Minor sequence differences were mostly in the intergenic regions with a preference to MK-0457 nmr AT-rich areas,
and were to a large extent SNP transitions (A/G and C/T) or single nucleotide insertions or deletions. The remaining differences were due to small insertions or deletions of 5-6 bp. The largest deletion (15bp) and the lowest sequence homology (86%) were observed in the intergenic region cox1- trnR2 (see Fig. 1). Figure 1 Genetic organization of (a) B. bassiana strain Bb147 and (b) B. brongniartii strain IMBST 95031 mtDNA. Protein-coding genes are marked with black arrows, and all other genes with gray arrows. Introns are shown with white arrows. Arrows indicate transcription orientation. Introns B. bassiana Bb147 contained five and B. brongniartii six introns, contributing to their total mtDNA genome size by 20.3% and 24.7%, respectively. All introns were group-I members, located in rnl, cob, cox1, cox2 and nad1 (Fig. 1; for details on exact positions of insertion and type of intron sub-group see Additional File 1, Table S1). All introns contained ORFs, i.e., the Rps3 homolog within the rnl gene (BbrnlI and BbrrnlI2),
putative GIY-YIG homing endonucleases (ABT 263 BbcobI1, cox2I1 and nad1I1) and the LAGLI-DADG endonuclease (Bbcox1I1 and Bbrcox1I1). The insertion positions of these introns were found to be conserved (identical sequences for at least 10 bp upstream and downstream of the insertion) for all known fungal complete mt genomes examined (36 in total). The only exception was the cox2 intron which was rarely encountered in other fungi. Interestingly, the additional LCL161 nmr intron detected in rnl of the B. brongniartii IMBST 95031 mt genome (positions 806-2102 of NC_011194 and Additional File 1, Table S1), was inserted at site not encountered before among the other complete mt genomes, i.e.,
the stem formed in domain II of rnl ‘s secondary structure. The target insertion sequence for the intron was GATAAGGTTG↓TGTATGTCAA and its intronic ORF encoded for a GIY-YIG endonuclease Dipeptidyl peptidase which shared homology (57% identity at the amino acid level) with I-PcI endonuclease of Podospora curvicolla (Acc. No. CAB 72450.1). Intergenic regions Both mt genomes contained 39 intergenic regions amounting for 5,985 bp in B. bassiana and 5,723 bp in B. brongniartii, and corresponding to 18.6% and 16.9% of their total mt genome, respectively. The A+T content was very similar for these regions in both mt genomes (~74.5%) and the largest intergenic region was located between cox1-trnR2 with sizes 1,314 bp for B. bassiana and 1,274 bp for B. brongniartii, respectively. Analysis of these particular regions revealed large unique putative ORFs (orf387 and orf368 for both genomes) with no significant similarity to any other ORFs in Genbank. Additionally, many direct repeats were also located in the same regions (maximum length 37 bp and 53 bp for B. bassiana and B. brongniartii, respectively).
No related posts.