Importance of appropriate genome information for the design of mating type primers in black and yellow morel populations
Abstract Morels are highly prized edible fungi where sexual reproduction is essential for fruiting-body production. As a result, a comprehensive understanding of their sexual reproduction is of great interest. Central to this is the identification of the reproductive strategies used by morels. Sexua...
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BMC
2022-08-01
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| Series: | IMA Fungus |
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| Online Access: | https://doi.org/10.1186/s43008-022-00101-6 |
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| author | Melissa Cravero Aaron J. Robinson Patrick Hilpisch Patrick S. Chain Saskia Bindschedler Pilar Junier |
| author_facet | Melissa Cravero Aaron J. Robinson Patrick Hilpisch Patrick S. Chain Saskia Bindschedler Pilar Junier |
| author_sort | Melissa Cravero |
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| description | Abstract Morels are highly prized edible fungi where sexual reproduction is essential for fruiting-body production. As a result, a comprehensive understanding of their sexual reproduction is of great interest. Central to this is the identification of the reproductive strategies used by morels. Sexual reproduction in fungi is controlled by mating-type (MAT) genes and morels are thought to be mainly heterothallic with two idiomorphs, MAT1-1 and MAT1-2. Genomic sequencing of black (Elata clade) and yellow (Esculenta clade) morel species has led to the development of PCR primers designed to amplify genes from the two idiomorphs for rapid genotyping of isolates from these two clades. To evaluate the design and theoretical performance of these primers we performed a thorough bioinformatic investigation, including the detection of the MAT region in publicly available Morchella genomes and in-silico PCR analyses. All examined genomes, including those used for primer design, appeared to be heterothallic. This indicates an inherent fault in the original primer design which utilized a single Morchella genome, as the use of two genomes with complementary mating types would be required to design accurate primers for both idiomorphs. Furthermore, potential off-targets were identified for some of the previously published primer sets, but verification was challenging due to lack of adequate genomic information and detailed methodologies for primer design. Examinations of the black morel specific primer pairs (MAT11L/R and MAT22L/R) indicated the MAT22 primers would correctly target and amplify the MAT1-2 idiomorph, but the MAT11 primers appear to be capable of amplifying incorrect off-targets within the genome. The yellow morel primer pairs (EMAT1-1 L/R and EMAT1-2 L/R) appear to have reporting errors, as the published primer sequences are dissimilar with reported amplicon sequences and the EMAT1-2 primers appear to amplify the RNA polymerase II subunit (RPB2) gene. The lack of the reference genome used in primer design and descriptive methodology made it challenging to fully assess the apparent issues with the primers for this clade. In conclusion, additional work is still required for the generation of reliable primers to investigate mating types in morels and to assess their performance on different clades and across multiple geographical regions. |
| format | Article |
| id | doaj-art-39e0a7352b8d47a38fd6a785000cf995 |
| institution | Kabale University |
| issn | 2210-6359 |
| language | English |
| publishDate | 2022-08-01 |
| publisher | BMC |
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| series | IMA Fungus |
| spelling | doaj-art-39e0a7352b8d47a38fd6a785000cf9952025-02-02T23:19:19ZengBMCIMA Fungus2210-63592022-08-011311610.1186/s43008-022-00101-6Importance of appropriate genome information for the design of mating type primers in black and yellow morel populationsMelissa Cravero0Aaron J. Robinson1Patrick Hilpisch2Patrick S. Chain3Saskia Bindschedler4Pilar Junier5Laboratory of Microbiology, Institute of Biology, University of NeuchâtelBioscience Division, Los Alamos National LaboratoryLaboratory of Microbiology, Institute of Biology, University of NeuchâtelBioscience Division, Los Alamos National LaboratoryLaboratory of Microbiology, Institute of Biology, University of NeuchâtelLaboratory of Microbiology, Institute of Biology, University of NeuchâtelAbstract Morels are highly prized edible fungi where sexual reproduction is essential for fruiting-body production. As a result, a comprehensive understanding of their sexual reproduction is of great interest. Central to this is the identification of the reproductive strategies used by morels. Sexual reproduction in fungi is controlled by mating-type (MAT) genes and morels are thought to be mainly heterothallic with two idiomorphs, MAT1-1 and MAT1-2. Genomic sequencing of black (Elata clade) and yellow (Esculenta clade) morel species has led to the development of PCR primers designed to amplify genes from the two idiomorphs for rapid genotyping of isolates from these two clades. To evaluate the design and theoretical performance of these primers we performed a thorough bioinformatic investigation, including the detection of the MAT region in publicly available Morchella genomes and in-silico PCR analyses. All examined genomes, including those used for primer design, appeared to be heterothallic. This indicates an inherent fault in the original primer design which utilized a single Morchella genome, as the use of two genomes with complementary mating types would be required to design accurate primers for both idiomorphs. Furthermore, potential off-targets were identified for some of the previously published primer sets, but verification was challenging due to lack of adequate genomic information and detailed methodologies for primer design. Examinations of the black morel specific primer pairs (MAT11L/R and MAT22L/R) indicated the MAT22 primers would correctly target and amplify the MAT1-2 idiomorph, but the MAT11 primers appear to be capable of amplifying incorrect off-targets within the genome. The yellow morel primer pairs (EMAT1-1 L/R and EMAT1-2 L/R) appear to have reporting errors, as the published primer sequences are dissimilar with reported amplicon sequences and the EMAT1-2 primers appear to amplify the RNA polymerase II subunit (RPB2) gene. The lack of the reference genome used in primer design and descriptive methodology made it challenging to fully assess the apparent issues with the primers for this clade. In conclusion, additional work is still required for the generation of reliable primers to investigate mating types in morels and to assess their performance on different clades and across multiple geographical regions.https://doi.org/10.1186/s43008-022-00101-6PCRMAT idiomorphsMorchellaHeterothallicHomothallicSexual reproduction |
| spellingShingle | Melissa Cravero Aaron J. Robinson Patrick Hilpisch Patrick S. Chain Saskia Bindschedler Pilar Junier Importance of appropriate genome information for the design of mating type primers in black and yellow morel populations IMA Fungus PCR MAT idiomorphs Morchella Heterothallic Homothallic Sexual reproduction |
| title | Importance of appropriate genome information for the design of mating type primers in black and yellow morel populations |
| title_full | Importance of appropriate genome information for the design of mating type primers in black and yellow morel populations |
| title_fullStr | Importance of appropriate genome information for the design of mating type primers in black and yellow morel populations |
| title_full_unstemmed | Importance of appropriate genome information for the design of mating type primers in black and yellow morel populations |
| title_short | Importance of appropriate genome information for the design of mating type primers in black and yellow morel populations |
| title_sort | importance of appropriate genome information for the design of mating type primers in black and yellow morel populations |
| topic | PCR MAT idiomorphs Morchella Heterothallic Homothallic Sexual reproduction |
| url | https://doi.org/10.1186/s43008-022-00101-6 |
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