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

IF 2.8 2区生物学 Q2 EVOLUTIONARY BIOLOGY Genome Biology and Evolution Pub Date : 2025-02-03 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

{"title":"Assembly and Annotation of the Tetraploid Salsola tragus (Russian Thistle) Genome.","authors":"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","doi":"10.1093/gbe/evaf014","DOIUrl":null,"url":null,"abstract":"<p><p>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 Gb. 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.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":2.8000,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11797066/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Genome Biology and Evolution","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1093/gbe/evaf014","RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"EVOLUTIONARY BIOLOGY","Score":null,"Total":0}

引用次数: 0

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 Gb. 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.

查看原文

微信好友朋友圈 QQ好友复制链接

本刊更多论文

俄罗斯蓟（Salsola tragus）四倍体基因组的组装与注释。

本文报道了异源四倍体沙漏（Salsola tragus）（2n=4x=36）的两个阶段染色体尺度基因组组装，填补了目前该物种基因组学资源的空白。流式细胞术估计1C基因组大小为1.319 Gbp。PacBio HiFi reads用Hi-C染色质接触图谱和Bionano光学图谱数据组装和搭建。为了进行注释，从根、茎、叶和花组织中生成PacBio Iso-Seq库，然后使用改进的Maker管道进行注释。组装的单倍体金黄色葡萄基因组每条包含18条染色体，其中9条染色体分配给亚基因组A， 9条染色体分配给亚基因组b。每个单倍体组装占流式细胞术估计的总基因组大小的95%。单倍体1和单倍体2分别包含43354和42221个被注释的基因。这种具有重要经济价值的杂草的高质量参考基因组的获得将有助于未来对金黄色葡萄进行组学分析，并更好地了解藜属植物。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

求助全文

约1分钟内获得全文去求助

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.