TEGR:一个综合性的杜鹃花科基因组资源数据库

doi:10.1016/j.jia.2023.11.026

摘要/Abstract

摘要：

杜鹃花科是一个分布在世界各地的开花植物类群，包括126属和4000多个物种。在本研究中，我们搭建了一个杜鹃花科基因组资源数据库(TEGR, http://www.tegr.com.cn)，这是一个基于16个杜鹃花科物种已发表基因组的综合性、用户友好的基于web的功能基因组数据库。TEGR数据库包含大量重要的功能基因，如生长素基因763个，开花基因2,407个，抗病基因20,432个，花青素相关基因617个，N6-甲基腺苷修饰基因470个。TEGR数据库中包含鉴定的599,174条特异的CRISPR引导序列。在TEGR数据库中对16个杜鹃花科物种进行了基因复制事件、共线性分析和同源性分析。TEGR数据库包含通过GO、Nr、Pfam、TrEMBL和Swiss-Prot数据库注释的614,821个功能基因。TEGR数据库提供Primer Design、Hmmsearch、Synteny、BLAST和JBrowse工具，帮助用户进行全面的比较基因组分析。所有高质量的参考基因组序列、基因组特征、基因注释和生物信息分析结果都可以从TEGR数据库下载。在未来，随着新基因组数据的出现，我们将继续完善更新TEGR数据库，为比较基因组学研究提供丰富的数据资源。

Abstract:

Ericaceae is a diverse family of flowering plants distributed nearly worldwide, and it includes 126 genera and more than 4,000 species. In the present study, we developed The Ericaceae Genome Resource (TEGR, ) as a comprehensive, user-friendly, web-based functional genomic database that is based on 16 published genomes from 16 Ericaceae species. The TEGR database contains information on many important functional genes, including 763 auxin genes, 2,407 flowering genes, 20,432 resistance genes, 617 anthocyanin-related genes, and 470 N⁶-methyladenosine (m⁶A) modification genes. We identified a total of 599,174 specific guide sequences for CRISPR in the TEGR database. The gene duplication events, synteny analysis, and orthologous analysis of the 16 Ericaceae species were performed using the TEGR database. The TEGR database contains 614,821 functional genes annotated through the GO, Nr, Pfam, TrEMBL, and Swiss-Prot databases. The TEGR database provides the Primer Design, Hmmsearch, Synteny, BLAST, and JBrowse tools for helping users perform comprehensive comparative genome analyses. All the high-quality reference genome sequences, genomic features, gene annotations, and bioinformatics results can be downloaded from the TEGR database. In the future, we will continue to improve the TEGR database with the latest data sets when they become available and to provide a useful resource that facilitates comparative genomic studies.

Key words: TEGR , Ericaceae , gene functional annotation , m⁶A , CRISPR , bioinformatic tools

Xiaojing Wang, Yunfeng Wei, Zhuo Liu, Tong Yu, Yanhong Fu, Xiaoming Song. TEGR:一个综合性的杜鹃花科基因组资源数据库[J]. Journal of Integrative Agriculture, 2025, 24(3): 1140-1151.

Xiaojing Wang, Yunfeng Wei, Zhuo Liu, Tong Yu, Yanhong Fu, Xiaoming Song. TEGR: A comprehensive Ericaceae genome resource database[J]. Journal of Integrative Agriculture, 2025, 24(3): 1140-1151.

参考文献

Ancillotti C, Ciofi L, Pucci D, Sagona E, Giordani E, Biricolti S, Gori M, Petrucci W A, Giardi F, Bartoletti R, Chiuminatto U, Orlandini S, Mosti S, Bubba M D. 2016. Polyphenolic profiles and antioxidant and antiradical activity of Italian berries from Vaccinium myrtillus L. and Vaccinium uliginosum L. subsp. gaultherioides (Bigelow) SB Young. Food Chemistry, 204, 176–184.

Bouche F, Lobet G, Tocquin P, Perilleux C. 2016. FLOR-ID: An interactive database of flowering-time gene networks in Arabidopsis thaliana. Nucleic Acids Research, 44, D1167–D1171.

