Inverted repeat

Abstract: Chloroplasts contain their own autonomously replicating DNA genome. The majority of proteins present in the chloroplasts are encoded by nuclear DNA, but the rest are encoded by chloroplast DNA and synthesized by the chloroplast transcription–translation machinery1–4. Although the nucleotide sequences of many chloroplast genes from various plant species have been determined, the entire gene organization of the chloroplast genome has not yet been elucidated for any species of plants. To improve our understanding of the chloroplast gene system, we have determined the complete sequence of the chloroplast DNA from a liverwort, Marchantia polymorpha, and deduced the gene organization. As reported here the liverwort chloroplast DNA contains 121,024 base pairs (bp), consisting of a set of large inverted repeats (IRA and IRB, each of 10,058 bp) separated by a small single-copy region (SSC, 19,813 bp) and a large single-copy region (LSC, 81,095 bp). We detected 128 possible genes throughout the liverwort chloroplast genome, including coding sequences for four kinds of ribosomal RNAs, 32 species of transfer RNAs and 55 identified open reading frames (ORFs) for proteins, which are separated by short A+T-rich spacers (Fig. 1). Twenty genes (8 encoding tRNAs, 12 encoding proteins) contain introns in their coding sequences. These introns can be classified as belonging to either group I or group II, as described for mitochondria5. Interestingly, seven of the identified ORFs show high homology to unidentified reading frames (URFs) found in human mitochondria6,7.

Abstract: The entire chloroplast genome of the monocot rice (Oryza sativa) has been sequenced and comprises 134525 bp. Predicted genes have been identified along with open reading frames (ORFs) conserved between rice and the previously sequenced chloroplast genomes, a dicot, tobacco (Nicotiana tabacum), and a liverwort (Marchantia polymorpha). The same complement of 30 tRNA and 4 rRNA genes has been conserved between rice and tobacco. Most ORFs extensively conserved betweenN. tabacum andM. polymorpha are also conserved intact in rice. However, several such ORFs are entirely absent in rice, or present only in severely truncated form. Structural changes are also apparent in the genome relative to tobacco. The inverted repeats, characteristic of chloroplast genome structure, have expanded outward to include several genes present only once per genome in tobacco and liverwort and the large single copy region has undergone a series of inversions which predate the divergence of the cereals. A chimeric tRNA pseudogene overlaps an apparent endpoint of the largest inversion, and a model invoking illegitimate recombination between tRNA genes is proposed which accounts simultaneously for the origin of this pseudogene, the large inversion and the creation of repeated sequences near the inversion endpoints.

Abstract: The complete nucleotide sequence of the adeno-associated virus 2 genome was determined The single-stranded genome is 4,675 nucleotides in length and contains inverted terminal repeats of 145 nucleotides, the first 125 nucleotides of which form a palindromic sequence Within the inverted terminal repetitions, there are two distinct sequences representing an inversion of 43 nucleotides that can exist on either terminus The 5' and 3' termini of three major mRNA transcripts, which are present in both spliced and unspliced forms, were also mapped on the viral genome Potential initiation and termination codons for efficient protein synthesis were identified, and genome segments were assigned that code for three major viral capsid proteins and, possibly, some as-yet-unidentified, nonstructural viral proteins