Tartary buckwheat database (TBD): an integrative platform for gene analysis of and biological information on Tartary buckwheat

Tartary buckwheat database (TBD): an integrative platform for gene analysis of and biological information on Tartary buckwheat 苦荞数据库：一个苦荞基因分析和生物信息的综合平台 1 2 first-author 1 3 1 1 corresp Hui CHEN, chenhui@sicau.edu.cn Hui CHEN, chenhui@sicau.edu.cn chenhui@sicau.edu.cn https://orcid.org/0000-0001-9185-1764 College of Life Science, Sichuan Agricultural University, Ya'an625014, China College of Life Science, Sichuan Agricultural University, Ya'an625014, China Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai200240, China Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai200240, China State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Key Laboratory of Major Crop Diseases and Rice Research Institute, Sichuan Agricultural University, Chengdu611130, China State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Key Laboratory of Major Crop Diseases and Rice Research Institute, Sichuan Agricultural University, Chengdu611130, China 本研究首次构建了苦荞数据库，该数据库提供了苦荞基因在不同组织和不同阶段果实中表达量，苦荞基因的荧光定量引物，以及苦荞转录因子家族生物信息学信息。我们在苦荞不同组织和不同发育阶段果实转录组数据中收集苦荞基因的表达图谱，共检测到31 839个基因，其中在根中表达的有26 426个基因，在茎中表达的有24 716基因，在叶中表达的有24 227个基因，在花中表达的有27 533个基因。并利用Primer 3软件为每个苦荞基因都提供了5对荧光定量引物。此外，我们还从苦荞基因组中鉴定到了14个转录因子家族中974个转录因子的基因结构、分子量、等电点、染色体位置和基因定位信息。 苦荞数据库 转录因子 表达谱 荧光定量PCR Rice, wheat, corn, and potatoes are four crops that provide a daily source of nutrition for humans, but there are many problems that have been found with these crops. First, they lack amino acids and minerals which are necessary for balanced nutrition, and they also are grown very widely and as monocultures, which increases the risk of the human food system being destroyed by climate change. Thus, by introducing coarse cereals with good characteristics, we can enrich human food resources, realize agricultural diversification, improve dietary structure, and mitigate risks. Tartary buckwheat ( Fagopyrum tataricum ) is a widely cultivated edible and medicinal crop with unique nutritional and excellent economic value. It contains flavonoids, such as rutin and quercetin, which are not found in cereal crops. Rutin is a major flavonoid that can enhance blood flow and aid in the use of vitamin C and the production of collagen. In addition, such antioxidants have been shown to effectively reduce cholesterol levels, blood clots, and hypertension, particularly for the prevention of inflammatory liver injury ( Middleton et al., 2000 Middleton et al., 2000 ; Lee et al., 2013 Lee et al., 2013 ; Suzuki et al., 2014 Suzuki et al., 2014 ; Huang et al., 2016 Huang et al., 2016 ; Nishimura et al., 2016 Nishimura et al., 2016 ). Meanwhile, Tartary buckwheat can tolerate poor climate and acidic soils containing high amounts of aluminum, which is toxic to other crops ( Wang et al., 2015 Wang et al., 2015 ). The self-pollination of Tartary buckwheat has resulted in a decrease in genomic heterozygosity, which is valuable for breeding and a stable production trait ( Wang and Campbell, 2007 Wang and Campbell, 2007 ). Therefore, Tartary buckwheat is an important minor crop, which is expected to become the target of many breeding efforts in the future. Due to the publication of the genome data for Tartary buckwheat, the pace of identification of key genes related to its development has accelerated ( Zhang et al., 2017 Zhang et al., 2017 ). Multiple transcription factors (TFs) involved in growth and development have been identified. For example, the auxin response factor (ARF) gene family of the Tartary buckwheat genome has been comprehensively and systematically analyzed ( Liu et al., 2018c Liu et al., 2018c ), and FtARF2 , which potentially regulates fruit size, has been further studied ( Liu et al., 2018b Liu et al., 2018b ). By systematic identification of MADS-box family members, the potential genes that regulate fruit cracking were also excavated ( Liu et al., 2019h Liu et al., 2019h ). Furthermore, various TF families, including APETALA2/ethylene-responsive factor (AP2/ERF) ( Liu et al., 2019d Liu et al., 2019d ), basic helix-loop-helix (bHLH) ( Sun et al., 2020a Sun et al., 2020a ), basic leucine zipper (bZIP) ( Liu et al., 2019b Liu et al., 2019b ), GRAS ( Liu et al., 2019g Liu et al., 2019g ), heat shock transcription factor (HSF) ( Liu et al., 2019c Liu et al., 2019c ), NAM, ATAF1/2, and CUC2 (NAC) ( Liu et al., 2019a Liu et al., 2019a ), squamosa promoter-binding protein-like (SPL) ( Liu et al., 2019f Liu et al., 2019f ), trihelix ( Ma et al., 2019 Ma et al., 2019 ), WRKY ( Sun et al., 2020b Sun et al., 2020b ), and zinc finger-homeodomain (ZF-HD) ( Liu et al., 2019e Liu et