Preprint Article Version 1 Preserved in Portico This version is not peer-reviewed

De Novo Assembly and Annotation of 11 Diverse Shrub Willow (Salix) Genomes Reveals Novel Gene Organization in Sex-Linked Regions

Brennan Hyden
ORCID logo ,
Kai Feng
,
Timothy B Yates
,
Sara Jawdy
,
Chelsea Cereghino
,
Lawrence B Smart
* ORCID logo ,
Wellington Muchero
*
Version 1 : Received: 8 December 2022 / Approved: 12 December 2022 / Online: 12 December 2022 (01:46:15 CET)

A peer-reviewed article of this Preprint also exists.

Hyden, B.; Feng, K.; Yates, T.B.; Jawdy, S.; Cereghino, C.; Smart, L.B.; Muchero, W. De Novo Assembly and Annotation of 11 Diverse Shrub Willow (Salix) Genomes Reveals Novel Gene Organization in Sex-Linked Regions. Int. J. Mol. Sci. 2023, 24, 2904. Hyden, B.; Feng, K.; Yates, T.B.; Jawdy, S.; Cereghino, C.; Smart, L.B.; Muchero, W. De Novo Assembly and Annotation of 11 Diverse Shrub Willow (Salix) Genomes Reveals Novel Gene Organization in Sex-Linked Regions. Int. J. Mol. Sci. 2023, 24, 2904.

Abstract

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 section 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.

Keywords

Salix; shrub willow; genome assembly; sex determination

Subject

Biology and Life Sciences, Plant Sciences

Copyright: This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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