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Comparative Genomic Analysis Reveals Genetic Variation and Adaptive Evolution in the Pathogenicity-Related Genes of Phytophthora capsici

Phytophthora capsici is an oomycete pathogen responsible for damping off, root rot, fruit rot, and foliar blight in popular vegetable and legume crops. The existence of distinct aggressiveness levels and physiological races among the P. capsici population is a major constraint to developing resistan...

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Autores principales: Lee, Joung-Ho, Siddique, Muhammad Irfan, Kwon, Jin-Kyung, Kang, Byoung-Cheorl
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8415033/
https://www.ncbi.nlm.nih.gov/pubmed/34484141
http://dx.doi.org/10.3389/fmicb.2021.694136
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author Lee, Joung-Ho
Siddique, Muhammad Irfan
Kwon, Jin-Kyung
Kang, Byoung-Cheorl
author_facet Lee, Joung-Ho
Siddique, Muhammad Irfan
Kwon, Jin-Kyung
Kang, Byoung-Cheorl
author_sort Lee, Joung-Ho
collection PubMed
description Phytophthora capsici is an oomycete pathogen responsible for damping off, root rot, fruit rot, and foliar blight in popular vegetable and legume crops. The existence of distinct aggressiveness levels and physiological races among the P. capsici population is a major constraint to developing resistant varieties of host crops. In the present study, we compared the genomes of three P. capsici isolates with different aggressiveness levels to reveal their genomic differences. We obtained genome sequences using short-read and long-read technologies, which yielded an average genome size of 76 Mbp comprising 514 contigs and 15,076 predicted genes. A comparative genomic analysis uncovered the signatures of accelerated evolution, gene family expansions in the pathogenicity-related genes among the three isolates. Resequencing two additional P. capsici isolates enabled the identification of average 1,023,437 SNPs, revealing the frequent accumulation of non-synonymous substitutions in pathogenicity-related gene families. Furthermore, pathogenicity-related gene families, cytoplasmic effectors and ATP binding cassette (ABC) transporters, showed expansion signals in the more aggressive isolates, with a greater number of non-synonymous SNPs. This genomic information explains the plasticity, difference in aggressiveness levels, and genome structural variation among the P. capsici isolates, providing insight into the genomic features related to the evolution and pathogenicity of this oomycete pathogen.
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spelling pubmed-84150332021-09-04 Comparative Genomic Analysis Reveals Genetic Variation and Adaptive Evolution in the Pathogenicity-Related Genes of Phytophthora capsici Lee, Joung-Ho Siddique, Muhammad Irfan Kwon, Jin-Kyung Kang, Byoung-Cheorl Front Microbiol Microbiology Phytophthora capsici is an oomycete pathogen responsible for damping off, root rot, fruit rot, and foliar blight in popular vegetable and legume crops. The existence of distinct aggressiveness levels and physiological races among the P. capsici population is a major constraint to developing resistant varieties of host crops. In the present study, we compared the genomes of three P. capsici isolates with different aggressiveness levels to reveal their genomic differences. We obtained genome sequences using short-read and long-read technologies, which yielded an average genome size of 76 Mbp comprising 514 contigs and 15,076 predicted genes. A comparative genomic analysis uncovered the signatures of accelerated evolution, gene family expansions in the pathogenicity-related genes among the three isolates. Resequencing two additional P. capsici isolates enabled the identification of average 1,023,437 SNPs, revealing the frequent accumulation of non-synonymous substitutions in pathogenicity-related gene families. Furthermore, pathogenicity-related gene families, cytoplasmic effectors and ATP binding cassette (ABC) transporters, showed expansion signals in the more aggressive isolates, with a greater number of non-synonymous SNPs. This genomic information explains the plasticity, difference in aggressiveness levels, and genome structural variation among the P. capsici isolates, providing insight into the genomic features related to the evolution and pathogenicity of this oomycete pathogen. Frontiers Media S.A. 2021-08-13 /pmc/articles/PMC8415033/ /pubmed/34484141 http://dx.doi.org/10.3389/fmicb.2021.694136 Text en Copyright © 2021 Lee, Siddique, Kwon and Kang. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Microbiology
Lee, Joung-Ho
Siddique, Muhammad Irfan
Kwon, Jin-Kyung
Kang, Byoung-Cheorl
Comparative Genomic Analysis Reveals Genetic Variation and Adaptive Evolution in the Pathogenicity-Related Genes of Phytophthora capsici
title Comparative Genomic Analysis Reveals Genetic Variation and Adaptive Evolution in the Pathogenicity-Related Genes of Phytophthora capsici
title_full Comparative Genomic Analysis Reveals Genetic Variation and Adaptive Evolution in the Pathogenicity-Related Genes of Phytophthora capsici
title_fullStr Comparative Genomic Analysis Reveals Genetic Variation and Adaptive Evolution in the Pathogenicity-Related Genes of Phytophthora capsici
title_full_unstemmed Comparative Genomic Analysis Reveals Genetic Variation and Adaptive Evolution in the Pathogenicity-Related Genes of Phytophthora capsici
title_short Comparative Genomic Analysis Reveals Genetic Variation and Adaptive Evolution in the Pathogenicity-Related Genes of Phytophthora capsici
title_sort comparative genomic analysis reveals genetic variation and adaptive evolution in the pathogenicity-related genes of phytophthora capsici
topic Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8415033/
https://www.ncbi.nlm.nih.gov/pubmed/34484141
http://dx.doi.org/10.3389/fmicb.2021.694136
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