Cargando…
Pan-Genomics Reveals a New Variation Pattern of Secreted Proteins in Pyricularia oryzae
(1) Background: Pyricularia oryzae, the causal agent of rice blast disease, is one of the major rice pathogens. The complex population structure of P. oryzae facilitates the rapid virulence variations, which make the blast disease a serious challenge for global food security. There is a large body o...
Autores principales: | , , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2022
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9785059/ https://www.ncbi.nlm.nih.gov/pubmed/36547571 http://dx.doi.org/10.3390/jof8121238 |
_version_ | 1784857960612102144 |
---|---|
author | Bao, Jiandong Wang, Zhe Chen, Meilian Chen, Shijie Chen, Xiaomin Xie, Jiahui Tang, Wei Zheng, Huakun Wang, Zonghua |
author_facet | Bao, Jiandong Wang, Zhe Chen, Meilian Chen, Shijie Chen, Xiaomin Xie, Jiahui Tang, Wei Zheng, Huakun Wang, Zonghua |
author_sort | Bao, Jiandong |
collection | PubMed |
description | (1) Background: Pyricularia oryzae, the causal agent of rice blast disease, is one of the major rice pathogens. The complex population structure of P. oryzae facilitates the rapid virulence variations, which make the blast disease a serious challenge for global food security. There is a large body of existing genomics research on P. oryzae, however the population structure at the pan-genome level is not clear, and the mechanism of genetic divergence and virulence variations of different sub-populations is also unknown. (2) Methods: Based on the genome data published in the NCBI, we constructed a pan-genome database of P. oryzae, which consisted of 156 strains (117 isolated from rice and 39 isolated from other hosts). (3) Results: The pan-genome contained a total of 24,100 genes (12,005 novel genes absent in the reference genome 70-15), including 16,911 (~70%) core genes (population frequency ≥95%) and 1378 (~5%) strain-specific genes (population frequency ≤5%). Gene presence-absence variation (PAV) based clustering analysis of the population structure of P. oryzae revealed four subgroups (three from rice and one from other hosts). Interestingly, the cloned avirulence genes and conventional secreted proteins (SPs, with signal peptides) were enriched in the high-frequency regions and significantly associated with transposable elements (TEs), while the unconventional SPs (without signal peptides) were enriched in the low-frequency regions and not associated significantly with TEs. This pan-genome will expand the breadth and depth of the rice blast fungus reference genome, and also serve as a new blueprint for scientists to further study the pathogenic mechanism and virulence variation of the rice blast fungus. |
format | Online Article Text |
id | pubmed-9785059 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-97850592022-12-24 Pan-Genomics Reveals a New Variation Pattern of Secreted Proteins in Pyricularia oryzae Bao, Jiandong Wang, Zhe Chen, Meilian Chen, Shijie Chen, Xiaomin Xie, Jiahui Tang, Wei Zheng, Huakun Wang, Zonghua J Fungi (Basel) Article (1) Background: Pyricularia oryzae, the causal agent of rice blast disease, is one of the major rice pathogens. The complex population structure of P. oryzae facilitates the rapid virulence variations, which make the blast disease a serious challenge for global food security. There is a large body of existing genomics research on P. oryzae, however the population structure at the pan-genome level is not clear, and the mechanism of genetic divergence and virulence variations of different sub-populations is also unknown. (2) Methods: Based on the genome data published in the NCBI, we constructed a pan-genome database of P. oryzae, which consisted of 156 strains (117 isolated from rice and 39 isolated from other hosts). (3) Results: The pan-genome contained a total of 24,100 genes (12,005 novel genes absent in the reference genome 70-15), including 16,911 (~70%) core genes (population frequency ≥95%) and 1378 (~5%) strain-specific genes (population frequency ≤5%). Gene presence-absence variation (PAV) based clustering analysis of the population structure of P. oryzae revealed four subgroups (three from rice and one from other hosts). Interestingly, the cloned avirulence genes and conventional secreted proteins (SPs, with signal peptides) were enriched in the high-frequency regions and significantly associated with transposable elements (TEs), while the unconventional SPs (without signal peptides) were enriched in the low-frequency regions and not associated significantly with TEs. This pan-genome will expand the breadth and depth of the rice blast fungus reference genome, and also serve as a new blueprint for scientists to further study the pathogenic mechanism and virulence variation of the rice blast fungus. MDPI 2022-11-23 /pmc/articles/PMC9785059/ /pubmed/36547571 http://dx.doi.org/10.3390/jof8121238 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Bao, Jiandong Wang, Zhe Chen, Meilian Chen, Shijie Chen, Xiaomin Xie, Jiahui Tang, Wei Zheng, Huakun Wang, Zonghua Pan-Genomics Reveals a New Variation Pattern of Secreted Proteins in Pyricularia oryzae |
title | Pan-Genomics Reveals a New Variation Pattern of Secreted Proteins in Pyricularia oryzae |
title_full | Pan-Genomics Reveals a New Variation Pattern of Secreted Proteins in Pyricularia oryzae |
title_fullStr | Pan-Genomics Reveals a New Variation Pattern of Secreted Proteins in Pyricularia oryzae |
title_full_unstemmed | Pan-Genomics Reveals a New Variation Pattern of Secreted Proteins in Pyricularia oryzae |
title_short | Pan-Genomics Reveals a New Variation Pattern of Secreted Proteins in Pyricularia oryzae |
title_sort | pan-genomics reveals a new variation pattern of secreted proteins in pyricularia oryzae |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9785059/ https://www.ncbi.nlm.nih.gov/pubmed/36547571 http://dx.doi.org/10.3390/jof8121238 |
work_keys_str_mv | AT baojiandong pangenomicsrevealsanewvariationpatternofsecretedproteinsinpyriculariaoryzae AT wangzhe pangenomicsrevealsanewvariationpatternofsecretedproteinsinpyriculariaoryzae AT chenmeilian pangenomicsrevealsanewvariationpatternofsecretedproteinsinpyriculariaoryzae AT chenshijie pangenomicsrevealsanewvariationpatternofsecretedproteinsinpyriculariaoryzae AT chenxiaomin pangenomicsrevealsanewvariationpatternofsecretedproteinsinpyriculariaoryzae AT xiejiahui pangenomicsrevealsanewvariationpatternofsecretedproteinsinpyriculariaoryzae AT tangwei pangenomicsrevealsanewvariationpatternofsecretedproteinsinpyriculariaoryzae AT zhenghuakun pangenomicsrevealsanewvariationpatternofsecretedproteinsinpyriculariaoryzae AT wangzonghua pangenomicsrevealsanewvariationpatternofsecretedproteinsinpyriculariaoryzae |