al., 2019e ), have been identified from the genome to excavate the genes that might improve Tartary buckwheat quality. The genes involved in regulating the synthesis of flavonoids in Tartary buckwheat were also found, including FtMYB13 , FtMYB14 , FtMYB15 , and FtMYB16 ( Zhou et al., 2017 Zhou et al., 2017 ). The construction of plant databases can effectively preserve and utilize large-scale datasets. One example is the maize database, which provides the expression of development-related genes and thus lays the foundation for improving maize quality ( Guillaumie et al., 2007 Guillaumie et al., 2007 ). Despite the many open species databases, comprehensive information databases about some crops with important agricultural significance and development potential are very limited ( Gayali et al., 2016 Gayali et al., 2016 ). Until now, there has been no available database to save, analyze, or utilize the important dataset of Tartary buckwheat. To promote the usage and application of identified TF families in Tartary buckwheat, we developed Tartary buckwheat database (TBD) ( http://tbd.sicau.edu.cn http://tbd.sicau.edu.cn ) as a highly integrated information platform with online query tools. TBD will provide comprehensive information and a query platform for researchers interested in understanding and improving Tartary buckwheat crop quality. To facilitate queries for gene information, we provide basic retrieval forms for Tartary buckwheat gene expression, TFs, and primers, and more. Users simply need to input a gene ID to retrieve specific gene information. Each gene has a detailed information page which is divided into several subsections for gene expression value (GEV), TF, and quantitative real-time polymerase chain reaction (qRT-PCR) primer (qPrimer). The TBD website includes six functional sections, including "Home," "GEV," "TF," "qPrimer," "Help," and "About Us." On the "Home" page, users can view a presentation, receive news updates, and see the current information in the TBD database ( Fig. 1 Fig. 1 a). In the "GEV" section, we provide a flexible interface for efficient retrieval of gene expression for all Tartary buckwheat genes. On this page, after one enters the Tartary buckwheat gene accession number and clicks "Run," all visualizations showing the absolute and relative expression of each gene in the roots, stems, flowers, leaves, and fruit (green fruit stage, 13 days after pollination (DAP); discoloration stage, 19 DAP; initial maturity stage, 25 DAP) are provided. The transcriptome data accession number of fruit at different developmental stages is GSE111937 ( Liu et al., 2018a Liu et al., 2018a ), and the transcriptional data accession number of different tissues of Tartary buckwheat (roots, stems, leaves, and flowers) is SRP103493 ( Zhang et al., 2017 Zhang et al., 2017 ). A total of 31 839 genes were detected, of which 26 426 genes were detected in roots, 24 716 genes were detected in stems, 24 227 genes were detected in leaves, 27 533 genes were detected in flowers, 27 569 genes were detected in early-development fruit (13 DAP), 26 673 genes were detected in mid-development fruit (19 DAP), and 25 767 genes were detected in late-development fruit (25 DAP) ( Fig. 1 Fig. 1 b). Moreover, there were 392 genes expressed only in roots, 28 genes expressed only in stems, 49 genes expressed only in leaves, 504 genes expressed only in flowers, and 288 genes (13 DAP, 153 genes; 19 DAP, 57 genes; 25 DAP, 49 genes) expressed only in fruit ( Fig. 1 Fig. 1 a). For each detected gene, we provide expression images for researchers to analyze, and attach specific values to the images. For example, a search for FtPinG0000001800.01 will return a detailed expression profile ( Fig. 1 Fig. 1 c). These specifically expressed genes provide candidates for researchers to study specific biological processes. The abundant data provide a rich selection for researchers to discover genes of interest. In the "TF" section, we provide biological information on 974 TFs from 14 major TF families, including AP2/ERF, ARF, bHLH, bZIP, GRAS, growth-regulating factor (GRF), HSF, MADS, v-myb avian myeloblastosis viral oncogene homolog (MYB), NAC, SPL, TEOSINTE-BRANCHED ‍1/cycloidea/PCF ‍(TCP), WRKY, and ZF-HD. To assist in the screening of important regulators, we also integrate the gene structure, grouping, and localization of these important TFs, which is advantageous for researchers when mining key genes. In addition, we provide a query function for identifying whether genes of interest to researchers belong to one of the 14 identified TF families ( Fig. 1 Fig. 1 d). By clicking on any TF family, researchers can obtain the intron/exon structural