四倍体刺沙蓬（俄罗斯刺沙蓬）基因组的组装与注释
Assembly and Annotation of the Tetraploid Salsola tragus (Russian Thistle) Genome.
作者信息
Lemas John M, Patterson Eric L, Cutti Luan, Morran Sarah, Johnson Nicholas A, Montgomery Jacob, Abdollahi Fatemeh, Nelson David R, Llaca Victor, Fengler Kevin, Westra Philip, Gaines Todd A
机构信息
Department of Agricultural Biology, Colorado State University, Fort Collins, CO 80523, USA.
Department of Plant, Soil, and Microbial Science, Michigan State University, East Lansing, MI 48823, USA.
出版信息
Genome Biol Evol. 2025 Feb 3;17(2). doi: 10.1093/gbe/evaf014.
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.
本报告展示了异源四倍体刺沙蓬（2n = 4x = 36）的两个阶段性染色体水平的基因组组装结果，填补了该物种当前基因组资源的空白。流式细胞术估计1C基因组大小为1.319 Gb。利用PacBio HiFi reads，并结合Hi-C染色质接触图谱和Bionano光学图谱数据进行组装和搭建支架。为了进行注释，从根、茎、叶和花组织中构建了一个PacBio Iso-Seq文库，随后使用改良的Maker流程进行注释。组装后的单倍体刺沙蓬基因组各包含18条染色体，其中9条染色体归为A亚基因组，9条染色体归为B亚基因组。每个单倍体基因组组装代表了流式细胞术估计的基因组总大小的95%。单倍体1和单倍体2分别包含433,54个和42,221个注释基因。这种具有经济重要性的杂草高质量参考基因组的可用性将有助于未来对刺沙蓬的组学分析，并更好地了解藜科植物。
Zotero 插件