Complete mitogenome sequence of Ricasolia amplissima (Lobariaceae) reveals extensive mitochondrial DNA rearrangement within the Peltigerales (lichenized ascomycetes)
[en] The structure of mitochondrial genomes varies among non-lichenized fungi in terms of their genic and intronic content and genic order. Whether lichenized fungal mitogenomes are equally labile is unknown due to the paucity of available mitogenomes. We assembled the mitogenome of Ricasolia amplissima (Peltigerales, Lobariaceae), using massive parallel sequencing, and compared its structure to that of two species of Peltigera (Peltigeraceae). The mitochondrial genome of R. amplissima comprised 82,333 bp, with a 29.8% G+C content, and holds 15 unique protein-coding genes, 29 tRNA genes, two rRNA genes, and one non-coding RNA gene. Although the protein-coding gene content in the mitogenome of Peltigera and Ricasolia was identical, the relative gene order differed substantially, revealing that significant gene rearrangements also characterize the evolution of mitogenomes of lichenized ascomycetes at a relatively shallow phylogenetic depth, such as within the order Peltigerales.
Disciplines :
Genetics & genetic processes
Author, co-author :
Simon, Antoine ; Université de Liège > Département de Biologie, Ecologie et Evolution > Biologie de l'évolution et de la conservation - aCREA-Ulg
Liu, Yang; University of Connecticut - UCONN > Ecology and Evolutionary Biology > Goffinet Lab
Sérusiaux, Emmanuël ; Université de Liège > Département de Biologie, Ecologie et Evolution > Biologie de l'évolution et de la conservation - aCREA-Ulg
Goffinet, Bernard; University of Connecticut - UCONN > Ecology and Evolutionary Biology > Goffinet Lab
Language :
English
Title :
Complete mitogenome sequence of Ricasolia amplissima (Lobariaceae) reveals extensive mitochondrial DNA rearrangement within the Peltigerales (lichenized ascomycetes)
Publication date :
16 August 2017
Journal title :
Bryologist
ISSN :
0007-2745
Publisher :
Amer Bryological Lichenological Society Inc, Omaha, United States - Nebraska
Aguileta, G., D. M. De Vienne, O. N. Ross, M. E. Hood, T. Giraud, E. Petit & T. Gabaldón. 2014. High variability of mitochondrial gene order among fungi. Genome Biology and Evolution 6: 451-465.
Altschul, S., W. Gish & W. Miller. 1990. Basic Local Alignment Search Tool. Journal of Molecular Biology 215: 403-410.
Bolger, A. M., M. Lohse & B. Usadel. 2014. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics 30: 2114-2120.
Fućiková, K., P. O. Lewis, D. González-Halphen & L. A. Lewis. 2014. Gene arrangement convergence, diverse intron content, and genetic code modifications in mitochondrial genomes of Sphaeropleales (Chlorophyta). Genome Biology and Evolution 6: 2170-2180.
Honegger, R. 2008. Mycobionts. Pages 27-39. In: T. H. Nash III(ed.), Lichen Biology. 2nd Edition. Cambridge University Press, Cambridge.
Koszul, R., A. Malpertuy, L. Frangeul, C. Bouchier, P. Wincker, A. Thierry, S. Duthoy, et al. 2003. The complete mitochondrial genome sequence of the pathogenic yeast Candida (Torulopsis) glabrata. FEBS Letters 534: 39-48.
Kirk, P. M., P. F. Cannon, D. W. Minter & J. A. Stalpers. 2008. Dictionary of the Fungi. 10th Edition. CAB International, Wallingford.
Liu, Y., J. Y. Xue, B. Wang, L. Li & Y. L. Qiu. 2011. The mitochondrial genomes of the early land plants Treubia lacunosa and Anomodon rugelii: Dynamic and conservative evolution. PLoS ONE 6: e25836.
Liu, Y., R. Medina & B. Goffinet. 2014. 350 my of mitochondrial genome stasis in mosses, an early land plant lineage. Molecular Biology and Evolution 31: 2586-2591.
Losada, L., S. B. Pakala, N. D. Fedorova, V. Joardar, S. A. Shabalina, J. Hostetler, S. M. Pakala, et al. 2014. Mobile elements and mitochondrial genome expansion in the soil fungus and potato pathogen Rhizoctonia solani AG-3. FEMS Microbiology Letters 352: 165-173.
Lowe, T. M. & S. R. Eddy. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Research 25: 955-964.
Lücking, R., B. P. Hodkinson & S. D. Leavitt. 2016 [2017]. The 2016 classification of lichenized fungi in the Ascomycota and Basidiomycota-Approaching one thousand genera. The Bryolo-gist 119: 361-416.
Mardanov, A. V., A. V. Beletsky, V. V. Kadnikov, A. N. Ignatov & N. V. Ravin. 2014. The 203 kbp mitochondrial genome of the phytopathogenic fungus Sclerotinia borealis reveals multiple invasions of introns and genomic duplications. PLoS ONE 9: e107536.
Miadlikowska, J., F. Kauff, F. Högnabba, J. C. Oliver, K. Molnár, E. Fraker, E. Gaya, et al. 2014. A multigene phylogenetic synthesis for the class Lecanoromycetes (Ascomycota): 1307 fungi representing 1139 infrageneric taxa, 317 genera and 66 families. Molecular Phylogenetics and Evolution 79:132-168.
Prieto, M. & M. Wedin. 2013. Dating the diversification of the major lineages of Ascomycota (Fungi). PLoS ONE 8: e65576.
Spribille, T. & L. Muggia. 2013. Expanded taxon sampling disentangles evolutionary relationships and reveals a new family in Peltigerales (Lecanoromycetidae, Ascomycota). Fungal Diversity 58: 171-184.
Tønsberg, T. & T. Goward. 2001. Sticta oroborealis sp. nov. and other Pacific North American lichens forming dendriscocauloid cyanotypes. The Bryologist 104: 12-23.
Xavier, B. B., V. P. W. Miao, Z. O. Jónsson & O. S. Andrésson. 2012. Mitochondrial genomes from the lichenized fungi Peltigera membranacea and Peltigera malacea: features and phylogeny. Fungal Biology 116: 802-814.