SesamumGDB: a comprehensive platform for Sesamum genetics and genomics analysis.

IF 3.4 4区生物学 Q1 MATHEMATICAL & COMPUTATIONAL BIOLOGY

Database: The Journal of Biological Databases and Curation Pub Date : 2024-10-19 DOI:10.1093/database/baae105

Cao Hengchun, Guo Hui, Yang Weifei, Li Guiting, Ju Ming, Duan Yinghui, Tian Qiuzhen, Ma Qin, Feng Xiaoxu, Zhang Zhanyou, Zhang Haiyang, Miao Hongmei

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引用次数: 0

Abstract

Sesame (Sesamum indicum L., 2n = 26) is a crucial oilseed crop cultivated worldwide. The ancient evolutionary position of the Sesamum genus highlights its value for genomics and molecular genetics research among the angiosperms of other genera. However, Sesamum is considered a small orphan genus with only a few genomic databases for cultivated sesame to date. The urgent need to construct comprehensive, curated genome databases that include genus-specific gene resources for both cultivated and wild Sesamum species is being recognized. In response, we developed Sesamum Genomics Database (SesamumGDB), a user-friendly genomic database that integrates extensive genomic resources from two cultivated sesame varieties (S. indicum) and seven wild Sesamum species, covering all three chromosome groups (2n = 26, 32, and 64). This database showcases a total of 352 471 genes, including 6026 related to lipid metabolism and 17 625 transcription factors within Sesamum. Equipped with an array of bioinformatics tools such as BLAST (basic local alignment search tool) and JBrowse (the Javascript browser), SesamumGDB facilitates data downloading, screening, visualization, and analysis. As the first centralized Sesamum genome database, SesamumGDB offers extensive insights into the genomics and genetics of sesame, potentially enhancing the molecular breeding of sesame and other oilseed crops in the future. Database URL: http://www.sgbdb.com/sgdb/.

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SesamumGDB：芝麻遗传学和基因组学分析综合平台。

芝麻（Sesamum indicum L.，2n = 26）是世界上重要的油料作物。在其他属的被子植物中，芝麻属的古老进化地位凸显了其在基因组学和分子遗传学研究方面的价值。然而，芝麻属被认为是一个小的孤儿属，迄今只有少数栽培芝麻的基因组数据库。人们认识到，迫切需要构建全面的、经过整理的基因组数据库，其中包括栽培芝麻和野生芝麻属的特异性基因资源。为此，我们开发了芝麻基因组数据库（SesamumGDB），这是一个用户友好型基因组数据库，整合了两个栽培芝麻品种（S. indicum）和七个野生芝麻物种的大量基因组资源，涵盖所有三个染色体组（2n = 26、32 和 64）。该数据库共展示了 352 471 个基因，包括 6026 个与脂质代谢有关的基因和 17 625 个芝麻转录因子。SesamumGDB 配备了一系列生物信息学工具，如 BLAST（基本局部比对搜索工具）和 JBrowse（Javascript 浏览器），为数据下载、筛选、可视化和分析提供了便利。作为第一个集中式芝麻基因组数据库，SesamumGDB 为芝麻的基因组学和遗传学提供了广泛的见解，有可能在未来提高芝麻和其他油料作物的分子育种水平。数据库网址：http://www.sgbdb.com/sgdb/.

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Database: The Journal of Biological Databases and Curation MATHEMATICAL & COMPUTATIONAL BIOLOGY-

CiteScore

9.00

自引率

3.40%

发文量

100

审稿时长

>12 weeks

期刊介绍： Huge volumes of primary data are archived in numerous open-access databases, and with new generation technologies becoming more common in laboratories, large datasets will become even more prevalent. The archiving, curation, analysis and interpretation of all of these data are a challenge. Database development and biocuration are at the forefront of the endeavor to make sense of this mounting deluge of data. Database: The Journal of Biological Databases and Curation provides an open access platform for the presentation of novel ideas in database research and biocuration, and aims to help strengthen the bridge between database developers, curators, and users.