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.