Carbon S, Douglass E, Good B M, Unni D R, Elser J. 2020. The Gene Ontology resource: Enriching a GOld mine. Nucleic Acids Research, 49, D325–D334.

Chen C, Chen H, Zhang Y, Thomas H R, Xia R. 2020. TBtools: An integrative toolkit developed for interactive analyses of big biological data. Molecular Plant, 13, 1194–1202.

Chen H, Wang T, He X, Cai X, Lin R, Liang J, Wu J, King G, Wang X. 2022. BRAD V3.0: An upgraded Brassicaceae database. Nucleic Acids Research, 50, D1432–D1441.

Cheng J, Zhao Z, Li B, Qin C, Wu Z, Trejo-Saavedra D, Luo X, Cui J, Rivera-Bustamante R F, Li S, Hu K. 2016. A comprehensive characterization of simple sequence repeats in pepper genomes provides valuable resources for marker development in Capsicum. Science Report, 6, 18919.

de la Concepción M C, Concepción M, Sargent D J, Šurbanovski N, Colgan R J, Moretto M. 2021. De novo sequencing and analysis of the transcriptome of two highbush blueberry (Vaccinium corymbosum L.) cultivars ‘Bluecrop’ and ‘Legacy’ at harvest and following post-harvest storage. PLoS ONE, 16, e0255139.

Debnath S C, Goyali J C. 2020. In vitro propagation and variation of antioxidant properties in micropropagated Vaccinium berry plants - A review. Molecules, 25, 788.

Diaz-Garcia L, Rodriguez-Bonilla L, Rohde J, Smith T, Zalapa J. 2019. Pacbio sequencing reveals identical organelle genomes between American cranberry (Vaccinium macrocarpon Ait.) and a wild relative. Genes, 10, 291.

El-Tantawy A A, Xie W, Li S, Wang J, Yang X. 2020. Changes of endogenous hormones during ovary development in Rhododendron delavayi×Rhododendron sinofalconeri and Rhododendron delavayi×Rhododendron cyanocarpum. European Journal of Horticultural Sciences, 85, 248–257.

Emms D M, Kelly S. 2019. OrthoFinder: Phylogenetic orthology inference for comparative genomics. Genome Biology, 20, 238.

Engelbrecht F A, Marean C W, Cowling R M, Engelbrecht C J, Neumann F H, Scott L, Ramapulana N, O’Neal D, Fisher E, Shook E, Franklin J, Thatcher M, McGregor J L, Van der M J, Dedekind Z, Difford M. 2019. Downscaling Last Glacial Maximum climate over southern Africa. Quaternary Science Reviews, 226, 105879.

Feng S, Liu Z, Chen H, Li N, Yu T, Zhou R, Nie F, Guo D, Ma X, Song X. 2024. PHGD: An integrative and user-friendly database for plant hormone-related genes. iMeta, 3, e164.

Garrison R R, Tobin P C. 2022. Susceptibility of Rhododendron to Azalea Lace Bug, Stephanitis pyrioides (Scott). Journal of Environmental Horticulture, 40, 94–102.

Giannoulatou E, Park S H, Humphreys D T, Ho J W K. 2014. Verification and validation of bioinformatics software without a gold standard: A case study of BWA and Bowtie. BMC Bioinformatics, 15, 1–8.

Gill S, Panthari P, Kharkwal H. 2015. Phytochemical investigation of high altitude medicinal plants Cinnamomum tamala (Buch-Ham) Nees and Eberm and Rhododendron arboreum Smith. American Journal of Clinical Dermatology, 3, 512–528.

Humann J L, Cheng C H, Lee T, Buble K, Jung S, Yu J, Zheng P, Hough H, Crabb J, Frank M. 2021. Using the Genome Database for Vaccinium for genetics, genomics, and breeding research. XII International Vaccinium Symposium, 1357, 115–122.

Jiang X, Liu B, Nie Z, Duan L, Xiong Q, Jin Z, Yang C, Chen Y. 2021. The role of m6A modification in the biological functions and diseases. Signal Transduction and Targeted Therapy, 6, 74.

