The complete mitochondrial genomes of two model ectomycorrhizal fungi (Laccaria): features, intron dynamics and phylogenetic implications

Laccaria amethystine and L. bicolor have served as model species for studying the life history and genetics of ectomycorrhizal fungi. However, the characterizations and variations of their mitogenomes are still unknown. In the present study, the mitogenomes of the two Laccaria species were assembled...

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Published inInternational journal of biological macromolecules Vol. 145; pp. 974 - 984
Main Authors Li, Qiang, Yang, Luxi, Xiang, Dabing, Wan, Yan, Wu, Qi, Huang, Wenli, Zhao, Gang
Format Journal Article
LanguageEnglish
Published Netherlands Elsevier B.V 15.02.2020
Subjects
Agaricales - genetics
Basidiomycota - classification
Basidiomycota - genetics
Bayes Theorem
Bayesian theory
circular DNA
Coprinopsis cinerea
Electron Transport Complex IV - genetics
Fungal Proteins - genetics
Gene Rearrangement
Genes, Mitochondrial - genetics
Genome, Mitochondrial - genetics
Intron
introns
Introns - genetics
Laccaria
Laccaria - classification
Laccaria - genetics
Laccaria bicolor
life history
mitochondrial genes
Mitochondrial genome
Mycorrhizae - classification
Mycorrhizae - genetics
mycorrhizal fungi
Phylogenetic analysis
Phylogeny
RNA - genetics
Sequence Analysis
statistical analysis
Phylogenetic analysis
Laccaria
Intron
Mitochondrial genome
Gene rearrangement
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Abstract Laccaria amethystine and L. bicolor have served as model species for studying the life history and genetics of ectomycorrhizal fungi. However, the characterizations and variations of their mitogenomes are still unknown. In the present study, the mitogenomes of the two Laccaria species were assembled, annotated, and compared. The two mitogenomes of L. amethystine and L. bicolor comprised circular DNA molecules, with the sizes of 65,156 bp and 95,304 bp, respectively. Genome collinearity analysis revealed large-scale gene rearrangements between the two Laccaria species. Comparative mitogenome analysis indicated the introns of cox1 genes in Agaricales experienced frequent lost/gain eveants, which promoted the organization and size variations in Agaricales mitogenomes. Evolutionary analysis indicated the core protein-coding genes in the two mitogenomes were subject to strong pressure of purifying selection. Phylogenetic analysis using the Bayesian inference (BI) and Maximum likelihood (ML) methods based on a combined mitochondrial gene set resulted in identical and well-supported tree topologies, wherein the two Laccaria species were most closely related to Coprinopsis cinerea. This study severed as the first study on the mitogenomes of Laccaria species, which promoted a comprehensive understanding of the genetics and evolution of the model ectomycorrhizal fungi.
AbstractList Laccaria amethystine and L. bicolor have served as model species for studying the life history and genetics of ectomycorrhizal fungi. However, the characterizations and variations of their mitogenomes are still unknown. In the present study, the mitogenomes of the two Laccaria species were assembled, annotated, and compared. The two mitogenomes of L. amethystine and L. bicolor comprised circular DNA molecules, with the sizes of 65,156 bp and 95,304 bp, respectively. Genome collinearity analysis revealed large-scale gene rearrangements between the two Laccaria species. Comparative mitogenome analysis indicated the introns of cox1 genes in Agaricales experienced frequent lost/gain eveants, which promoted the organization and size variations in Agaricales mitogenomes. Evolutionary analysis indicated the core protein-coding genes in the two mitogenomes were subject to strong pressure of purifying selection. Phylogenetic analysis using the Bayesian inference (BI) and Maximum likelihood (ML) methods based on a combined mitochondrial gene set resulted in identical and well-supported tree topologies, wherein the two Laccaria species were most closely related to Coprinopsis cinerea. This study severed as the first study on the mitogenomes of Laccaria species, which promoted a comprehensive understanding of the genetics and evolution of the model ectomycorrhizal fungi.
