Kanzi, Aquillah M.Wingfield, Brenda D.Steenkamp, Emma TheodoraNaidoo, SanushkaVan der Merwe, Nicolaas Albertus (Albie)2016-07-132016-07-132016-06-06Kanzi AM, Wingfield BD, Steenkamp ET, Naidoo S, van der Merwe NA (2016) Intron Derived Size Polymorphism in the Mitochondrial Genomes of Closely Related Chrysoporthe Species. PLoS ONE 11(6): e0156104. DOI: 10.1371/journal.pone.0156104.1932-620310.1371/journal.pone.0156104http://hdl.handle.net/2263/55525S1 Fig. Midrooted phylogenetic tree of rnpb genes. Rnpb genes were mannualy retrieved from annotated fungal mt genomes publicly available in GenBank. Phylogenetic analysis was performed using maximum likelihood method implemented in RAxML with HKY model of selection. Branch support was calculated using 1000 bootstrap replicates. Green boxes depict atp6 gene, red; small sub-unit of ribosomal RNA (rns) and dark red; small sub-unit of ribosomal RNA (rnl). (PDF)S2 Fig. Maximum likelihood phylogeny of Rps3. Phylogenetic analysis of orf540, orf551 and orf551 from C. austroafricana, C. cubensis and C. deuterocubensis which show sequence similarity to C. parasitica S5 ribosomal protein/maturase fusion protein. Sequences used in this phylogeny were retrieved from GenBank using BLAST. The LG+G model of substitution was used. Branch support for was calculated using the bootstrap method with 1000 replicates. (PDF)S3 Fig. RPKM values for 14 OXPHOS genes. The graph shows the average expression for genes that are involved in oxidative phosphorylation and electron transport and the rnpb gene of Chrysoporthe austroafricana grown in complete and minimal media. (PDF)S4 Fig. Physical maps of the mt genomes of C. austroafricana, C. cubensis, C. deuterocubensis and C. parasitica showing locations of all intronic and intergenic ORFs. Intronic ORFs are depicted by yellow arrowed boxes on introns of genes where found and are labelled according to the gene and intron position. Intergenic ORFs are also depicted by yellow arrowed boxes and are labelled with “IN” prefix. (PDF)S1 Table. Accession number and species names for sequences used for rps3 gene phylogeny. (PDF)S2 Table. Codon usage analysis. Comparison of codon usage and tRNAs for the 14 genes involved in oxidative phosphorylation and electron transport in the mitochondrial genomes of Chrysoporthe austroafricana, C. cubensis, C. deuterocubensis and Cryphonectria parasitica. (PDF)S3 Table. BLAST analysis of all identified introns against mt genome sequences deposited in NCBI GenBank. The best hits for each query (intron) is shown. Default BLAST parameters were used. The prefix CA, CC, CD and CP is added to the intron names for clarity. (PDF)S4 Table. BLAST analysis of identified intron encoded and free standing HEG protein sequences. Results from all possible comparisons were calculated. Only Blast hits with a threshold of over 50% alignment coverage, 50% sequence identity and E-value of 0.00005 are shown. (PDF)S5 Table. BLAST analysis of intronic and free standing HEG protein sequences against mt genomes deposited in NCBI GenBank database. HEG type were annotated using the NCBI Conserved Domain Database (CDD). (PDF)In this study, the complete mitochondrial (mt) genomes of Chrysoporthe austroafricana (190,834 bp), C. cubensis (89,084 bp) and C. deuterocubensis (124,412 bp) were determined. Additionally, the mitochondrial genome of another member of the Cryphonectriaceae, namely Cryphonectria parasitica (158,902 bp), was retrieved and annotated for comparative purposes. These genomes showed high levels of synteny, especially in regions including genes involved in oxidative phosphorylation and electron transfer, unique open reading frames (uORFs), ribosomal RNAs (rRNAs) and transfer RNAs (tRNAs), as well as intron positions. Comparative analyses revealed signatures of duplication events, intron number and length variation, and varying intronic ORFs which highlighted the genetic diversity of mt genomes among the Cryphonectriaceae. These mt genomes showed remarkable size polymorphism. The size polymorphism in the mt genomes of these closely related Chrysoporthe species was attributed to the varying number and length of introns, coding sequences and to a lesser extent, intergenic sequences. Compared to publicly available fungal mt genomes, the C. austroafricana mt genome is the second largest in the Ascomycetes thus far.en© 2016 Kanzi et al. This is an open access article distributed under the terms of the Creative Commons Attribution License.MitochondrialChrysoporthe austroafricanaCryphonectria parasiticaCryphonectriaceaeArticle