HybridMine: A Pipeline for Allele Inheritance and Gene Copy Number Prediction in Hybrid Genomes and Its Application to Industrial Yeasts
Genome-scale computational approaches are opening opportunities to model and predict favorable combination of traits for strain development. However, mining the genome of complex hybrids is not currently an easy task, due to the high level of redundancy and presence of homologous. For example, <i...
| Main Authors: | , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2020-10-01
|
| Series: | Microorganisms |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2076-2607/8/10/1554 |
| _version_ | 1827704662153756672 |
|---|---|
| author | Soukaina Timouma Jean-Marc Schwartz Daniela Delneri |
| author_facet | Soukaina Timouma Jean-Marc Schwartz Daniela Delneri |
| author_sort | Soukaina Timouma |
| collection | DOAJ |
| description | Genome-scale computational approaches are opening opportunities to model and predict favorable combination of traits for strain development. However, mining the genome of complex hybrids is not currently an easy task, due to the high level of redundancy and presence of homologous. For example, <i>Saccharomyces pastorianus</i> is an allopolyploid sterile yeast hybrid used in brewing to produce lager-style beers. The development of new yeast strains with valuable industrial traits such as improved maltose utilization or balanced flavor profiles are now a major ambition and challenge in craft brewing and distilling industries. Moreover, no genome annotation for most of these industrial strains have been published. Here, we developed HybridMine, a new user-friendly, open-source tool for functional annotation of hybrid aneuploid genomes of any species by predicting parental alleles including paralogs. Our benchmark studies showed that HybridMine produced biologically accurate results for hybrid genomes compared to other well-established software. As proof of principle, we carried out a comprehensive structural and functional annotation of complex yeast hybrids to enable system biology prediction studies. HybridMine is developed in Python, Perl, and Bash programming languages and is available in GitHub. |
| first_indexed | 2024-03-10T15:46:21Z |
| format | Article |
| id | doaj.art-0056384ecc4a43418fae74d519d9b05c |
| institution | Directory Open Access Journal |
| issn | 2076-2607 |
| language | English |
| last_indexed | 2024-03-10T15:46:21Z |
| publishDate | 2020-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Microorganisms |
| spelling | doaj.art-0056384ecc4a43418fae74d519d9b05c2023-11-20T16:25:03ZengMDPI AGMicroorganisms2076-26072020-10-01810155410.3390/microorganisms8101554HybridMine: A Pipeline for Allele Inheritance and Gene Copy Number Prediction in Hybrid Genomes and Its Application to Industrial YeastsSoukaina Timouma0Jean-Marc Schwartz1Daniela Delneri2Manchester Institute of Biotechnology, Faculty of Biology Medicine and Health, University of Manchester, M1 7DN Manchester, UKDivision of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, M13 9PT Manchester, UKManchester Institute of Biotechnology, Faculty of Biology Medicine and Health, University of Manchester, M1 7DN Manchester, UKGenome-scale computational approaches are opening opportunities to model and predict favorable combination of traits for strain development. However, mining the genome of complex hybrids is not currently an easy task, due to the high level of redundancy and presence of homologous. For example, <i>Saccharomyces pastorianus</i> is an allopolyploid sterile yeast hybrid used in brewing to produce lager-style beers. The development of new yeast strains with valuable industrial traits such as improved maltose utilization or balanced flavor profiles are now a major ambition and challenge in craft brewing and distilling industries. Moreover, no genome annotation for most of these industrial strains have been published. Here, we developed HybridMine, a new user-friendly, open-source tool for functional annotation of hybrid aneuploid genomes of any species by predicting parental alleles including paralogs. Our benchmark studies showed that HybridMine produced biologically accurate results for hybrid genomes compared to other well-established software. As proof of principle, we carried out a comprehensive structural and functional annotation of complex yeast hybrids to enable system biology prediction studies. HybridMine is developed in Python, Perl, and Bash programming languages and is available in GitHub.https://www.mdpi.com/2076-2607/8/10/1554hybridspredictionparental allelesorthologsyeast |
| spellingShingle | Soukaina Timouma Jean-Marc Schwartz Daniela Delneri HybridMine: A Pipeline for Allele Inheritance and Gene Copy Number Prediction in Hybrid Genomes and Its Application to Industrial Yeasts Microorganisms hybrids prediction parental alleles orthologs yeast |
| title | HybridMine: A Pipeline for Allele Inheritance and Gene Copy Number Prediction in Hybrid Genomes and Its Application to Industrial Yeasts |
| title_full | HybridMine: A Pipeline for Allele Inheritance and Gene Copy Number Prediction in Hybrid Genomes and Its Application to Industrial Yeasts |
| title_fullStr | HybridMine: A Pipeline for Allele Inheritance and Gene Copy Number Prediction in Hybrid Genomes and Its Application to Industrial Yeasts |
| title_full_unstemmed | HybridMine: A Pipeline for Allele Inheritance and Gene Copy Number Prediction in Hybrid Genomes and Its Application to Industrial Yeasts |
| title_short | HybridMine: A Pipeline for Allele Inheritance and Gene Copy Number Prediction in Hybrid Genomes and Its Application to Industrial Yeasts |
| title_sort | hybridmine a pipeline for allele inheritance and gene copy number prediction in hybrid genomes and its application to industrial yeasts |
| topic | hybrids prediction parental alleles orthologs yeast |
| url | https://www.mdpi.com/2076-2607/8/10/1554 |
| work_keys_str_mv | AT soukainatimouma hybridmineapipelineforalleleinheritanceandgenecopynumberpredictioninhybridgenomesanditsapplicationtoindustrialyeasts AT jeanmarcschwartz hybridmineapipelineforalleleinheritanceandgenecopynumberpredictioninhybridgenomesanditsapplicationtoindustrialyeasts AT danieladelneri hybridmineapipelineforalleleinheritanceandgenecopynumberpredictioninhybridgenomesanditsapplicationtoindustrialyeasts |