Jones M S, Vanhanen H, Peltola R, Drummond F. 2014. A global review of arthropod-mediated ecosystem-services in Vaccinium berry agroecosystems. Terrestrial Arthropod Reviews, 7, 41–78.

Krebs S L. 2018. Rhododendron. Ornamental Crops, 11, 673–718.

Kumar V, Suri S, Prasad R, Gat Y, Sangma C, Jakhu H, Sharma M. 2019. Bioactive compounds, health benefits and utilization of Rhododendron: A comprehensive review. Agriculture Food Security, 8, 1–7.

Li H, Fan Y, Yu J, Chai L, Zhang J, Jiang J, Cui C, Zheng B, Jiang L, Kun L. 2018. Genome-wide identification of flowering-time genes in Brassica species and reveals a correlation between selective pressure and expression patterns of vernalization-pathway genes in Brassica napus. International Journal of Molecular Sciences, 19, 3632.

Li H, Guo Q, Li Q, Yang L. 2020. Long-reads reveal that Rhododendron delavayi plastid genome contains extensive repeat sequences, and recombination exists among plastid genomes of photosynthetic Ericaceae. PeerJ, 8, e9048.

Li P, Quan X, Jia G, Xiao J, Cloutier S, Frank M. 2016. RGAugury: A pipeline for genomewide prediction of resistance gene analogs (RGAs) in plants. BMC Genomics, 17, 852.

Liu N, Zhang L, Zhou Y, Tu M, Wu Z, Gui D, Ma Y, Wang J, Zhang C. 2012. The Rhododendron Plant Genome Database (RPGD): A comprehensive online omics database for Rhododendron. BMC Genomics, 22, 1–10.

Liu Q, Liaquat F, He Y, Munis M F H, Zhang C. 2021. Functional annotation of a full-length transcriptome and identification of genes associated with flower development in Rhododendron simsii (Ericaceae). Plants, 10, 649.

Liu Z, Li N, Yu T, Wang Z, Wang J, Ren J, He J, Huang Y, Shi K, Yang Q, Wu T, Lin H, Song X. 2022. The Brassicaceae genome resource (TBGR): A comprehensive genome platform for Brassicaceae plants. Plant Physiology, 190, 226–237.

Liu Z, Shen S, Li C, Zhang C, Chen X, Fu Y, Yu T, Zhou R, Liu D, Yang Q, Song X. 2024. SoIR: a comprehensive Solanaceae information resource for comparative and functional genomic study. Nucleic Acids Research, 2024, gkae1040.

Martau G A, Bernadette-Emőke T, Odocheanu R, Soporan D A, Bochis M, Simon E, Vodnar D C. 2023. Vaccinium species (Ericaceae): Phytochemistry and biological properties of medicinal plants. Molecules, 28, 1533.

Meng F, Tang Q, Chu T, Li X, Lin Y, Song X, Chen W. 2022. TCMPG: An integrative database for traditional Chinese medicine plant genomes. Horticulture Research, 9, uhac060.

Mistry J, Chuguransky S, Williams L, Qureshi M, Salazar G A, Sonnhammer E L L, Tosatto S C, Paladin L, Raj S, Richardson L J, Finn R D, Bateman A. 2021. Pfam: The protein families database in 2021. Nucleic Acids Research, 49, D412–D419.

Pandey T, Kumar P, Pratap O, Jyoti B, Singh I, Kumar V, Gusain Y S, Chaudhary S. 2019. A marvelous hide and speculation in the life of Rhododendron species at a glance. International Journal of Conservation Science, 7, 3158–3168.

Rodriguez-Bonilla L, Williams K A, Bonilla F R, Matusinec D, Maule A, Coe K, Wiesman E, Diaz-Garcia L, Zalapa J. 2020. The genetic diversity of cranberry crop wild relatives, Vaccinium macrocarpon Aiton and V. oxycoccos L., in the US, with special emphasis on National Forests. Plants, 9, 1446.

Rose A E S, Senthilkumar S. 2016. Studies on the mycorrhizal association of Rhododendron arboreum Sm. ssp nilagiricum (Zenker) Tagg. Tropical Ecology, 57, 69–76.

