Characterisation and comparative analysis of mitochondrial genomes of false, yellow, black and blushing morels provide insights on their structure and evolution

<i>Morchella</i> species have considerable significance in terrestrial ecosystems, exhibiting a range of ecological lifestyles along the saprotrophism-to-symbiosis continuum. However, the mitochondrial genomes of these ascomycetous fungi have not been thoroughly studied, thereby impeding a comprehensive understanding of their genetic makeup and ecological role. In this study, we analysed the mitogenomes of 30 <i>Morchellaceae</i> species, including yellow, black, blushing and false morels. These mitogenomes are either circular or linear DNA molecules with lengths ranging from 217 to 565 kbp and GC content ranging from 38% to 48%. Fifteen core protein-coding genes, 28-37 <i>tRNA</i> genes and 3-8 <i>rRNA</i> genes were identified in these <i>Morchellaceae</i> mitogenomes. The gene order demonstrated a high level of conservation, with the <i>cox1</i> gene consistently positioned adjacent to the <i>rnS</i> gene and <i>cob</i> gene flanked by <i>apt</i> genes. Some exceptions were observed, such as the rearrangement of <i>atp6</i> and <i>rps3</i> in <i>Morchellaimportuna</i> and the reversed order of <i>atp6</i> and <i>atp8</i> in certain morel mitogenomes. However, the arrangement of the <i>tRNA</i> genes remains conserved. We additionally investigated the distribution and phylogeny of homing endonuclease genes (HEGs) of the LAGLIDADG (LAGs) and GIY-YIG (GIYs) families. A total of 925 LAG and GIY sequences were detected, with individual species containing 19-48HEGs. These HEGs were primarily located in the <i>cox1</i>, <i>cob</i>, <i>cox2</i> and <i>nad5</i> introns and their presence and distribution displayed significant diversity amongst morel species. These elements significantly contribute to shaping their mitogenome diversity. Overall, this study provides novel insights into the phylogeny and evolution of the <i>Morchellaceae</i>.