De Novo Assembly and Annotation of 11 Diverse Shrub Willow (<i>Salix</i>) Genomes Reveals Novel Gene Organization in Sex-Linked Regions
Poplar and willow species in the Salicaceae are dioecious, yet have been shown to use different sex determination systems located on different chromosomes. Willows in the subgenus <i>Vetrix</i> are interesting for comparative studies of sex determination systems, yet genomic resources fo...
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-02-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/24/3/2904 |
| _version_ | 1797624248959762432 |
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| author | Brennan Hyden Kai Feng Timothy B. Yates Sara Jawdy Chelsea Cereghino Lawrence B. Smart Wellington Muchero |
| author_facet | Brennan Hyden Kai Feng Timothy B. Yates Sara Jawdy Chelsea Cereghino Lawrence B. Smart Wellington Muchero |
| author_sort | Brennan Hyden |
| collection | DOAJ |
| description | Poplar and willow species in the Salicaceae are dioecious, yet have been shown to use different sex determination systems located on different chromosomes. Willows in the subgenus <i>Vetrix</i> are interesting for comparative studies of sex determination systems, yet genomic resources for these species are still quite limited. Only a few annotated reference genome assemblies are available, despite many species in use in breeding programs. Here we present de novo assemblies and annotations of 11 shrub willow genomes from six species. Copy number variation of candidate sex determination genes within each genome was characterized and revealed remarkable differences in putative master regulator gene duplication and deletion. We also analyzed copy number and expression of candidate genes involved in floral secondary metabolism, and identified substantial variation across genotypes, which can be used for parental selection in breeding programs. Lastly, we report on a genotype that produces only female descendants and identified gene presence/absence variation in the mitochondrial genome that may be responsible for this unusual inheritance. |
| first_indexed | 2024-03-11T09:40:13Z |
| format | Article |
| id | doaj.art-c27935ddc48e4eda8d92b47cbea2850a |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-11T09:40:13Z |
| publishDate | 2023-02-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-c27935ddc48e4eda8d92b47cbea2850a2023-11-16T17:04:05ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672023-02-01243290410.3390/ijms24032904De Novo Assembly and Annotation of 11 Diverse Shrub Willow (<i>Salix</i>) Genomes Reveals Novel Gene Organization in Sex-Linked RegionsBrennan Hyden0Kai Feng1Timothy B. Yates2Sara Jawdy3Chelsea Cereghino4Lawrence B. Smart5Wellington Muchero6Horticulture Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, USABiosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USABiosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USABiosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USABiosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USAHorticulture Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, USABiosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USAPoplar and willow species in the Salicaceae are dioecious, yet have been shown to use different sex determination systems located on different chromosomes. Willows in the subgenus <i>Vetrix</i> are interesting for comparative studies of sex determination systems, yet genomic resources for these species are still quite limited. Only a few annotated reference genome assemblies are available, despite many species in use in breeding programs. Here we present de novo assemblies and annotations of 11 shrub willow genomes from six species. Copy number variation of candidate sex determination genes within each genome was characterized and revealed remarkable differences in putative master regulator gene duplication and deletion. We also analyzed copy number and expression of candidate genes involved in floral secondary metabolism, and identified substantial variation across genotypes, which can be used for parental selection in breeding programs. Lastly, we report on a genotype that produces only female descendants and identified gene presence/absence variation in the mitochondrial genome that may be responsible for this unusual inheritance.https://www.mdpi.com/1422-0067/24/3/2904<i>Salix</i>shrub willowgenome assemblysex determination |
| spellingShingle | Brennan Hyden Kai Feng Timothy B. Yates Sara Jawdy Chelsea Cereghino Lawrence B. Smart Wellington Muchero De Novo Assembly and Annotation of 11 Diverse Shrub Willow (<i>Salix</i>) Genomes Reveals Novel Gene Organization in Sex-Linked Regions International Journal of Molecular Sciences <i>Salix</i> shrub willow genome assembly sex determination |
| title | De Novo Assembly and Annotation of 11 Diverse Shrub Willow (<i>Salix</i>) Genomes Reveals Novel Gene Organization in Sex-Linked Regions |
| title_full | De Novo Assembly and Annotation of 11 Diverse Shrub Willow (<i>Salix</i>) Genomes Reveals Novel Gene Organization in Sex-Linked Regions |
| title_fullStr | De Novo Assembly and Annotation of 11 Diverse Shrub Willow (<i>Salix</i>) Genomes Reveals Novel Gene Organization in Sex-Linked Regions |
| title_full_unstemmed | De Novo Assembly and Annotation of 11 Diverse Shrub Willow (<i>Salix</i>) Genomes Reveals Novel Gene Organization in Sex-Linked Regions |
| title_short | De Novo Assembly and Annotation of 11 Diverse Shrub Willow (<i>Salix</i>) Genomes Reveals Novel Gene Organization in Sex-Linked Regions |
| title_sort | de novo assembly and annotation of 11 diverse shrub willow i salix i genomes reveals novel gene organization in sex linked regions |
| topic | <i>Salix</i> shrub willow genome assembly sex determination |
| url | https://www.mdpi.com/1422-0067/24/3/2904 |
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