AprGPD: the apricot genomic and phenotypic database

Plant Methods - 2021
Chen Chen1,2, Huimin Liu2,1, Ningning Gou1,2, Mengzhen Huang1,2, Wei Xu1,2, Xuchun Zhu1,2, Mingyu Yin1,2, Haikun Bai1,2, Lin Wang1,2, Tana Wuyun1,2
1Kernel-Apricot Engineering and Technology Research Center of State Forestry and Grassland Administration, Zhengzhou, China
2State Key Laboratory of Tree Genetics and Breeding, Non-timber Forest Research and Development Center, Chinese Academy of Forestry, Zhengzhou, China

Tóm tắt

Abstract Background Apricot is cultivated worldwide because of its high nutritive content and strong adaptability. Its flesh is delicious and has a unique and pleasant aroma. Apricot kernel is also consumed as nuts. The genome of apricot has been sequenced, and the transcriptome, resequencing, and phenotype data have been increasely generated. However, with the emergence of new information, the data are expected to integrate, and disseminate. Results To better manage the continuous addition of new data and increase convenience, we constructed the apricot genomic and phenotypic database (AprGPD, http://apricotgpd.com). At present, AprGPD contains three reference genomes, 1692 germplasms, 306 genome resequencing data, 90 RNA sequencing data. A set of user-friendly query, analysis, and visualization tools have been implemented in AprGPD. We have also performed a detailed analysis of 59 transcription factor families for the three genomes of apricot. Conclusion Six modules are displayed in AprGPD, including species, germplasm, genome, variation, product, tools. The data integrated by AprGPD will be helpful for the molecular breeding of apricot.

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Tài liệu tham khảo

Rehder A. Manual of cultivated trees and shrubs hardy in North America. Taxon. 1927;27(4):424.

Kafkaletou M, Kalantzis I, Karantzi A, Christopoulos MV, Tsantili E. Phytochemical characterization in traditional and modern apricot (Prunus armeniaca L.) cultivars—nutritional value and its relation to origin. Sci Horticult. 2019;253:195–202.

Zhebentyayeva TN, Ledbetter C, Burgos L, Llácer G. Fruit breeding. In: Handbook of plant breeding. New York: Springer; 2012. p. 415–58.

Zhang JT, Zhang J. Chinese fruit tree: apricot. Beijing: China Forestry Press; 2003. p. 18–26.

Zhang QP, Liu WS, Ning L, Zhang YP, Ming X. Allelic variation of simple sequence repeats markers linked to PPV resistance in Chinese apricot. Hortic Sci. 2017;44(1):6–13.

Liu S, Decroocq S, Harte E, Tricon D, Decroocq V. Genetic diversity and population structure analyses in the Alpine plum (Prunus brigantina Vill.) confirm its affiliation to the Armeniaca section. Tree Genet Genomes. 2020;17(1):1–12.

Wang YZ, Sun H, Li Y, Zhang J. Classification criteria of some quantitative characteristics of apricot germplasm resources. Chin Agric Sci Bull. 2008;24:147–51.

Zhou HT, Wang FH, Jiang ZL, Hao CH, Wang W, Liu TF. Studies on the classify standard for quantitative characters of sorghum DUS testing in Jilin province I. Measurement of single characters. Jilin Agric Sci. 2015;40(5):21–5.

Minoru K, Susumu G, Yoko S, Miho F, Mao T. KEGG for integration and interpretation of large-scale molecular datasets. Nucleic Acids Res. 2012;40(D1):D109–14.

Srikanth A, Schmid M. Regulation of flowering time:all roads lead to Rome. Cell Mol Life Sci. 2011;68(12):2013–37.

Langfelder P, Horvath S. WGCNA: an R package for weighted correlation network analysis. BMC Bioinform. 2008;9(1):559.

Eddy SR. A new generation of homology search tools based on probabilistic inference. Genome Inf. 2009;23:205–11.

Yi Z, Chen J, Sun H, Rosli HG, Pombo MA, Zhang P, et al. iTAK: a program for genome-wide prediction and classification of plant transcription factors, transcriptional regulators, and protein kinases. Mol Plant. 2016;9(012):1667–70.

Schultz J, Milpetz F, Bork P, Ponting CP. SMART: a simple modular architecture research tool: Identification of signaling domains. Proc Natl Acad Sci. 1998;95(11):5857–64.

Aron MB, Lu S, Anderson JB, Farideh C, Derbyshire MK, Carol DWS, et al. CDD: a conserved domain database for the functional annotation of proteins. Nucleic Acids Res. 2011;39(Database):D225–9.

Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, Mcwilliam H, et al. ClustalW and ClustalX version 2. Bioinformatics. 2007;23(21):2947–8.

Sudhir K, Glen S, Koichiro T. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol. 2016;33(7):1870–4.

Bailey TL, Mikael B, Buske FA, Martin F, Grant CE, Luca C, et al. MEME Suite: tools for motif discovery and searching. Nucleic Acids Res. 2009;37(Web Server issue):W202–8.

Wang Y, Tang H, Debarry JD, Tan X, Li J, Wang X, Tae-Ho L, Jin H, Barry M, Guo H. MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res. 2012;40(7):e49–e49.

Chen C, Chen H, Zhang Y, Thomas HR, Xia R. TBtools: an integrative toolkit developed for interactive analyses of big biological data. Mol Plant. 2020;13(8):1194–202.

Letunic I, Bork P. Interactive Tree Of Life (iTOL) v4: recent updates and new developments. Nucleic Acids Res. 2019;47(W1):W256–9.

Jin J, Zhang H, Kong L, Gao G, Luo J. PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors. Nucleic Acids Res. 2014;42(D1):1182–7.

Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira M, Bender D, et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Human Genet. 2007;81(3):559–75.

Wang K, Mingyao L, Hakonarson H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 2010;16:e164.

Skinner ME, Uzilov AV, Stein LD, Mungall CJ, Holmes IH. JBrowse: a next-generation genome browser. Genome Res. 2009;19(9):1630–8.

Wuyun T, Zhu XC, Zhu GP, Zhao H. Extraction and refining technology of Siberian apricot kernel oil (CN 105950277 B), China, Patent. June, 11, 2019.

Wuyun T, Jiang ZM, Zhu XC, Zhu XC, Zhao H. Production method of Siberian apricot kernel tofu ice cream (CN 105913934 B), China, Patent. June, 11, 2019.

Deng WJ, Nickle DN, Learn GH, Maust B, Mullins J. ViroBLAST: a stand-alone BLAST web server for flexible queries of multiple databases and user's datasets. Bioinformatics. 2007;23(17):2334–2336.

Tal G, Alan O, Jonathan S, Carson S. heatmaply: an R package for creating interactive cluster heatmaps for online publishing. Bioinformatics. 2017;34(9): 1600–2.

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