Hamilton John P, Brose Julia, Buell C Robin
Department of Crop & Soil Sciences, University of Georgia, Athens, GA 30602, USA.
Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, USA.
Genetics. 2025 Mar 17;229(3). doi: 10.1093/genetics/iyae205.
Potato is a key food crop with a complex, polyploid genome. Advancements in sequencing technologies coupled with improvements in genome assembly algorithms have enabled generation of phased, chromosome-scale genome assemblies for cultivated tetraploid potato. The SpudDB database houses potato genome sequence and annotation, with the doubled monoploid DM 1-3 516 R44 (hereafter DM) genome serving as the reference genome and haplotype. Diverse annotation data types for DM genes are provided through a suite of Gene Report Pages including gene expression profiles across 438 potato samples. To further annotate potato genes based on expression, 65 gene co-expression modules were constructed that permit the identification of tightly co-regulated genes within DM across development and responses to wounding, abiotic stress, and biotic stress. Genome browser views of DM and 28 other potato genomes are provided along with a download page for genome sequence and annotation. To link syntenic genes within and between haplotypes, syntelogs were identified across 25 cultivated potato genomes. Through access to potato genome sequences and associated annotations, SpudDB can enable potato biologists, geneticists, and breeders to continue to improve this key food crop.
马铃薯是一种具有复杂多倍体基因组的关键粮食作物。测序技术的进步以及基因组组装算法的改进，使得能够为栽培四倍体马铃薯生成定相的、染色体级别的基因组组装。SpudDB数据库存储了马铃薯基因组序列和注释，以双单倍体DM 1-3 516 R44（以下简称DM）基因组作为参考基因组和单倍型。通过一套基因报告页面提供了DM基因的多种注释数据类型，包括438个马铃薯样本的基因表达谱。为了基于表达进一步注释马铃薯基因，构建了65个基因共表达模块，这些模块允许在DM中鉴定在发育过程以及对伤口、非生物胁迫和生物胁迫的响应中紧密共调控的基因。提供了DM和其他28个马铃薯基因组的基因组浏览器视图以及基因组序列和注释的下载页面。为了连接单倍型内和单倍型间的同线基因，在25个栽培马铃薯基因组中鉴定了同线同源基因。通过访问马铃薯基因组序列和相关注释，SpudDB可以使马铃薯生物学家、遗传学家和育种者继续改良这种关键粮食作物。
