加强玉米遗传学和基因组学数据库的泛基因组资源。

IF 3.3 3区 生物学 Genetics Pub Date : 2024-04-05 DOI:10.1093/genetics/iyae036
Ethalinda K Cannon, John L Portwood, Rita K Hayford, Olivia C Haley, Jack M Gardiner, Carson M Andorf, Margaret R Woodhouse
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引用次数: 0

摘要

泛基因组包括一个支系内基因组集合中发现的全部基因序列,比单一参考基因组更有助于研究物种多样性。对于像玉米这样基因组特别多样和复杂的物种来说尤其如此。展示泛基因组数据、分析和可视化具有挑战性,尤其是对于多样性物种来说,而当泛基因组数据与广泛的基因模型和基因数据(包括经典基因信息、标记、插入、表达和蛋白质组数据以及蛋白质结构)相连接时,挑战性就更大了,玉米基因组数据库(MaizeGDB)就是这种情况。在这里,我们介绍了 MaizeGDB 的扩展情况,它将玉米泛基因组的基因子集纳入了一个泛基因数据中心,该数据中心的特色是由 MaizeGDB 托管的玉米基因组,以及来自 Pan-Andropoganeae 项目的外群茶籽玉米基因组。新数据中心提供各种浏览和可视化工具,包括序列比对可视化、基因树和其他工具,以探索由 Pandagma 管道计算的玉米泛基因。综合这些数据,将有助于玉米研究人员研究玉米的复杂性和多样性,并利用比较功能验证选定基因模型的泛基因关系。
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Enhanced pan-genomic resources at the maize genetics and genomics database.
Pan-genomes, encompassing the entirety of genetic sequences found in a collection of genomes within a clade, are more useful than single reference genomes for studying species diversity. This is especially true for a species like Zea mays, which has a particularly diverse and complex genome. Presenting pan-genome data, analyses, and visualization is challenging, especially for a diverse species, but more so when pan-genomic data is linked to extensive gene model and gene data, including classical gene information, markers, insertions, expression and proteomic data, and protein structures as is the case at MaizeGDB. Here, we describe MaizeGDB's expansion to include the genic subset of the Zea pan-genome in a pan-gene data center featuring the maize genomes hosted at MaizeGDB, and the outgroup teosinte Zea genomes from the Pan-Andropoganeae project. The new data center offers a variety of browsing and visualization tools, including sequence alignment visualization, gene trees and other tools, to explore pan-genes in Zea that were calculated by the pipeline Pandagma. Combined, these data will help maize researchers study the complexity and diversity of Zea, and to use the comparative functions to validate pan-gene relationships for a selected gene model.
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来源期刊
Genetics
Genetics 生物-遗传学
CiteScore
6.20
自引率
6.10%
发文量
177
期刊介绍: GENETICS is published by the Genetics Society of America, a scholarly society that seeks to deepen our understanding of the living world by advancing our understanding of genetics. Since 1916, GENETICS has published high-quality, original research presenting novel findings bearing on genetics and genomics. The journal publishes empirical studies of organisms ranging from microbes to humans, as well as theoretical work. While it has an illustrious history, GENETICS has changed along with the communities it serves: it is not your mentor''s journal. The editors make decisions quickly – in around 30 days – without sacrificing the excellence and scholarship for which the journal has long been known. GENETICS is a peer reviewed, peer-edited journal, with an international reach and increasing visibility and impact. All editorial decisions are made through collaboration of at least two editors who are practicing scientists. GENETICS is constantly innovating: expanded types of content include Reviews, Commentary (current issues of interest to geneticists), Perspectives (historical), Primers (to introduce primary literature into the classroom), Toolbox Reviews, plus YeastBook, FlyBook, and WormBook (coming spring 2016). For particularly time-sensitive results, we publish Communications. As part of our mission to serve our communities, we''ve published thematic collections, including Genomic Selection, Multiparental Populations, Mouse Collaborative Cross, and the Genetics of Sex.
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