The mitochondrial genome of Morchella importuna (272.2 kb) is the largest among fungi and contains numerous introns, mitochondrial non-conserved open reading frames and repetitive sequences

Liu, Wei; Cai, Yingli; Zhang, Qianqian; Chen, Lianfu; Fang, Shu; Ma, Xiaolong; Bian, Yinbing

doi:10.1016/j.ijbiomac.2019.12.056

Cited by 45 publications

(48 citation statements)

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“…Morchella species seem to have a special mitochondrial structure. The present mitochondrial genome of M. crassipes and that of M. importuna were the two largest ones of all fungi so far [29]. Except for a nad4L gene between cox1 and nad6 genes in the mitochondrial genome of M. importuna, and a truncated nad4_2 gene fragment between nad4 and cox1 in that of M. crassipes, the two species were consistent in the conservative gene sequence.…”

Section: Comparative Analysis Of Mitochondrial Genomementioning

confidence: 60%

“…The sequence length of 51 introns accounted for 53.67% of the total mitochondria genome length, with a length of more than 5 kb for 19 of the 51 introns, much larger than that of other fungi, thus increasing the difficulty of predicting conservative genes. These large introns were also present in M. importuna and considered as a manifestation of greater mitochondrial tolerance [29]. Another distinct feature was sequence repetition within mitochondria.…”

Section: Comparative Analysis Of Mitochondrial Genomementioning

confidence: 91%

“…Another distinct feature was sequence repetition within mitochondria. The repetitive sequences in M. importuna were about 18%, while those in M. crassipes were as high as 51.31%, with no definite repetitive features (no transposable features), just like R. solani and M. importuna [29,36]. A comparative analysis of the mitochondrial genome with the nuclear genome and other public databases (nr/nt, refseq_genomes, wgs, HTGS and gss) unveiled that no collinearity existed, suggesting that the main reason for the increase of the mitochondrial genome of MK527108) can been, and on the left, the mitochondrial genome of M. crassipes with a size of 531 kb (GenBank accession number: MN542893) can be seen.…”

Section: Comparative Analysis Of Mitochondrial Genomementioning

confidence: 95%

“…Due to the ineffectiveness of conventional assembly strategies in mitochondrial genome assembly caused by the large proportion of repetitive sequences, the gradual extension strategy was carried out as described in our recent work [29]. The mitochondrial ORFs were identified automatically with MFannot and RNAweasel using genetic code 4 (http://megasun.bch.umontreal.ca/RNAweasel/), and the prediction results were corrected by the homology comparison method.…”

Section: Mitochondrial Genome Assembly Gene Annotation and Bioinformmentioning

confidence: 99%

“…Mitochondria, typically referred to as the power factories of cells due to their contribution to energy supply, also participate in ion homeostasis, intermediary metabolism and cell senescence and apoptosis [27,28]. Compared with other fungi, the mitochondria of M. importuna have distinct characteristics in genome size, ncORF (non-conserved open reading frames), intron, and repeat sequence, with its mitochondrial genome once being regarded as the largest in size [29]. However, whether the mitochondrial genome of M. crassipes also has the same characteristics is not known, and a comparative analysis of the mitochondria of neighboring species will help to understand their evolution.…”

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Subchromosome-Scale Nuclear and Complete Mitochondrial Genome Characteristics of Morchella crassipes

