The 206 kbp mitochondrial genome of Phanerochaete carnosa reveals dynamics of introns, accumulation of repeat sequences and plasmid-derived genes
In this study, the mitogenome of Phanerochaete carnosa was sequenced and assembled by the next-generation sequencing. The P. carnosa mitogenome was composed of circular DNA molecules, with a total size of 206,437 bp. Intron sequence, repeat sequence and plasmid-derived genes together promoted the P....
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| Published in: | International journal of biological macromolecules Vol. 162; pp. 209 - 219 |
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| Main Authors: | , , , , , , |
| Format: | Journal Article |
| Language: | English |
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Elsevier B.V
01.11.2020
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| ISSN: | 0141-8130, 1879-0003, 1879-0003 |
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| Abstract | In this study, the mitogenome of Phanerochaete carnosa was sequenced and assembled by the next-generation sequencing. The P. carnosa mitogenome was composed of circular DNA molecules, with a total size of 206,437 bp. Intron sequence, repeat sequence and plasmid-derived genes together promoted the P. carnosa mitogenome to become the second largest mitogenome in Basidiomycota. Gene arrangement analysis revealed large-scale gene rearrangements between Polyporales mitogenomes, and P. carnosa contained a unique gene order. The number and position classes of introns varied between 14 Polyporales species tested, indicated numerous intron loss/gain events occurred in the evolution of Polyporales. Most core PCGs in the 14 Polyporales species we tested were found subjected to purifying selection. However, the Ka/Ks values of rps3 gene were found >1 between some Polyporales species, indicating pressure of positive selection may exist. Phylogenetic analysis based on the combined mitochondrial gene set obtained well-supported tree topologies, and P. carnosa was identified as a sister species to Phlebia radiata. This study served as the first report on the mitogenome in the family Phanerochaetaceae, which will promote the understanding of the phylogeny, population genetics, and evolution of this white-rot fungus and related fungi. |
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| AbstractList | In this study, the mitogenome of Phanerochaete carnosa was sequenced and assembled by the next-generation sequencing. The P. carnosa mitogenome was composed of circular DNA molecules, with a total size of 206,437 bp. Intron sequence, repeat sequence and plasmid-derived genes together promoted the P. carnosa mitogenome to become the second largest mitogenome in Basidiomycota. Gene arrangement analysis revealed large-scale gene rearrangements between Polyporales mitogenomes, and P. carnosa contained a unique gene order. The number and position classes of introns varied between 14 Polyporales species tested, indicated numerous intron loss/gain events occurred in the evolution of Polyporales. Most core PCGs in the 14 Polyporales species we tested were found subjected to purifying selection. However, the Ka/Ks values of rps3 gene were found >1 between some Polyporales species, indicating pressure of positive selection may exist. Phylogenetic analysis based on the combined mitochondrial gene set obtained well-supported tree topologies, and P. carnosa was identified as a sister species to Phlebia radiata. This study served as the first report on the mitogenome in the family Phanerochaetaceae, which will promote the understanding of the phylogeny, population genetics, and evolution of this white-rot fungus and related fungi. In this study, the mitogenome of Phanerochaete carnosa was sequenced and assembled by the next-generation sequencing. The P. carnosa mitogenome was composed of circular DNA molecules, with a total size of 206,437 bp. Intron sequence, repeat sequence and plasmid-derived genes together promoted the P. carnosa mitogenome to become the second largest mitogenome in Basidiomycota. Gene arrangement analysis revealed large-scale gene rearrangements between Polyporales mitogenomes, and P. carnosa contained a unique gene order. The number and position classes of introns varied between 14 Polyporales species tested, indicated numerous intron loss/gain events occurred in the evolution of Polyporales. Most core PCGs in the 14 Polyporales species we tested were found subjected to purifying selection. However, the Ka/Ks values of rps3 gene were found >1 between some Polyporales species, indicating pressure of positive selection may exist. Phylogenetic analysis based on the combined mitochondrial gene set obtained well-supported tree topologies, and P. carnosa was identified as a sister species to Phlebia radiata. This study served as the first report on the mitogenome in the family Phanerochaetaceae, which will promote the understanding of the phylogeny, population genetics, and evolution of this white-rot fungus and