doi:10.48130/BPR-2021-0005

[1]

Xia E, Zhang H, Sheng J, Li K, Zhang Q, et al. 2017. The tea tree genome provides insights into tea flavor and independent evolution of caffeine biosynthesis. Molecular Plant 10:866−77 doi: 10.1016/j.molp.2017.04.002

[2]

Chen Y, Yu M, Xu J, Chen X, Shi J. 2009. Differentiation of eight tea (Camellia sinensis) cultivars in China by elemental fingerprint of their leaves. Journal of the Science of Food and Agriculture 89:2350−55 doi: 10.1002/jsfa.3716

[3]

Juneja LR, Chu DC, Okubo T, Nagato Y, Yokogoshi H. 1999. L-theanine - a unique amino acid of green tea and its relaxation effect in humans. Trends in Food Science & Technology 10:199−204 doi: 10.1016/S0924-2244(99)00044-8

[4]

Mukhtar H, Ahmad N. 2000. Tea polyphenols: prevention of cancer and optimizing health. The American Journal of Clinical Nutrition 71:1698S−1702S doi: 10.1093/ajcn/71.6.1698S

[5]

Koshiishi C, Kato A, Yama S, Crozier A, Ashihara H. 2001. A new caffeine biosynthetic pathway in tea leaves: utilisation of adenosine released from the S-adenosyl-L-methionine cycle. FEBS Letters 499:50−54 doi: 10.1016/S0014-5793(01)02512-1

[6]

Zhang Z, Li Y, Qi L, Wan X. 2006. Antifungal activities of major tea leaf volatile constituents toward Colletorichum camelliae Massea. Journal of Agricultural and Food Chemistry 54:3936−40 doi: 10.1021/jf060017m

[7]

Zhang S, Xuan H, Zhang L, Fu S, Wang Y, et al. 2017. TBC2health: a database of experimentally validated health-beneficial effects of tea bioactive compounds. Briefings in Bioinformatics 18:830−36 doi: 10.1093/bib/bbw055

[8]

Xia E H, Tong W, Wu Q, Wei S, Zhao J, et al. 2020. Tea plant genomics: achievements, challenges and perspectives. Horticulture Research 7:7 doi: 10.1038/s41438-019-0225-4

[9]

Ott J, Wang J, Leal SM. 2015. Genetic linkage analysis in the age of whole-genome sequencing. Nature Reviews Genetics 16:275−84 doi: 10.1038/nrg3908

[10]

Zhang C, Wang L, Wei K, Wu L, Li H, et al. 2016. Transcriptome analysis reveals self-incompatibility in the tea plant (Camellia sinensis) might be under gametophytic control. BMC Genomics 17:359 doi: 10.1186/s12864-016-2703-5

[11]

Kang M, Wu H, Yang Q, Huang L, Hu Q, et al. 2020. A chromosome-scale genome assembly of Isatis indigotica, an important medicinal plant used in traditional Chinese medicine. Horticulture Research 7:18 doi: 10.1038/s41438-020-0240-5

[12]

Wei S, Yang Y, Yin T. 2020. The chromosome-scale assembly of the willow genome provides insight into Salicaceae genome evolution. Horticulture Research 7:45 doi: 10.1038/s41438-020-0268-6

[13]

Li S, Wang J, Dong R, Zhu H, Lan L, et al. 2020. Chromosome-level genome assembly, annotation and evolutionary analysis of the ornamental plant Asparagus setaceus. Horticulture Research 7:48 doi: 10.1038/s41438-020-0271-y

[14]

Gao S, Wang B, Xie S, Xu X, Zhang J, et al. 2020. A high-quality reference genome of wild Cannabis sativa. Horticulture Research 7:73 doi: 10.1038/s41438-020-0295-3

[15]

Xue T, Zheng X, Chen D, Liang L, Chen N, et al. 2020. A high-quality genome provides insights into the new taxonomic status and genomic characteristics of Cladopus chinensis (Podostemaceae). Horticulture Research 7:46 doi: 10.1038/s41438-020-0269-5

