|
Centromeric
satellite repeats |
|
CMCM002 |
||
|
Unclassified
Centromere Sequences |
|
CMCMOOT |
||
|
|
||||
|
Telomere-related
sequences |
Telomere |
|
TRTM000 |
|
|
Telomere-associated |
|
TRTA000 |
||
|
|
||||
|
Ribosomal
RNA genes |
45S rDNA |
|
RGRR000 |
|
|
5S rDNA |
|
RGRR005 |
||
|
|
||||
|
Unclassified |
|
|
OTOT000 |
|
a: Ning, J. and Wessler, S.R. Plant Cell 13:2553-2564 2001.
b: Tarchini, R., Biddle, P., Wineland, R., Tingey, S. and Rafalski A. Plant Cell 12:381-391 2000.