Laccaria amethystine and L. bicolor have served as model species for studying the life history and genetics of ectomycorrhizal fungi. However, the characterizations and variations of their mitogenomes are still unknown. In the present study, the mitogenomes of the two Laccaria species were assembled, annotated, and compared. The two mitogenomes of L. amethystine and L. bicolor comprised circular DNA molecules, with the sizes of 65,156 bp and 95,304 bp, respectively. Genome collinearity analysis revealed large-scale gene rearrangements between the two Laccaria species. Comparative mitogenome analysis indicated the introns of cox1 genes in Agaricales experienced frequent lost/gain eveants, which promoted the organization and size variations in Agaricales mitogenomes. Evolutionary analysis indicated the core protein-coding genes in the two mitogenomes were subject to strong pressure of purifying selection. Phylogenetic analysis using the Bayesian inference (BI) and Maximum likelihood (ML) methods based on a combined mitochondrial gene set resulted in identical and well-supported tree topologies, wherein the two Laccaria species were most closely related to Coprinopsis cinerea. This study severed as the first study on the mitogenomes of Laccaria species, which promoted a comprehensive understanding of the genetics and evolution of the model ectomycorrhizal fungi.Laccaria amethystine and L. bicolor have served as model species for studying the life history and genetics of ectomycorrhizal fungi. However, the characterizations and variations of their mitogenomes are still unknown. In the present study, the mitogenomes of the two Laccaria species were assembled, annotated, and compared. The two mitogenomes of L. amethystine and L. bicolor comprised circular DNA molecules, with the sizes of 65,156 bp and 95,304 bp, respectively. Genome collinearity analysis revealed large-scale gene rearrangements between the two Laccaria species. Comparative mitogenome analysis indicated the introns of cox1 genes in Agaricales experienced frequent lost/gain eveants, which promoted the organization and size variations in Agaricales mitogenomes. Evolutionary analysis indicated the core protein-coding genes in the two mitogenomes were subject to strong pressure of purifying selection. Phylogenetic analysis using the Bayesian inference (BI) and Maximum likelihood (ML) methods based on a combined mitochondrial gene set resulted in identical and well-supported tree topologies, wherein the two Laccaria species were most closely related to Coprinopsis cinerea. This study severed as the first study on the mitogenomes of Laccaria species, which promoted a comprehensive understanding of the genetics and evolution of the model ectomycorrhizal fungi.
Laccaria amethystine and L. bicolor have served as model species for studying the life history and genetics of ectomycorrhizal fungi. However, the characterizations and variations of their mitogenomes are still unknown. In the present study, the mitogenomes of the two Laccaria species were assembled, annotated, and compared. The two mitogenomes of L. amethystine and L. bicolor comprised circular DNA molecules, with the sizes of 65,156 bp and 95,304 bp, respectively. Genome collinearity analysis revealed large-scale gene rearrangements between the two Laccaria species. Comparative mitogenome analysis indicated the introns of cox1 genes in Agaricales experienced frequent lost/gain eveants, which promoted the organization and size variations in Agaricales mitogenomes. Evolutionary analysis indicated the core protein-coding genes in the two mitogenomes were subject to strong pressure of purifying selection. Phylogenetic analysis using the Bayesian inference (BI) and Maximum likelihood (ML) methods based on a combined mitochondrial gene set resulted in identical and well-supported tree topologies, wherein the two Laccaria species were most closely related to Coprinopsis cinerea. This study severed as the first study on the mitogenomes of Laccaria species, which promoted a comprehensive understanding of the genetics and evolution of the model ectomycorrhizal fungi.
Author Wu, Qi
Li, Qiang
Xiang, Dabing
Yang, Luxi
Huang, Wenli
Wan, Yan
Zhao, Gang
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  surname: Wan
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Keywords Phylogenetic analysis
Laccaria
Intron
Mitochondrial genome
Gene rearrangement
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Snippet Laccaria amethystine and L. bicolor have served as model species for studying the life history and genetics of ectomycorrhizal fungi. However, the...
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SubjectTerms Agaricales - genetics
Basidiomycota - classification
Basidiomycota - genetics
Bayes Theorem
Bayesian theory
circular DNA
Coprinopsis cinerea
Electron Transport Complex IV - genetics
Fungal Proteins - genetics
Gene Rearrangement
Genes, Mitochondrial - genetics
Genome, Mitochondrial - genetics
Intron
introns
Introns - genetics
Laccaria
Laccaria - classification
Laccaria - genetics
Laccaria bicolor
life history
mitochondrial genes
Mitochondrial genome
Mycorrhizae - classification
Mycorrhizae - genetics
mycorrhizal fungi
Phylogenetic analysis
Phylogeny
RNA - genetics
Sequence Analysis
statistical analysis
Title The complete mitochondrial genomes of two model ectomycorrhizal fungi (Laccaria): features, intron dynamics and phylogenetic implications
URI https://dx.doi.org/10.1016/j.ijbiomac.2019.09.188
https://www.ncbi.nlm.nih.gov/pubmed/31669472
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https://www.proquest.com/docview/2352433780
Volume 145
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