The Gene Rearrangement, Loss, Transfer, and Deep Intronic Variation in Mitochondrial Genomes of Conidiobolus

Abstract

The genus Conidiobolus s.s. was newly delimited from Conidiobolus s.l. In order to gain insight into its mitochondrial genetic background, this study sequenced six mitochondrial genomes of the genus Conidiobolus s.s. These mitogenomes were all composed of circular DNA molecules, ranging from 29,253 to 48,417 bp in size and from 26.61 to 27.90% in GC content. The order and direction for 14 core protein-coding genes (PCGs) were identical, except for the atp8 gene lost in Conidiobolus chlamydosporus, Conidiobolus polyspermus, and Conidiobolus polytocus, and rearranged in the other Conidiobolus s.s. species. Besides, the atp8 gene split the cox1 gene in Conidiobolus taihushanensis. Phylogenomic analysis based on the 14 core PCGs confirmed that all Conidiobolus s.s. species formed a monophyly in the Entomophthoromycotina lineage. The number and length of introns were the main factors contributing to mitogenomic size, and deep variations and potential transfer were detected in introns. In addition, gene transfer occurred between the mitochondrial and nuclear genomes. This study promoted the understanding of the evolution and phylogeny of the Conidiobolus s.s. genus.

The Early Terrestrial Fungal Lineage of Conidiobolus—Transition from Saprotroph to Parasitic Lifestyle

“…Phylogenetic reconstruction suggests polyphyletic origins of conidiobolus-like fungi, and not a single origin. The polyphyletic origin of this composite fungal group was already suggested by our previous works [ 7 , 21 , 22 , 23 , 24 ], and one of the tasks of this study was to determine the corresponding taxonomic levels of the main branches. Alternatively, the whole group should be treated as a single family (the Entomophthoraceae), and all genera could be subsumed into it.…”

Genome-wide survey reveals the phylogenomic relationships of Chirolophis japonicus Herzenstein, 1890 (Stichaeidae, Perciformes)

“…The quality of the assembled genome was evaluated by Quast v. 5.0.2 and BUSCO v. 5.3.2 ( Simão et al 2015 ). The mitochondrial DNA analyses followed the method of previous studies ( Yang et al 2016 , 2021 ; Nie et al 2021 ). In brief, the software NOVOPlasty v. 4.2.1 ( Dierckxsens et al 2017 ) and GetOrganelle v. 1.7.6.1 ( Jin et al 2020 ) were used to assemble the mitogenome with clean data.…”