related fungi.In this study, the mitogenome of Phanerochaete carnosa was sequenced and assembled by the next-generation sequencing. The P. carnosa mitogenome was composed of circular DNA molecules, with a total size of 206,437 bp. Intron sequence, repeat sequence and plasmid-derived genes together promoted the P. carnosa mitogenome to become the second largest mitogenome in Basidiomycota. Gene arrangement analysis revealed large-scale gene rearrangements between Polyporales mitogenomes, and P. carnosa contained a unique gene order. The number and position classes of introns varied between 14 Polyporales species tested, indicated numerous intron loss/gain events occurred in the evolution of Polyporales. Most core PCGs in the 14 Polyporales species we tested were found subjected to purifying selection. However, the Ka/Ks values of rps3 gene were found >1 between some Polyporales species, indicating pressure of positive selection may exist. Phylogenetic analysis based on the combined mitochondrial gene set obtained well-supported tree topologies, and P. carnosa was identified as a sister species to Phlebia radiata. This study served as the first report on the mitogenome in the family Phanerochaetaceae, which will promote the understanding of the phylogeny, population genetics, and evolution of this white-rot fungus and related fungi. In this study, the mitogenome of Phanerochaete carnosa was sequenced and assembled by the next-generation sequencing. The P. carnosa mitogenome was composed of circular DNA molecules, with a total size of 206,437 bp. Intron sequence, repeat sequence and plasmid-derived genes together promoted the P. carnosa mitogenome to become the second largest mitogenome in Basidiomycota. Gene arrangement analysis revealed large-scale gene rearrangements between Polyporales mitogenomes, and P. carnosa contained a unique gene order. The number and position classes of introns varied between 14 Polyporales species tested, indicated numerous intron loss/gain events occurred in the evolution of Polyporales. Most core PCGs in the 14 Polyporales species we tested were found subjected to purifying selection. However, the Ka/Ks values of rps3 gene were found >1 between some Polyporales species, indicating pressure of positive selection may exist. Phylogenetic analysis based on the combined mitochondrial gene set obtained well-supported tree topologies, and P. carnosa was identified as a sister species to Phlebia radiata. This study served as the first report on the mitogenome in the family Phanerochaetaceae, which will promote the understanding of the phylogeny, population genetics, and evolution of this white-rot fungus and related fungi. |
| Author | Chen, Mingyue Li, Qiang Wang, Xu Liu, Na Song, Andong Li, Xiao Wang, Fengqin |
| Author_xml | – sequence: 1 givenname: Xu surname: Wang fullname: Wang, Xu organization: College of Life Sciences, Henan Agricultural University, Zhengzhou, Henan 450002, China – sequence: 2 givenname: Andong surname: Song fullname: Song, Andong organization: College of Life Sciences, Henan Agricultural University, Zhengzhou, Henan 450002, China – sequence: 3 givenname: Fengqin surname: Wang fullname: Wang, Fengqin organization: College of Life Sciences, Henan Agricultural University, Zhengzhou, Henan 450002, China – sequence: 4 givenname: Mingyue surname: Chen fullname: Chen, Mingyue organization: College of Life Sciences, Henan Agricultural University, Zhengzhou, Henan 450002, China – sequence: 5 givenname: Xiao surname: Li fullname: Li, Xiao organization: College of Life Sciences, Henan Agricultural University, Zhengzhou, Henan 450002, China – sequence: 6 givenname: Qiang surname: Li fullname: Li, Qiang email: leeq110@126.com organization: College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, Sichuan 610106, China – sequence: 7 givenname: Na surname: Liu fullname: Liu, Na email: naliu@henau.edu.cn organization: College of Life Sciences, Henan Agricultural University, Zhengzhou, Henan 450002, China |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/32562727$$D View this record in MEDLINE/PubMed |
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| Keywords | Phylogenetic analysis Repeat sequence Phanerochaete carnosa Protein coding gene Mitochondrial genome Gene rearrangement |
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| SubjectTerms | circular DNA Codon Usage Cyclooxygenase 1 - genetics Evolution, Molecular Gene Order Gene Rearrangement Genes, Mitochondrial Genome, Mitochondrial Genomics High-Throughput Nucleotide Sequencing Introns mitochondrial genes Mitochondrial genome Phanerochaete - genetics Phanerochaete carnosa Phlebia Phylogenetic analysis Phylogeny Plasmids - genetics Polyporales - genetics Protein coding gene Repeat sequence Repetitive Sequences, Nucleic Acid trees white-rot fungi |
| Title | The 206 kbp mitochondrial genome of Phanerochaete carnosa reveals dynamics of introns, accumulation of repeat sequences and plasmid-derived genes |
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