Assembly and Annotation of the Tetraploid Salsola tragus (Russian thistle) Genome.

IF 3.2 2区生物学 Q2 EVOLUTIONARY BIOLOGY Genome Biology and Evolution Pub Date : 2025-01-25 DOI:10.1093/gbe/evaf014

John M Lemas, Eric L Patterson, Luan Cutti, Sarah Morran, Nicholas A Johnson, Jacob Montgomery, Fatemeh Abdollahi, David R Nelson, Victor Llaca, Kevin Fengler, Philip Westra, Todd A Gaines

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Abstract

This report presents two phased chromosome-scale genome assemblies of allotetraploid Salsola tragus (2n=4x=36) and fills the current genomics resource gap for this species. Flow cytometry estimated 1C genome size was 1.319 Gbp. PacBio HiFi reads were assembled and scaffolded with Hi-C chromatin contact mapping and Bionano optical mapping data. For annotation, a PacBio Iso-Seq library was generated from root, stem, leaf, and floral tissues followed by annotation using a modified Maker pipeline. The assembled haploid S. tragus genomes contained 18 chromosomes each, with 9 chromosomes assigned to subgenome A and 9 chromosomes to subgenome B. Each haplome assembly represented 95% of the total flow cytometry estimated genome size. Haplome 1 and haplome 2 contained 43,354 and 42,221 annotated genes, respectively. The availability of high-quality reference genomes for this economically important weed will facilitate future omics analysis of S. tragus and a better understanding of chenopod plants.

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来源期刊

Genome Biology and Evolution EVOLUTIONARY BIOLOGY-GENETICS & HEREDITY

CiteScore

5.80

自引率

6.10%

发文量

169

审稿时长

1 months

期刊介绍： About the journal Genome Biology and Evolution (GBE) publishes leading original research at the interface between evolutionary biology and genomics. Papers considered for publication report novel evolutionary findings that concern natural genome diversity, population genomics, the structure, function, organisation and expression of genomes, comparative genomics, proteomics, and environmental genomic interactions. Major evolutionary insights from the fields of computational biology, structural biology, developmental biology, and cell biology are also considered, as are theoretical advances in the field of genome evolution. GBE’s scope embraces genome-wide evolutionary investigations at all taxonomic levels and for all forms of life — within populations or across domains. Its aims are to further the understanding of genomes in their evolutionary context and further the understanding of evolution from a genome-wide perspective.