Rose J P, Kleist T J, Löfstrand S D, Drew B T, Schoenenberger J, Sytsma K J. 2018. Phylogeny, historical biogeography, and diversification of angiosperm order Ericales suggest ancient Neotropical and East Asian connections. Molecular Phylogenetics and Evolution, 122, 59–79.

Sekhwal M K, Li P, Lam I, Wang X, Cloutier S, Frank M. 2015. Disease resistance gene analogs (RGAs) in plants. International Journal of Molecular Sciences, 16, 19248–19290.

Shinde H, Dudhate A, Kadam U S, Chan J. 2023. RNA methylation in plants: An overview. Frontiers in Plant Science, 14, 1132959.

Song X, Yang Q, Bai Y, Gong K, Ma X. 2021. Comprehensive analysis of SSRs and database construction using all complete gene-coding sequences in major horticultural and representative plants. Horticulture Research, 8, 122.

Sosnovsky Y, Nachychko V, Prokopiv A, Honcharenko V. 2017. Leaf architecture in Rhododendron subsection Rhododendron (Ericaceae) from the Alps and Carpathian Mountains: Taxonomic and evolutionary implications. Flora, 230, 26–38.

Soza V L, Lindsley D, Waalkes A, Ramage E, Patwardhan R, Burton J, Adey A, Kumar A, Qiu R, Shendure J, Hall B. 2019. The Rhododendron genome and chromosomal organization provide insight into shared whole-genome duplications across the heath family (Ericaceae). Genome Biology and Evolution, 11, 3353–3371.

Tian X, Chang Y, Neilsen J, Wang S, Ma Y. 2019. A new species of Rhododendron (Ericaceae) from northeastern Yunnan. China Phytotaxa, 395, 66–70.

Tundis R, Tenuta M C, Loizzo M R, Bonesi M, Finetti F, Trabalzini L, Deguin B. 2021. Vaccinium species (Ericaceae): From chemical composition to bio-functional activities. Applied Sciences, 11, 5655.

Wang Y, Tang H, Debarry J D, Tan X, Li J, Wang X, Tae-ho L, Jin H, Barry M, Guo H. 2012. MCScanX: A toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Research, 40, e49.

Wu T, Feng S, Yang Q, Preetidt J, Gong K, Cui C, Song J, Ping X, Pei Q, Yu T, Song X. 2021. Integration of metabolome and transcriptome reveals the metabolites or genes related to nutritional and medicinal value in Coriandrum sativum. Journal of Integrative Agriculture, 20, 1807–1818.

Wu T, Liu Z, Yu T, Zhou R, Yang Q, Cao R, Nie F, Ma X, Bai Y, Song X. 2024. Flowering genes identification, network analysis, and database construction for 837 plants. Horticulture Research, 11, uhae013.

Xiao Z, Su J, Sun X, Li C, He L, Cheng S, Liu X. 2018. De novo transcriptome analysis of Rhododendron molle G. Don flowers by Illumina sequencing. Genes Genomic, 40, 591–601.

Yu T, Bai Y, Liu Z, Wang Z, Yang Q, Wu T, Feng S, Zhang Y, Shen S, Li Q, Gu L, Song X. 2022a. Large-scale analyses of heat shock transcription factors and database construction based on whole-genome genes in horticultural and representative plants. Horticulture Research, 9, uhac035.

Yu T, Ma X, Liu Z, Feng X, Wang Z, Ren J, Cao R, Zhang Y, Nie F, Song X. 2022b. TVIR: A comprehensive vegetable information resource database for comparative and functional genomic studies. Horticulture Research, 9, uhac213.

Yang Y, Hsu P J, Chen Y S, Yang Y G. 2018. Dynamic transcriptomic m6A decoration: Writers, erasers, readers and functions in RNA metabolism. Cell Research, 28, 616–624.

Zhang Y, Zhang Y, Li B, Tan X, Zhu C, Wu T, Feng S, Yang Q, Shen S, Yu T, Liu Z, Song X. 2022. Polyploidy events shaped the expansion of transcription factors in Cucurbitaceae and exploitation of genes for tendril development. Horticultural Plant Journal, 8, 562–574.