Whole genome sequencing data of greater burdock (Arctium lappa) naturalized in the United States of America

IF 1 Q3 MULTIDISCIPLINARY SCIENCES

Data in Brief Pub Date : 2025-03-21 DOI:10.1016/j.dib.2025.111508

Danae Kala Rodriguez Bardaji, Girish Kumar, Samantha Tran, Gabriella Fedus, Michael A. Savka, Dawn Carter, André O. Hudson

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引用次数: 0

Abstract

This dataset comprises whole genome sequencing burdock (Arctium lappa) naturalized in a residential yard in Rochester, New York, USA. Total DNA was extracted from a leaf sample and processed using the Illumina Nextera XT DNA library preparation kit. Sequencing on the NextSeq 2000 platform produced 127.4 GB of raw data, yielding 125.8 GB of high-quality reads after filtering, with an average genome coverage of 75x. The genome was assembled de novo into 792,817 contigs, achieving a total genome length of 1,075,454,921 base pairs with a GC content of 37.03 %. Scaffolding against a Chinese A. lappa reference genome improved genome completeness from 49.1 % to 94.93 %, successfully recovering the majority of protein-coding genes.

Variant analysis identified approximately 20.8 million Single Nucleotide Polymorphisms (SNPs) and 1.3 million indels, including functionally significant mutations. The Internal Transcribed Spacer 2 (ITS2) ribosomal region was isolated and compared with global references, revealing significant genetic differentiation between the U.S.A and Chinese populations. This comprehensive genomic dataset has been deposited in publicly accessible repositories, including National Center for Biotechnology Information (NC and Zenodo. The sequencing of this sample provides a valuable resource for comparative genomics, population genetics, and investigations into bioactive compounds with antimicrobial properties, supporting agricultural and pharmaceutical applications. Direct access to the dataset is available at 10.5281/zenodo.14607136

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在美国归化的大牛蒡（Arctium lappa）的全基因组测序数据

该数据集包括全基因组测序牛蒡（牛蒡）归化在一个住宅院子在罗切斯特，纽约，美国。从叶片样品中提取总DNA，并使用Illumina Nextera XT DNA文库制备试剂盒进行处理。NextSeq 2000平台测序产生127.4 GB原始数据，过滤后产生125.8 GB高质量reads，平均基因组覆盖率为75倍。基因组从头组装为792,817个contigs，基因组总长度为1,075,454,921个碱基对，GC含量为37.03%。对中国黄颡鱼参考基因组构建后，基因组完整性从49.1%提高到94.93%，成功恢复了大部分蛋白质编码基因。变异分析确定了大约2080万个单核苷酸多态性（snp）和130万个索引，包括功能显著的突变。我们分离了ITS2核糖体区域，并与全球参考文献进行了比较，揭示了美国和中国人群之间显著的遗传差异。这个全面的基因组数据集已经存放在公众可访问的存储库中，包括国家生物技术信息中心（NC）和Zenodo。该样品的测序为比较基因组学、群体遗传学和具有抗菌特性的生物活性化合物的研究提供了宝贵的资源，支持农业和制药应用。可以在10.5281/zenodo.14607136直接访问该数据集

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

Data in Brief MULTIDISCIPLINARY SCIENCES-

CiteScore

3.10

自引率

0.00%

发文量

996

审稿时长

70 days

期刊介绍： Data in Brief provides a way for researchers to easily share and reuse each other''s datasets by publishing data articles that: -Thoroughly describe your data, facilitating reproducibility. -Make your data, which is often buried in supplementary material, easier to find. -Increase traffic towards associated research articles and data, leading to more citations. -Open up doors for new collaborations. Because you never know what data will be useful to someone else, Data in Brief welcomes submissions that describe data from all research areas.