characteristics of all genes in that family. For example, clicking on GRF provides structural information for 12 genes ( Fig. 1 Fig. 1 e). Detailed information on protein length, molecular weight (MW), isoelectric point (pI), chromosome location, and localization of the corresponding gene can also be viewed ( Fig. 1 Fig. 1 e). In "qPrimer," TBD offers a user-friendly interface for conveniently downloading the best or all primer sequences for the target gene. We provide 1–5 pairs of the best primers for each of 31 839 Tartary buckwheat genes ( Fig. 1 Fig. 1 f). For example, when searching for FtPinG0000001800.01 , researchers will be given five pairs of different primers, and can select primer pairs that meet the experimental requirements with regard to parameters such as sequence, melting temperature, and GC content ( Fig. 1 Fig. 1 f). The "Help" page starts with an overview of TBD. It also details the features of each page of the website to help new users understand the design and layout of the site and become proficient with the database. "About Us" provides an avenue for users with new discoveries to contact us to submit their data requests. Our database will be updated regularly based on user feedback. In conclusion, we developed TBD as the central portal for genetic study of this promising crop. TBD stores expression profiles of all Tartary buckwheat genes, qPrimers of all genes, and bioinformatics information of important TF family genes. Since the database is manually integrated, all raw data collected/submitted are processed through our own custom pipeline. The processed data are also correlated to the retrieval analysis module that performs the main functions of TBD, including various query and visualization tasks ( Fig. 2 Fig. 2 ). We believe that this database will not only promote research on improving Tartary buckwheat breeding, but also bring increased attention to the genetic improvement of other important crops. TBD is a platform based on the currently sequenced Tartary buckwheat genome and will be updated in the future. As research progresses, we will continuously update information on the other TF families, while also providing evolutionary and expansion information on corresponding families in multiple species. Meanwhile, we will provide bioinformatics tools such as a Genome Browser and BLAST sequence search in the next version of TBD. Future research is not limited to improving Tartary buckwheat breeding, but will also provide valuable information for other important species. References Gayali S , Acharya S , Lande NV , et al. , 2016 . CicerTransDB 1.0: a resource for expression and functional study of chickpea transcription factors . 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The Tartary buckwheat genome provides insights into rutin biosynthesis and abiotic stress tolerance . Mol Plant , 10 ( 9 ): 1224 - 1237 . https://doi.org/10.1016/j.molp.2017.08.013 https://doi.org/10.1016/j.molp.2017.08.013 The Tartary buckwheat genome provides insights into rutin biosynthesis and abiotic stress tolerance Zhou ML , Sun ZM , Ding MQ , et al. , 2017 . FtSAD2 and FtJAZ1 regulate activity of the FtMYB11 transcription repressor of the phenylpropanoid pathway in Fagopyrum tataricum . New Phytol , 216 ( 3 ): 814 - 828 . https://doi.org/10.1111/nph.14692 https://doi.org/10.1111/nph.14692 FtSAD2 and FtJAZ1 regulate activity of the FtMYB11 transcription repressor of the phenylpropanoid pathway in Fagopyrum tataricum Moyang LIU and Hui CHEN designed research. Moyang LIU, Wenjun SUN, and Zhaotang MA performed research. Zhaotang MA, Yuan HU, and Hui CHEN analyzed data. Wenjun SUN and Yuan HU wrote the paper. Hui CHEN, Wenjun SUN, and Moyang LIU revised the manuscript. All authors have read and approved the final manuscript, and therefore, have full access to all the data in the study and take responsibility for the integrity and security of the data. This work was supported by the National Key R&D Program (No. 2018YFD1000706) and the Sichuan Science and Technology Program (No. 2021YFH0086), China. 10.1631/jzus.B2100319 1673-1581（2021）11-0954-05 This work was supported by the National Key R&D Program (No. 2018YFD1000706) and the Sichuan Science and Technology Program (No. 2021YFH0086), China. 2021-04-07 2021-07-12 2021-11-15 2022-05-09 2021-10-19 Copyright © Zhejiang University and Springer-Verlag GmbH Germany, part of Springer Nature 2021 2021 浙江大学出版社 Moyang LIU, Wenjun SUN, Zhaotang MA, Yuan HU, and Hui CHEN declare that they have no conflict of interest. This article does not contain any studies with human or animal subjects performed by any of the authors. Compliance with ethics guidelines 浙江大学学报（英文版）（B辑：生物医学和生物技术） 11 22