The intraspecific variability of mitochondrial genes of Agaricus bisporus reveals an extensive group I intron mobility combined with low nucleotide substitution rates

Abstract

Intraspecific mitochondrial variability was studied in ten strains of A. bisporus var. bisporus, in a strain representative of A. bisporus var. eurotetrasporus and in a strain of the closely related species Agaricus devoniensis. In A. bisporus, the cox1 gene is the richest in group I introns harboring homing endonuclease genes (heg). This study led to identify group I introns as the main source of cox1 gene polymorphism. Among the studied introns, two groups were distinguished according to the heg they contained. One group harbored heg maintained putatively functional. The other group was composed of eroded heg sequences that appeared to evolve toward their elimination. Low nucleotide substitution rates were found in both types of intronic sequences. This feature was also shared by all types of studied mitochondrial sequences, not only intronic but also genic and intergenic ones, when compared with nuclear sequences. Hence, the intraspecific evolution of A. bisporus mitochondrial genome appears characterized by both an important mobility (presence/absence) of large group I introns and by low nt substitution rates. This stringent conservation of mitochondrial sequences, when compared with their nuclear counterparts, appears irrespective of their apparent functionality and contrasts to what is widely accepted in fungal sequence evolution. This strengthens the usefulness of mtDNA sequences to get clues on intraspecific evolution.

Evolution of group I introns in Porifera: new evidence for intron mobility and implications for DNA barcoding

“…We wonder whether this could be linked to a lower mt mutation rate in the Spirophorina with respect to other sponges, as suggested for some intron hotspot fungi groups [44]. We show that co-occurrence of two introns in cox1 is unique among metazoans, but not uncommon in sponges.…”

“…In fact, the mitochondrial genomes of the sponge classes Homoscleromorpha and Demospongiae possess features shared with non-metazoan opisthokonts rather than Bilateria such as the presence of intergenic regions, genes of foreign origin, a low substitution rate, selfish elements and introns [50]. Mt introns are also found in plants [28], fungi [44], Placozoa [76], and Hexacorallia [13, 37, 74] all known to have slow rates of evolution. It is assumed that this lower substitution rate slows down the elimination of ribozyme activities within group I introns, therefore HEGs would degenerate slower in most fungi [23], anthozoans [27, 31] and placozoans [9].…”

The Coevolution of Fungal Mitochondrial Introns and Their Homing Endonucleases (GIY-YIG and LAGLIDADG)

“…However, fungal mt genomes present significant size variability which is partly attributed to the abundance of introns ( Kouvelis et al. 2004 ; Hausner 2012 ; Jalalzadeh et al. 2015 ).…”

The mitochondrial genome of Endoconidiophora resinifera is intron rich

“…Recent papers have noted that fungal mitochondrial genomes are dynamic with regards to their structure and composition due to the presence of mobile elements (such as group I and group II introns) and duplication events 20 , 42 , 48 . This study found 81 introns in the mtDNAs of E .…”