Characterization and Phylogenetic Analysis of the Complete Mitogenomes of <i>Valsa mali</i> and <i>Valsa pyri</i>
Apple Valsa canker, caused by <i>Valsa mali</i> and <i>Valsa pyri</i>, is a devastating disease of apple trees and poses a severe threat to the sustainable development of apple production. Although the two species’ whole genomes have been sequenced, their mitochondrial genome...
Saved in:
| Main Authors: | , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2025-04-01
|
| Series: | Journal of Fungi |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2309-608X/11/5/348 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1849327268088774656 |
|---|---|
| author | Guoqing Xing Shunpei Xie Zhanxiang Qiao Qingzhou Ma Chao Xu Yuehua Geng Yashuang Guo Rui Zang Meng Zhang |
| author_facet | Guoqing Xing Shunpei Xie Zhanxiang Qiao Qingzhou Ma Chao Xu Yuehua Geng Yashuang Guo Rui Zang Meng Zhang |
| author_sort | Guoqing Xing |
| collection | DOAJ |
| description | Apple Valsa canker, caused by <i>Valsa mali</i> and <i>Valsa pyri</i>, is a devastating disease of apple trees and poses a severe threat to the sustainable development of apple production. Although the two species’ whole genomes have been sequenced, their mitochondrial genomes are still uncharacterized. In this study, the complete mitochondrial genomes of <i>V. mali</i> and <i>V. pyri</i> were assembled, annotated, and compared by bioinformatic methods. The results indicate that the mitogenomes are both circular DNA molecules with sizes of 213,406 bp and 128,022 bp, respectively. The AT skew values of the two <i>Valsa</i> species’ mitogenomes were positive, while the GC skew values were negative. Comparative mitogenome analysis revealed that the length and base composition of protein-coding genes (PCGs), rRNA genes, and tRNA genes differed between the two <i>Valsa</i> species. It was found that the expansion of <i>V. mali</i> was primarily attributable to the intronic regions. There are large numbers of interspersed repetitive sequences (IRS) in both <i>Valsa</i> mitogenomes; however, the proportion of IRS in <i>V. mali</i> (43.56%) was much higher than that in <i>V. pyri</i> (2.41%). The alignment of large fragments between the mitochondrial and nuclear genomes of both <i>V. mali</i> (1.73 kb) and <i>V. pyri</i> (5.17 kb) indicates that gene transfer between mitochondrial and nuclear genomes occurred during evolution. The ka/ks ratios for 15 core PCGs were below one, suggesting that these genes were subjected to purifying selection pressure. Comparative mitogenomics revealed that the two fungi had significant mitogenomic collinearity and large-scale gene rearrangements. The results of phylogenetic analysis based on Bayesian inference (BI) and maximum likelihood (ML) using a combined mitochondrial gene set confirmed that <i>V. mali</i> and <i>V. pyri</i> were fully independent taxa with a high bootstrap value of 100 (ML) and a high posterior probability of 1.0 (BI). This is the first report on the mitogenomes within the genus <i>Valsa</i>. These results will pave the way to understanding the evolution and differentiation of mitogenomes in the genus <i>Valsa</i>. |
| format | Article |
| id | doaj-art-c735e0bd2ac74032a2f12523c5b660d5 |
| institution | Kabale University |
| issn | 2309-608X |
| language | English |
| publishDate | 2025-04-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Journal of Fungi |
| spelling | doaj-art-c735e0bd2ac74032a2f12523c5b660d52025-08-20T03:47:54ZengMDPI AGJournal of Fungi2309-608X2025-04-0111534810.3390/jof11050348Characterization and Phylogenetic Analysis of the Complete Mitogenomes of <i>Valsa mali</i> and <i>Valsa pyri</i>Guoqing Xing0Shunpei Xie1Zhanxiang Qiao2Qingzhou Ma3Chao Xu4Yuehua Geng5Yashuang Guo6Rui Zang7Meng Zhang8College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, ChinaCollege of Plant Protection, Henan Agricultural University, Zhengzhou 450002, ChinaCollege of Plant Protection, Henan Agricultural University, Zhengzhou 450002, ChinaCollege of Plant Protection, Henan Agricultural University, Zhengzhou 450002, ChinaCollege of Plant Protection, Henan Agricultural University, Zhengzhou 450002, ChinaCollege of Plant Protection, Henan Agricultural University, Zhengzhou 450002, ChinaCollege of Plant Protection, Henan Agricultural University, Zhengzhou 450002, ChinaCollege of Plant Protection, Henan Agricultural University, Zhengzhou 450002, ChinaCollege of Plant Protection, Henan Agricultural University, Zhengzhou 450002, ChinaApple Valsa canker, caused by <i>Valsa mali</i> and <i>Valsa pyri</i>, is a devastating disease of apple trees and poses a severe threat to the sustainable development of apple production. Although the two species’ whole genomes have been sequenced, their mitochondrial genomes are still uncharacterized. In this study, the complete mitochondrial genomes of <i>V. mali</i> and <i>V. pyri</i> were assembled, annotated, and compared by bioinformatic methods. The results indicate that the mitogenomes are both circular DNA molecules with sizes of 213,406 bp and 128,022 bp, respectively. The AT skew values of the two <i>Valsa</i> species’ mitogenomes were positive, while the GC skew values were negative. Comparative mitogenome analysis revealed that the length and base composition of protein-coding genes (PCGs), rRNA genes, and tRNA genes differed between the two <i>Valsa</i> species. It was found that the expansion of <i>V. mali</i> was primarily attributable to the intronic regions. There are large numbers of interspersed repetitive sequences (IRS) in both <i>Valsa</i> mitogenomes; however, the proportion of IRS in <i>V. mali</i> (43.56%) was much higher than that in <i>V. pyri</i> (2.41%). The alignment of large fragments between the mitochondrial and nuclear genomes of both <i>V. mali</i> (1.73 kb) and <i>V. pyri</i> (5.17 kb) indicates that gene transfer between mitochondrial and nuclear genomes occurred during evolution. The ka/ks ratios for 15 core PCGs were below one, suggesting that these genes were subjected to purifying selection pressure. Comparative mitogenomics revealed that the two fungi had significant mitogenomic collinearity and large-scale gene rearrangements. The results of phylogenetic analysis based on Bayesian inference (BI) and maximum likelihood (ML) using a combined mitochondrial gene set confirmed that <i>V. mali</i> and <i>V. pyri</i> were fully independent taxa with a high bootstrap value of 100 (ML) and a high posterior probability of 1.0 (BI). This is the first report on the mitogenomes within the genus <i>Valsa</i>. These results will pave the way to understanding the evolution and differentiation of mitogenomes in the genus <i>Valsa</i>.https://www.mdpi.com/2309-608X/11/5/348mitochondrial genomecollinearitygene rearrangementphylogenetic analysis<i>Valsa mali</i><i>Valsa pyri</i> |
| spellingShingle | Guoqing Xing Shunpei Xie Zhanxiang Qiao Qingzhou Ma Chao Xu Yuehua Geng Yashuang Guo Rui Zang Meng Zhang Characterization and Phylogenetic Analysis of the Complete Mitogenomes of <i>Valsa mali</i> and <i>Valsa pyri</i> Journal of Fungi mitochondrial genome collinearity gene rearrangement phylogenetic analysis <i>Valsa mali</i> <i>Valsa pyri</i> |
| title | Characterization and Phylogenetic Analysis of the Complete Mitogenomes of <i>Valsa mali</i> and <i>Valsa pyri</i> |
| title_full | Characterization and Phylogenetic Analysis of the Complete Mitogenomes of <i>Valsa mali</i> and <i>Valsa pyri</i> |
| title_fullStr | Characterization and Phylogenetic Analysis of the Complete Mitogenomes of <i>Valsa mali</i> and <i>Valsa pyri</i> |
| title_full_unstemmed | Characterization and Phylogenetic Analysis of the Complete Mitogenomes of <i>Valsa mali</i> and <i>Valsa pyri</i> |
| title_short | Characterization and Phylogenetic Analysis of the Complete Mitogenomes of <i>Valsa mali</i> and <i>Valsa pyri</i> |
| title_sort | characterization and phylogenetic analysis of the complete mitogenomes of i valsa mali i and i valsa pyri i |
| topic | mitochondrial genome collinearity gene rearrangement phylogenetic analysis <i>Valsa mali</i> <i>Valsa pyri</i> |
| url | https://www.mdpi.com/2309-608X/11/5/348 |
| work_keys_str_mv | AT guoqingxing characterizationandphylogeneticanalysisofthecompletemitogenomesofivalsamaliiandivalsapyrii AT shunpeixie characterizationandphylogeneticanalysisofthecompletemitogenomesofivalsamaliiandivalsapyrii AT zhanxiangqiao characterizationandphylogeneticanalysisofthecompletemitogenomesofivalsamaliiandivalsapyrii AT qingzhouma characterizationandphylogeneticanalysisofthecompletemitogenomesofivalsamaliiandivalsapyrii AT chaoxu characterizationandphylogeneticanalysisofthecompletemitogenomesofivalsamaliiandivalsapyrii AT yuehuageng characterizationandphylogeneticanalysisofthecompletemitogenomesofivalsamaliiandivalsapyrii AT yashuangguo characterizationandphylogeneticanalysisofthecompletemitogenomesofivalsamaliiandivalsapyrii AT ruizang characterizationandphylogeneticanalysisofthecompletemitogenomesofivalsamaliiandivalsapyrii AT mengzhang characterizationandphylogeneticanalysisofthecompletemitogenomesofivalsamaliiandivalsapyrii |