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Introduction

Alfalfa (Medicago sativa L.) is a versatile and valuable crop that has been cultivated for over 2,000 years. As a perennial flowering plant in the legume family, Fabaceae, it is also known as lucerne and is widely grown as a forage crop for livestock. Originally native to Europe and Asia, it is now grown in many parts of the world, including the United States, Canada, Australia, and South Africa. It is a highly nutritious plant that is rich in protein, minerals, and vitamins. This feature have allowed it to be cultivated in many parts of the world, making it a valuable crop for farmers and consumers alike. The accumulation of multidimensional and multi-omics data for alfalfa has been made possible by recent advancements in high-throughput techniques. The integration of this information holds great potential to expedite genetic research and facilitate advancements in alfalfa agronomic traits. To this goal, we have developed a comprehensive database named MODMS, which incorporates multiple reference genomes, annotations, comparative genomics, transcriptomes, high-quality genetic variants, proteomics, and metabolomics.

Portals

Genomics

This module is a tool designed for analyzing and interpreting genomic data. It collects four alfalfa varieties genome assemblies and one genome assembly of M. truncatula.

Transcriptomics

This module comprises 18 transcriptome datasets obtained from distinct tissues or subjected to different treatment conditions.

Variation

This module is designed to collect annotations of polymorphic variations, including SNPs, InDels, and SVs from populations of 200 individuals.

Proteomics

This module collected thirteen proteomics datasets from other research groups and provides the functionality to visualize the expression patterns of paralogs for selected genes at the protein level under different treatments.

Metabolomics

This module collected fourteen metabolomics datasets and provided a user-friendly portal that supports researchers in identifying differential metabolites among various conditions by inputting the treatments and the name of alfalfa varieties.

gRNA

This module is an innovative tool that serves as a comprehensive platform for designing guide RNA (gRNA) sequences targeted to specific genes for gene editing.

Tools

Blast

Design Primer

Enrichment

Muscle

Lastz

Genewise

How to cite us

Fang Longfa, Liu Tao, Li Mingyu, Dong Xueming, Han Yuling, Xu Congzhuo, Li Siqi, Zhang Jia, He Xiaojuan, Zhou Qiang, Luo Dong, Liu Zhipeng*. MODMS: a multi-omics database for facilitating biological studies on alfalfa (Medicago sativa L.). Horticulture Research, 2024, 11: 245

Liu zhipeng (http://caoye.lzu.edu.cn/lzupage/2009/12/07/N20091207181858.html) : lzp@lzu.edu.cn

fanglongfa (http://caoye.lzu.edu.cn/lzupage/2020/09/14/N20200914173154.html) : fanglf@lzu.edu.cn

Important data source

1. Luo Dong, Zhou Qiang, Wu, Yuguo, Chai Xutian, Liu Wenxian, Wang Yanrong, Yang, Qingchuan, Wang Zengyu, and Liu Zipeng. 2019. Full-length transcript sequencing and comparative transcriptomic analysis to evaluate the contribution of osmotic and ionic stress components towards salinity tolerance in the roots of cultivated alfalfa (Medicago sativa L.). BMC Plant Biology, 2019, 19:1-20

2. Shen Chen, Du Huilong, Chen Zhuo, Lu Hongwei, Zhu Fugui, Chen Hong, Meng Xiangzhao, Liu Qianwen, Liu Peng, Zheng Lihua, Li Xiuxiu, Dong Jiangli, Liang Chengzhi, Wang Tao. The chromosome-level genome sequence of the autotetraploid alfalfa and resequencing of core germplasms provide genomic resources for alfalfa research. Molecular Plant. 2020, 13(9):1250-61

3. Chen Haitao, Zeng Yan, Yang Yongzhi, Huang Lingli, Tang Bolin, Zhang He, Hao Fei, Liu Wei, Li Youhan, Liu Yanbin, Zhang Xiaohua, Zhang Ru, Zhang Yesheng, Li Yongxin, Wang Kun, He Hua, Wang Zhongkai, Fan Guangyi, Yang Hui, Bao Aike, Shang Zhanhuan, Chen Jianghua, Wang Wen, Qiu Qiang. Allele-aware chromosome-level genome assembly and efficient transgene-free genome editing for the autotetraploid cultivated alfalfa. Nature Communications. 2020, 11:2494.