Haas BJ, Zeng Q, Pearson MD, Cuomo CA, Wortman JR. Approaches to Fungal Genome Annotation. Mycology. 2011 Oct 3;2(3):118-141. doi: 10.1080/21501203.2011.606851. PMID: 22059117; PMCID: PMC3207268.
Fungal mitochondrions also contain non-coding RNA genes. The mitochondrial rRNA genes are single copy genes for the large and small ribosomal RNAs (rrl and rrs). These are significantly shorter than their counterpart in the nuclear genome and cannot be identified by RNAmmer(Lagesen, Hallin, Rodland, Staerfeldt, Rognes and Ussery 2007). Instead, they are identified by a combination of RFAM and BLASTN against a rRNA database. This approach has been used for the annotation of multiple fungal mitochondrial genomes, such as Cryptococcus gattii R265(D’Souza et al. 2011). Most fungal species contain tRNAs for all 20 amino acids. In some fungal mitochondrial genomes that appear be deficient in tRNA content, it is likely that these “absent” tRNAs are nuclear encoded and later imported into the mitochondrion(Forget, Ustinova, Wang, Huss and Lang 2002). tRNA genes can be identified with tRNAScan using the organelle option and the sensitive mode(Lowe and Eddy 1997). The fungal mitochondrial tRNA genes tend to form clusters, often around the rRNA genes (rnl and rns), but the clusters can also be dispersed throughout the mitochondrial genome. The order of tRNA genes is largely conserved among closely related fungal species(Cardoso, Tambor and Nobrega 2007, Woo, Zhen, Cai, Yu, Lau, Wang, Teng, Wong, Tse, Chen, Yang, Liu and Yuen 2003, Torriani, Goodwin, Kema, Pangilinan and McDonald 2008).
Haas BJ, Zeng Q, Pearson MD, Cuomo CA, Wortman JR. Approaches to Fungal Genome Annotation. Mycology. 2011 Oct 3;2(3):118-141. doi: 10.1080/21501203.2011.606851. PMID: 22059117; PMCID: PMC3207268.
