Comparative genomic analysis of pleurotus species reveals insights into the evolution and coniferous utilization of Pleurotus placentodes
Pleurotus placentodes (PPL) and Pleurotus cystidiosus (PCY) are economically valuable species. PPL grows on conifers, while PCY grows on broad-leaved trees. To reveal the genetic mechanism behind PPL’s adaptability to conifers, we performed de novo genome sequencing and comparative analysis of PPL a...
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Frontiers Media S.A.
2023-11-01
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| Series: | Frontiers in Molecular Biosciences |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmolb.2023.1292556/full |
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| author | Lei Sun Lei Sun Xiaolei Yin Xiaolei Yin Frederick Leo Sossah Frederick Leo Sossah Xuerong Han Xuerong Han Yu Li Yu Li |
| author_facet | Lei Sun Lei Sun Xiaolei Yin Xiaolei Yin Frederick Leo Sossah Frederick Leo Sossah Xuerong Han Xuerong Han Yu Li Yu Li |
| author_sort | Lei Sun |
| collection | DOAJ |
| description | Pleurotus placentodes (PPL) and Pleurotus cystidiosus (PCY) are economically valuable species. PPL grows on conifers, while PCY grows on broad-leaved trees. To reveal the genetic mechanism behind PPL’s adaptability to conifers, we performed de novo genome sequencing and comparative analysis of PPL and PCY. We determined the size of the genomes for PPL and PCY to be 36.12 and 42.74 Mb, respectively, and found that they contain 10,851 and 15,673 protein-coding genes, accounting for 59.34% and 53.70% of their respective genome sizes. Evolution analysis showed PPL was closely related to P. ostreatus with the divergence time of 62.7 MYA, while PCY was distantly related to other Pleurotus species with the divergence time of 111.7 MYA. Comparative analysis of carbohydrate-active enzymes (CAZYmes) in PPL and PCY showed that the increase number of CAZYmes related to pectin and cellulose degradation (e.g., AA9, PL1) in PPL may be important for the degradation and colonization of conifers. In addition, geraniol degradation and peroxisome pathways identified by comparative genomes should be another factors for PPL’s tolerance to conifer substrate. Our research provides valuable genomes for Pleurotus species and sheds light on the genetic mechanism of PPL’s conifer adaptability, which could aid in breeding new Pleurotus varieties for coniferous utilization. |
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| institution | Directory Open Access Journal |
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| language | English |
| last_indexed | 2024-03-11T12:23:50Z |
| publishDate | 2023-11-01 |
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| series | Frontiers in Molecular Biosciences |
| spelling | doaj.art-7572118c2be844159f1aab86da80644f2023-11-06T16:06:35ZengFrontiers Media S.A.Frontiers in Molecular Biosciences2296-889X2023-11-011010.3389/fmolb.2023.12925561292556Comparative genomic analysis of pleurotus species reveals insights into the evolution and coniferous utilization of Pleurotus placentodesLei Sun0Lei Sun1Xiaolei Yin2Xiaolei Yin3Frederick Leo Sossah4Frederick Leo Sossah5Xuerong Han6Xuerong Han7Yu Li8Yu Li9Jilin Province Key Laboratory of Fungal Phenomics, Jilin Agricultural University, Changchun, ChinaInternational Cooperation Research Center of China for New Germplasm Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, ChinaJilin Province Key Laboratory of Fungal Phenomics, Jilin Agricultural University, Changchun, ChinaInternational Cooperation Research Center of China for New Germplasm Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, ChinaJilin Province Key Laboratory of Fungal Phenomics, Jilin Agricultural University, Changchun, ChinaCouncil for Scientific and Industrial Research (CSIR), Oil Palm Research Institute, Coconut Research Programme, Sekondi, GhanaJilin Province Key Laboratory of Fungal Phenomics, Jilin Agricultural University, Changchun, ChinaInternational Cooperation Research Center of China for New Germplasm Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, ChinaJilin Province Key Laboratory of Fungal Phenomics, Jilin Agricultural University, Changchun, ChinaInternational Cooperation Research Center of China for New Germplasm Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, ChinaPleurotus placentodes (PPL) and Pleurotus cystidiosus (PCY) are economically valuable species. PPL grows on conifers, while PCY grows on broad-leaved trees. To reveal the genetic mechanism behind PPL’s adaptability to conifers, we performed de novo genome sequencing and comparative analysis of PPL and PCY. We determined the size of the genomes for PPL and PCY to be 36.12 and 42.74 Mb, respectively, and found that they contain 10,851 and 15,673 protein-coding genes, accounting for 59.34% and 53.70% of their respective genome sizes. Evolution analysis showed PPL was closely related to P. ostreatus with the divergence time of 62.7 MYA, while PCY was distantly related to other Pleurotus species with the divergence time of 111.7 MYA. Comparative analysis of carbohydrate-active enzymes (CAZYmes) in PPL and PCY showed that the increase number of CAZYmes related to pectin and cellulose degradation (e.g., AA9, PL1) in PPL may be important for the degradation and colonization of conifers. In addition, geraniol degradation and peroxisome pathways identified by comparative genomes should be another factors for PPL’s tolerance to conifer substrate. Our research provides valuable genomes for Pleurotus species and sheds light on the genetic mechanism of PPL’s conifer adaptability, which could aid in breeding new Pleurotus varieties for coniferous utilization.https://www.frontiersin.org/articles/10.3389/fmolb.2023.1292556/fullPleurotus placentodesgenome sequencingconiferous utilizationevolutionadaption |
| spellingShingle | Lei Sun Lei Sun Xiaolei Yin Xiaolei Yin Frederick Leo Sossah Frederick Leo Sossah Xuerong Han Xuerong Han Yu Li Yu Li Comparative genomic analysis of pleurotus species reveals insights into the evolution and coniferous utilization of Pleurotus placentodes Frontiers in Molecular Biosciences Pleurotus placentodes genome sequencing coniferous utilization evolution adaption |
| title | Comparative genomic analysis of pleurotus species reveals insights into the evolution and coniferous utilization of Pleurotus placentodes |
| title_full | Comparative genomic analysis of pleurotus species reveals insights into the evolution and coniferous utilization of Pleurotus placentodes |
| title_fullStr | Comparative genomic analysis of pleurotus species reveals insights into the evolution and coniferous utilization of Pleurotus placentodes |
| title_full_unstemmed | Comparative genomic analysis of pleurotus species reveals insights into the evolution and coniferous utilization of Pleurotus placentodes |
| title_short | Comparative genomic analysis of pleurotus species reveals insights into the evolution and coniferous utilization of Pleurotus placentodes |
| title_sort | comparative genomic analysis of pleurotus species reveals insights into the evolution and coniferous utilization of pleurotus placentodes |
| topic | Pleurotus placentodes genome sequencing coniferous utilization evolution adaption |
| url | https://www.frontiersin.org/articles/10.3389/fmolb.2023.1292556/full |
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