利用公共档案中的基因数据填补昆虫保护方面的知识空白。

IF 3.4 4区 生物学 Q1 MATHEMATICAL & COMPUTATIONAL BIOLOGY
Serena Baini, Alessio De Biase
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引用次数: 0

摘要

近年来,昆虫数量下降已成为一个日益令人担忧的问题,研究显示,一些类群的数量下降速度令人震惊。我们对昆虫遗传空间模式和进化历史的了解仍然存在巨大差距,这阻碍了我们有效保护和管理昆虫种群和物种的能力。基因数据可为我们提供有关昆虫物种和种群多样性及进化关系的宝贵见解。公共资料库,如 GenBank 和 BOLD,包含大量遗传数据档案和相关元数据,为研究人员提供了不可替代的资源,有助于我们了解物种多样性、种群结构和进化关系。然而,在使用这些数据时也存在一些问题,因为这些数据通常比较分散,而且由于采样协议不一致和信息不完整,可能会缺乏准确性。在本文中,我们介绍了一个由 GenBank 和 BOLD 收集的基因数据组成的地理参照数据库,该数据库针对的是被列入世界自然保护联盟(IUCN)意大利红色名录的昆虫(蜻蜓、蜜蜂、无患子甲虫和蝴蝶)。在查询这些资料库后,我们进行了质量控制和数据标准化步骤。我们创建了一个数据集,其中包含四个昆虫名录中 1466 个物种的约 33000 个线粒体序列以及相关的分类学、采集地点、地理坐标和 IUCN 红色名录状态等元数据。我们描述了意大利红色名录中不同保护状态物种的地理元数据在查询库中的现状,以量化数据缺口,从而为确定保护行动的优先次序扫清障碍。我们策划的数据集可用于数据再利用和分析,使研究人员能够开展比较研究。我们强调填补昆虫多样性和分布方面的知识空白的重要性,并强调该数据集在促进其他研究领域(如系统地理学、宏基因遗传学和保护战略)方面的潜力。我们的数据库可以通过 Zenodo 存储库以 SQL 格式下载。数据库网址:https://zenodo.org/records/8375181.
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Filling knowledge gaps in insect conservation by leveraging genetic data from public archives.

Insect decline has become a growing concern in recent years, with studies showing alarming declines in populations of several taxa. Our knowledge about genetic spatial patterns and evolutionary history of insects still exhibits significant gaps hindering our ability to effectively conserve and manage insect populations and species. Genetic data may provide valuable insights into the diversity and the evolutionary relationships of insects' species and populations. Public repositories, such as GenBank and BOLD, containing vast archives of genetic data with associated metadata, offer an irreplaceable resource for researchers contributing to our understanding of species diversity, population structure and evolutionary relationships. However, there are some issues in using these data, as they are often scattered and may lack accuracy due to inconsistent sampling protocols and incomplete information. In this paper we describe a curated georeferenced database of genetic data collected in GenBank and BOLD, for insects listed in the International Union for Conservation of Nature (IUCN) Italian Red Lists (dragonflies, bees, saproxylic beetles and butterflies). After querying these repositories, we performed quality control and data standardization steps. We created a dataset containing approximately 33 000 mitochondrial sequences and associated metadata about taxonomy, collection localities, geographic coordinates and IUCN Red List status for 1466 species across the four insect lists. We describe the current state of geographical metadata in queried repositories for species listed under different conservation status in the Italian Red Lists to quantify data gaps posing barriers to prioritization of conservation actions. Our curated dataset is available for data repurposing and analysis, enabling researchers to conduct comparative studies. We emphasize the importance of filling knowledge gaps in insect diversity and distribution and highlight the potential of this dataset for promoting other research fields like phylogeography, macrogenetics and conservation strategies. Our database can be downloaded through the Zenodo repository in SQL format. Database URL:  https://zenodo.org/records/8375181.

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来源期刊
Database: The Journal of Biological Databases and Curation
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.
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