Pan-Genomes Provide Insights into the Genetic Basis of <i>Auricularia heimuer</i> Domestication
In order to reveal the genetic variation signals of <i>Auricularia heimuer</i> that have occurred during their domestication and to find potential functional gene families, we constructed a monokaryotic pan-genome of <i>A. heimuer</i> representing four cultivated strains and...
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MDPI AG
2022-05-01
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| Series: | Journal of Fungi |
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| Online Access: | https://www.mdpi.com/2309-608X/8/6/581 |
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| author | Yuxiu Guo Zhenhua Liu Yongping Fu Yu Li Yueting Dai Shijun Xiao |
| author_facet | Yuxiu Guo Zhenhua Liu Yongping Fu Yu Li Yueting Dai Shijun Xiao |
| author_sort | Yuxiu Guo |
| collection | DOAJ |
| description | In order to reveal the genetic variation signals of <i>Auricularia heimuer</i> that have occurred during their domestication and to find potential functional gene families, we constructed a monokaryotic pan-genome of <i>A. heimuer</i> representing four cultivated strains and four wild strains. The pan-genome contained 14,089 gene families, of which 67.56% were core gene families and 31.88% were dispensable gene families. We screened substrate utilization-related genes such as the chitinase gene <i>ahchi1</i> of the glycoside hydrolase (GH) 18 family and a carbohydrate-binding module (CBM)-related gene from the dispensable families of cultivated populations. The genomic difference in the <i>ahchi1</i> gene between the wild and cultivated genomes was caused by a 33 kb presence/absence variation (PAV). The detection rate of the <i>ahchi1</i> gene was 93.75% in the cultivated population, significantly higher than that in the wild population (17.39%), indicating that it has been selected in cultivated strains. Principal component analysis (PCA) of the polymorphic markers in fragments near the <i>ahchi1</i> gene was enriched in cultivated strains, and this was caused by multiple independent instances of artificial selection. We revealed for the first time the genetic basis of the <i>ahchi1</i> gene in domestication, thereby providing a foundation for elucidating the potential function of the <i>ahchi1</i> gene in the breeding of <i>A. heimuer</i>. |
| first_indexed | 2024-03-09T23:22:09Z |
| format | Article |
| id | doaj.art-22a66bfc39df48329463f5d0e7081666 |
| institution | Directory Open Access Journal |
| issn | 2309-608X |
| language | English |
| last_indexed | 2024-03-09T23:22:09Z |
| publishDate | 2022-05-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Journal of Fungi |
| spelling | doaj.art-22a66bfc39df48329463f5d0e70816662023-11-23T17:24:28ZengMDPI AGJournal of Fungi2309-608X2022-05-018658110.3390/jof8060581Pan-Genomes Provide Insights into the Genetic Basis of <i>Auricularia heimuer</i> DomesticationYuxiu Guo0Zhenhua Liu1Yongping Fu2Yu Li3Yueting Dai4Shijun Xiao5Life Science College, Northeast Normal University, Changchun 130024, ChinaEngineering Research Center, Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, ChinaEngineering Research Center, Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, ChinaEngineering Research Center, Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, ChinaEngineering Research Center, Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, ChinaEngineering Research Center, Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, ChinaIn order to reveal the genetic variation signals of <i>Auricularia heimuer</i> that have occurred during their domestication and to find potential functional gene families, we constructed a monokaryotic pan-genome of <i>A. heimuer</i> representing four cultivated strains and four wild strains. The pan-genome contained 14,089 gene families, of which 67.56% were core gene families and 31.88% were dispensable gene families. We screened substrate utilization-related genes such as the chitinase gene <i>ahchi1</i> of the glycoside hydrolase (GH) 18 family and a carbohydrate-binding module (CBM)-related gene from the dispensable families of cultivated populations. The genomic difference in the <i>ahchi1</i> gene between the wild and cultivated genomes was caused by a 33 kb presence/absence variation (PAV). The detection rate of the <i>ahchi1</i> gene was 93.75% in the cultivated population, significantly higher than that in the wild population (17.39%), indicating that it has been selected in cultivated strains. Principal component analysis (PCA) of the polymorphic markers in fragments near the <i>ahchi1</i> gene was enriched in cultivated strains, and this was caused by multiple independent instances of artificial selection. We revealed for the first time the genetic basis of the <i>ahchi1</i> gene in domestication, thereby providing a foundation for elucidating the potential function of the <i>ahchi1</i> gene in the breeding of <i>A. heimuer</i>.https://www.mdpi.com/2309-608X/8/6/581artificial selectionchitinasedispensable geneglycoside hydrolase 18 familywood ear |
| spellingShingle | Yuxiu Guo Zhenhua Liu Yongping Fu Yu Li Yueting Dai Shijun Xiao Pan-Genomes Provide Insights into the Genetic Basis of <i>Auricularia heimuer</i> Domestication Journal of Fungi artificial selection chitinase dispensable gene glycoside hydrolase 18 family wood ear |
| title | Pan-Genomes Provide Insights into the Genetic Basis of <i>Auricularia heimuer</i> Domestication |
| title_full | Pan-Genomes Provide Insights into the Genetic Basis of <i>Auricularia heimuer</i> Domestication |
| title_fullStr | Pan-Genomes Provide Insights into the Genetic Basis of <i>Auricularia heimuer</i> Domestication |
| title_full_unstemmed | Pan-Genomes Provide Insights into the Genetic Basis of <i>Auricularia heimuer</i> Domestication |
| title_short | Pan-Genomes Provide Insights into the Genetic Basis of <i>Auricularia heimuer</i> Domestication |
| title_sort | pan genomes provide insights into the genetic basis of i auricularia heimuer i domestication |
| topic | artificial selection chitinase dispensable gene glycoside hydrolase 18 family wood ear |
| url | https://www.mdpi.com/2309-608X/8/6/581 |
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