The 203 kbp Mitochondrial Genome of the Phytopathogenic Fungus Sclerotinia borealis Reveals Multiple Invasions of Introns and Genomic Duplications

Abstract

Here we report the complete sequence of the mitochondrial (mt) genome of the necrotrophic phytopathogenic fungus Sclerotinia borealis, a member of the order Helotiales of Ascomycetes. The 203,051 bp long mtDNA of S. borealis represents one of the largest sequenced fungal mt genomes. The large size is mostly determined by the presence of mobile genetic elements, which include 61 introns. Introns contain a total of 125,394 bp, are scattered throughout the genome, and are found in 12 protein-coding genes and in the ribosomal RNA genes. Most introns contain complete or truncated ORFs that are related to homing endonucleases of the LAGLIDADG and GIY-YIG families. Integrations of mobile elements are also evidenced by the presence of two regions similar to fragments of inverton-like plasmids. Although duplications of some short genome regions, resulting in the appearance of truncated extra copies of genes, did occur, we found no evidences of extensive accumulation of repeat sequences accounting for mitochondrial genome size expansion in some other fungi. Comparisons of mtDNA of S. borealis with other members of the order Helotiales reveal considerable gene order conservation and a dynamic pattern of intron acquisition and loss during evolution. Our data are consistent with the hypothesis that horizontal DNA transfer has played a significant role in the evolution and size expansion of the S. borealis mt genome.

Comparative genomics in plant fungal pathogens (Mycosphaerellaceae): variation in mitochondrial composition due to at least five independent intron invasions

“…However, it is not common to find highly fragmented genes as the cox1 of Sphaerulina populicola (Figure 5). A similar case was reported in the mitochondrial genome of Sclerotinia borealis, where researchers found thirteen introns of cox1 and truncated copies of ETC genes (Mardanov et al, 2014).…”

“…Invasion of mobile elements and accessory genes as main source of size variability among the genomes of phylogenetically related organisms was observed before in a study where nine mitochondrial genomes of Aspergillus and Penicilium were compared (Joardar et al, 2012). In the phytopathogenic fungus Sclerotinia borealis, they also found expansion of the genome due to plasmid like sequences integrated in the mitochondrial DNA and HEG related ORFs (Mardanov et al, 2014).…”

“…Mitochondrial gene duplication is seldom described in fungi. Maradanov et al (2014) found duplications of some mitochondrial regions, resulting in the appearance of truncated extra copies of atp9 and atp6 in phytopathogenic fungus Sclerotinia borealis (Mardanov et al, 2014).…”

Complete mitochondrial genome sequence of the phytopathogenic fungi Sclerotinia sclerotiorum JX-21

“…Most of them are available for members of the Eurotiomycetes and Sordariomycetes with only partial non-annotated genomes or draft annotations available for helotialean species (Du o et al 2012). Only three mitochondrial genomes belong to members of the Sclerotiniaceae: S. sclerotiorum, S. borealia (Mardanov et al 2014), and Botryotinia fuckeliana. Here, we resequenced the complete nucleotide sequence of the mt genome of S. sclerotiorum with different strains isolate obtained from the infected stems of Brassica campestris L., which was collected from March to April in 2012 from Wangjiang County (30 13 0 N and 116 68 0 E), Anhui Province, China and the strain was stored in the Chinese common microbe bacterial preservation administration centre with the preservation number CGMCC3.18027.…”

“…The remaining two clusters were located around rRNA gene: five around rnl and three around rps3, while the remaining four tRNA genes occurred, respectively. The phylogenetic analysis of S. sclerotiorum JX-21 was performed by comparison with 15 core mt proteins of other 21 species in Ascomycota (Mardanov et al 2014) and was constructed by a maximum-likelihood analysis of MEGA 6.0 (Hachioji, Tokyo, Japan) (Tamura et al 2013) program using 1000 bootstrap replicates. Result shows JX-21 is closely related to S. sclerotiorum1980 UF-70, S. borealia F-4128, and B. fuckeliana B05.10 which are another three members in the family Sclerotiniaceae with high bootstrap value supported (Figure 1).…”