Liu

Cai

Zhang

et al. 2020

IJMS

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Morchella crassipes (Vent.) Pers., a typical yellow morel species with high economic value, is mainly distributed in the low altitude plains of Eurasia. However, rare research has been performed on its genomics and polarity, thus limiting its research and development. Here, we reported a fine physical map of the nuclear genome at the subchromosomal-scale and the complete mitochondrial genome of M. crassipes. The complete size of the nuclear genome was 56.7 Mb, and 23 scaffolds were assembled, with eight of them being complete chromosomes. A total of 11,565 encoding proteins were predicted. The divergence time analysis showed that M. crassipes representing yellow morels differentiated with black morels at ~33.98 Mya (million years), with 150 gene families contracted and expanded in M. crassipes versus the two black morels (M. snyderi and M. importuna). Furthermore, 409 CAZYme genes were annotated in M. crassipes, containing almost all plant cell wall degrading enzymes compared with the mycorrhizal fungi (truffles). Genomic annotation of mating type loci and amplification of the mating genes in the monospore population was conducted, the results indicated that M. crassipes is a heterothallic fungus. Additionally, a complete circular mitochondrial genome of M. crassipes was assembled, the size reached as large as 531,195 bp. It can be observed that the strikingly large size was the biggest up till now, coupled with 14 core conserved mitochondrial protein-coding genes, two rRNAs, 31 tRNAs, 51 introns, and 412 ncORFs. The total length of intron sequences accounted for 53.67% of the mitochondrial genome, with 19 introns having a length over 5 kb. Particularly, 221 of 412 ncORFs were distributed within 51 introns, and the total length of the ncORFs sequence accounted for 40.83% of the mitochondrial genome, and 297 ncORFs had expression activity in the mycelium stage, suggesting their potential functions in M. crassipes. Meanwhile, there was a high degree of repetition (51.31%) in the mitochondria of M. crassipes. Thus, the large number of introns, ncORFs and internal repeat sequences may contribute jointly to the largest fungal mitochondrial genome to date. The fine physical maps of nuclear genome and mitochondrial genome obtained in this study will open a new door for better understanding of the mysterious species of M. crassipes.

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Section: Comparative Analysis Of Mitochondrial Genomementioning

confidence: 60%

Section: Comparative Analysis Of Mitochondrial Genomementioning

confidence: 91%

Section: Comparative Analysis Of Mitochondrial Genomementioning

confidence: 95%

Section: Mitochondrial Genome Assembly Gene Annotation and Bioinformmentioning

confidence: 99%

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confidence: 99%

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Subchromosome-Scale Nuclear and Complete Mitochondrial Genome Characteristics of Morchella crassipes

Liu

Cai

Zhang

et al. 2020

IJMS

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Comparative analysis of the complete mitochondrial genomes of four cordyceps fungi

Zhong

Jin

Zhou

et al. 2022

Ecology and Evolution

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Cordyceps is a large group of entomogenous, medicinally important fungi. In this study, we sequenced, assembled, and annotated the entire mitochondrial genome of Ophiocordyceps xuefengensis , in addition to comparing it against other three complete cordyceps mitogenomes that were previously published. Comparative analysis indicated that the four complete mitogenomes are all composed of circular DNA molecules, although their sizes significantly differ due to high variability in intron and intergenic region sizes in the Ophiocordyceps sinensis and O . xuefengensis mitogenomes. All mitogenomes contain 14 conserved genes and two ribosomal RNA genes, but varying numbers of tRNA introns. The Ka/Ks ratios for all 14 PCGs and rps3 were all less than 1, indicating that these genes have been subject to purifying selection. Phylogenetic analysis was conducted using concatenated amino acid and nucleotide sequences of the 14 PCGs and rps3 using two different methods (Maximum Likelihood and Bayesian analysis), revealing highly supported relationships between O . xuefengensis and other Ophiocordyceps species, in addition to a close relationship with O . sinensis . Further, the analyses indicated that cox1 and rps3 play important roles in population differentiation. These mitogenomes will allow further study of the population genetics, taxonomy, and evolutionary biology of medicinally important cordyceps species.

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Panorama of intron dynamics and gene rearrangements in the phylum Basidiomycota as revealed by the complete mitochondrial genome of Turbinellus floccosus

Cheng

Luo

Ren

et al. 2021

Appl Microbiol Biotechnol

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The mitochondrial genome of Morchella importuna (272.2 kb) is the largest among fungi and contains numerous introns, mitochondrial non-conserved open reading frames and repetitive sequences

Cited by 45 publications

References 54 publications

Subchromosome-Scale Nuclear and Complete Mitochondrial Genome Characteristics of Morchella crassipes

Subchromosome-Scale Nuclear and Complete Mitochondrial Genome Characteristics of Morchella crassipes

Comparative analysis of the complete mitochondrial genomes of four cordyceps fungi

Panorama of intron dynamics and gene rearrangements in the phylum Basidiomycota as revealed by the complete mitochondrial genome of Turbinellus floccosus

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