Coffee Retro-Transposon Sequences

PCR-amplification of the tract between this RNAse H motif and a restriction site in the adjacent LTR sequence, it is possible to isolate and characterize sequences containing the necessary part of the LTR, without the need to construct a DNA library. In this way we have isolated a total of 43 Retro-Transposon based sequences. click on teh link to access the sequences

Retrotransposons

What are retrotransposons?

The presence of mobile elements, capable of moving from one region of the genome to another, has been known and thoroughly studied since the 1950’s. These elements are capable of exciding and inserting themselves from one region of the chromatin to another, through their peculiar terminal repeat regions. This process is mediated by enzymes encoded by the transposon itself.
Retrotransposons are a class of mobile elements, widespread in plant genomes, where they account for a significant part of noncoding DNA. Barley, for example, contains thousands of copies of the Bare-1 element, dispersed throughout the euchromatic regions of chromosomes and exhibiting sequence identity higher than 95% to each other.

Unlike other classes of mobile elements, retrotransposons insert into the genome via an RNA intermediate, sinthetized by their own reverse transcriptase, without the loss of the parental copy. Unique sequence properties show that retrotransposons of the Ty1-copia group are close to retroviruses, and their mode of integration in the host genome is also very similar.

The number and exact point of insertion of retrotransposons may differ from one individual to another and this can be exploited to characterize individuals, varieties or species, depending on how recent the transpositional event is. Furthermore, insertion of a retrotransposon is an irreversible event, a characteristic that can be helpful when tracing an ancestry.

Retrotransposons are suitable to be used as molecular markers by means of their Long Terminal Repeat (LTR) sequences. These are stretches of DNA, variable in length and sequence, repeated at both ends of the retrotransposon. LTRs can be found by “mining” public databases with suitable search programs, but this method is only suitable for a restricted number of well-known species. Alternatively, it is possible to screen libraries for other, more conserved sequences closely related to LTRs, such as conserved domains of the transposon genes rt and rnh

Retrotransposons

What are retrotransposons?

The presence of mobile elements, capable of moving from one region of the genome to another, has been known and thoroughly studied since the 1950’s. These elements are capable of exciding and inserting themselves from one region of the chromatin to another, through their peculiar terminal repeat regions. This process is mediated by enzymes encoded by the transposon itself.
Retrotransposons are a class of mobile elements, widespread in plant genomes, where they account for a significant part of noncoding DNA. Barley, for example, contains thousands of copies of the Bare-1 element, dispersed throughout the euchromatic regions of chromosomes and exhibiting sequence identity higher than 95% to each other.

Unlike other classes of mobile elements, retrotransposons insert into the genome via an RNA intermediate, sinthetized by their own reverse transcriptase, without the loss of the parental copy. Unique sequence properties show that retrotransposons of the Ty1-copia group are close to retroviruses, and their mode of integration in the host genome is also very similar.

The number and exact point of insertion of retrotransposons may differ from one individual to another and this can be exploited to characterize individuals, varieties or species, depending on how recent the transpositional event is. Furthermore, insertion of a retrotransposon is an irreversible event, a characteristic that can be helpful when tracing an ancestry.

Retrotransposons are suitable to be used as molecular markers by means of their Long Terminal Repeat (LTR) sequences. These are stretches of DNA, variable in length and sequence, repeated at both ends of the retrotransposon. LTRs can be found by “mining” public databases with suitable search programs, but this method is only suitable for a restricted number of well-known species. Alternatively, it is possible to screen libraries for other, more conserved sequences closely related to LTRs, such as conserved domains of the transposon genes rt and rnh