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De Novo Assembly and Annotation of 11 Diverse Shrub Willow (Salix) 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 Vetrix are interesting for comparative studies of sex determination systems, yet genomic resources for these species are...

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Autores principales: Hyden, Brennan, Feng, Kai, Yates, Timothy B., Jawdy, Sara, Cereghino, Chelsea, Smart, Lawrence B., Muchero, Wellington
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9917877/
https://www.ncbi.nlm.nih.gov/pubmed/36769224
http://dx.doi.org/10.3390/ijms24032904
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author Hyden, Brennan
Feng, Kai
Yates, Timothy B.
Jawdy, Sara
Cereghino, Chelsea
Smart, Lawrence B.
Muchero, Wellington
author_facet Hyden, Brennan
Feng, Kai
Yates, Timothy B.
Jawdy, Sara
Cereghino, Chelsea
Smart, Lawrence B.
Muchero, Wellington
author_sort Hyden, Brennan
collection PubMed
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 Vetrix 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.
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spelling pubmed-99178772023-02-11 De Novo Assembly and Annotation of 11 Diverse Shrub Willow (Salix) Genomes Reveals Novel Gene Organization in Sex-Linked Regions Hyden, Brennan Feng, Kai Yates, Timothy B. Jawdy, Sara Cereghino, Chelsea Smart, Lawrence B. Muchero, Wellington Int J Mol Sci Article 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 Vetrix 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. MDPI 2023-02-02 /pmc/articles/PMC9917877/ /pubmed/36769224 http://dx.doi.org/10.3390/ijms24032904 Text en © 2023 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
Hyden, Brennan
Feng, Kai
Yates, Timothy B.
Jawdy, Sara
Cereghino, Chelsea
Smart, Lawrence B.
Muchero, Wellington
De Novo Assembly and Annotation of 11 Diverse Shrub Willow (Salix) Genomes Reveals Novel Gene Organization in Sex-Linked Regions
title De Novo Assembly and Annotation of 11 Diverse Shrub Willow (Salix) Genomes Reveals Novel Gene Organization in Sex-Linked Regions
title_full De Novo Assembly and Annotation of 11 Diverse Shrub Willow (Salix) Genomes Reveals Novel Gene Organization in Sex-Linked Regions
title_fullStr De Novo Assembly and Annotation of 11 Diverse Shrub Willow (Salix) Genomes Reveals Novel Gene Organization in Sex-Linked Regions
title_full_unstemmed De Novo Assembly and Annotation of 11 Diverse Shrub Willow (Salix) Genomes Reveals Novel Gene Organization in Sex-Linked Regions
title_short De Novo Assembly and Annotation of 11 Diverse Shrub Willow (Salix) Genomes Reveals Novel Gene Organization in Sex-Linked Regions
title_sort de novo assembly and annotation of 11 diverse shrub willow (salix) genomes reveals novel gene organization in sex-linked regions
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9917877/
https://www.ncbi.nlm.nih.gov/pubmed/36769224
http://dx.doi.org/10.3390/ijms24032904
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