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

Brennan Hyden; Kai Feng; Timothy B. Yates; Sara Jawdy; Chelsea Cereghino; Lawrence B. Smart; Wellington Muchero

doi:10.3390/ijms24032904

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

Brennan Hyden, Kai Feng, Timothy B. Yates, Sara Jawdy, Chelsea Cereghino, Lawrence B. Smart, Wellington Muchero

Plant Systems Biology

Research output: Contribution to journal › Article › peer-review

2 Scopus citations

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 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.

Original language	English
Article number	2904
Journal	International Journal of Molecular Sciences
Volume	24
Issue number	3
DOIs	https://doi.org/10.3390/ijms24032904
State	Published - Feb 2023

Funding

This work was partially supported by the U.S. Department of Energy (DOE) Office of Science Early Career Research Program under the Biological and Environmental Research office. BH was supported by a fellowship from the DOE Office of Science Graduate Student Research (SCGSR) Program and by a Pre-doctoral Research Fellowship from the United States Department of Agriculture National Institute for Food and Agriculture (award #2021-67034-35116). Oak Ridge National Laboratory is managed by UT-Battelle, LLC for the U.S. Department of Energy under Contract Number DE-AC05-00OR22725. Part of this work was performed at the Oak Ridge Leadership Computing Facility (OLCF) including resources of the Compute and Data Environment for Science (CADES) at Oak Ridge National Laboratory. Partial funding for this research was also provided by grants from the National Science Foundation (DEB-1542486) and from the USDA National Institute for Food and Agriculture (2015-67009-23957).

Keywords

Salix
genome assembly
sex determination
shrub willow

Access to Document

10.3390/ijms24032904

Cite this

@article{7437faa6037e4cb5ba333738cf35abdf,

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

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 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.",

keywords = "Salix, genome assembly, sex determination, shrub willow",

author = "Brennan Hyden and Kai Feng and Yates, {Timothy B.} and Sara Jawdy and Chelsea Cereghino and Smart, {Lawrence B.} and Wellington Muchero",

note = "Publisher Copyright: {\textcopyright} 2023 by the authors.",

year = "2023",

month = feb,

doi = "10.3390/ijms24032904",

language = "English",

volume = "24",

journal = "International Journal of Molecular Sciences",

issn = "1661-6596",

publisher = "MDPI",

number = "3",

}

TY - JOUR

T1 - De Novo Assembly and Annotation of 11 Diverse Shrub Willow (Salix) Genomes Reveals Novel Gene Organization in Sex-Linked Regions

AU - Hyden, Brennan

AU - Feng, Kai

AU - Yates, Timothy B.

AU - Jawdy, Sara

AU - Cereghino, Chelsea

AU - Smart, Lawrence B.

AU - Muchero, Wellington

PY - 2023/2

Y1 - 2023/2

N2 - 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.

AB - 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.

KW - Salix

KW - genome assembly

KW - sex determination

KW - shrub willow

UR - http://www.scopus.com/inward/record.url?scp=85147894305&partnerID=8YFLogxK

U2 - 10.3390/ijms24032904

DO - 10.3390/ijms24032904

M3 - Article

C2 - 36769224

AN - SCOPUS:85147894305

SN - 1661-6596

VL - 24

JO - International Journal of Molecular Sciences

JF - International Journal of Molecular Sciences

IS - 3

M1 - 2904

ER -

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

Abstract

Funding

Keywords

Access to Document

Other files and links

Fingerprint

Cite this