[16]

Xanthopoulou A, Manioudaki M, Bazakos C, Kissoudis C, Farsakoglou AM, et al. 2020. Whole genome re-sequencing of sweet cherry (Prunus avium L.) yields insights into genomic diversity of a fruit species. Horticulture Research 7:60 doi: 10.1038/s41438-020-0281-9

[17]

Hu M, Sun W, Tsai WC, Xiang S, Lai X, et al. 2020. Chromosome-scale assembly of the Kandelia obovata genome. Horticulture Research 7:60 doi: 10.1038/s41438-020-0300-x

[18]

Fan Y, Sahu SK, Yang T, Mu W, Wei J, et al. 2020. Dissecting the genome of star fruit (Averrhoa carambola L.). Horticulture Research 7:94 doi: 10.1038/s41438-020-0306-4

[19]

Peace CP, Bianco L, Troggio M, van de Weg E, Howard NP, et al. 2019. Apple whole genome sequences: recent advances and new prospects. Horticulture Research 6:59 doi: 10.1038/s41438-019-0141-7

[20]

Li Q, Qi J, Qin X, Dou W, Lei T, et al. 2020. CitGVD: a comprehensive database of citrus genomic variations. Horticulture Research 7:12 doi: 10.1038/s41438-019-0234-3

[21]

Liu T, Li M, Liu Z, Ai X, Li Y. 2021. Reannotation of the cultivated strawberry genome and establishment of a strawberry genome database. Horticulture research 8(1):41 doi: 10.1038/s41438-021-00476-4

[22]

Yue J, Liu J, Tang W, Wu Y, Tang X, et al. 2020. Kiwifruit Genome Database (KGD): a comprehensive resource for kiwifruit genomics. Horticulture Research 7:117 doi: 10.1038/s41438-020-0338-9

[23]

Yano K, Aoki K, Shibata D. 2007. Genomic Databases for Tomato. Plant Biotechnology 24:17−25 doi: 10.5511/plantbiotechnology.24.17

[24]

Xu H, Yu Q, Shi Y, Hua X, Tang H, et al. 2018. PGD: Pineapple Genomics Database. Horticulture Research 5:66 doi: 10.1038/s41438-018-0078-2

[25]

Kim C, Park D, Seol Y, Yoon U, Lee G, et al. 2012. An online database for genome information of agricultural plants. Bioinformation 8:1059−61 doi: 10.6026/97320630081059

[26]

Chen J, Zheng C, Ma J, Jiang C, Ercisli S, et al. 2020. The chromosome-scale genome reveals the evolution and diversification after the recent tetraploidization event in tea plant. Horticulture Research 7:63 doi: 10.1038/s41438-020-0288-2

[27]

Xia E, Tong W, Hou Y, An Y, Chen L, et al. 2020. The reference genome of tea plant and resequencing of 81 diverse accessions provide insights into its genome evolution and adaptation. Molecular Plant 13:1013−26 doi: 10.1016/j.molp.2020.04.010

[28]

Wang X, Feng H, Chang Y, Ma C, Wang L, et al. 2020. Population sequencing enhances understanding of tea plant evolution. Nature Communications 11:4447 doi: 10.1038/s41467-020-18228-8

[29]

Zhang Q, Li W, Li K, Nan H, Shi C, et al. 2020. The chromosome-level reference genome of tea tree unveils recent bursts of non-autonomous LTR retrotransposons in driving genome size evolution. Molecular Plant 13:935−38 doi: 10.1016/j.molp.2020.04.009

[30]

Zhang W, Zhang Y, Qiu H, Guo Y, Wan H, et al. 2020. Genome assembly of wild tea tree DASZ reveals pedigree and selection history of tea varieties. Nature Communications 11:3719 doi: 10.1038/s41467-020-17498-6

[31]

Wei C, Yang H, Wang S, Zhao J, Liu C, et al. 2018. Draft genome sequence of Camellia sinensis var. sinensis provides insights into the evolution of the tea genome and tea quality. PNAS 115:E4151−E4158 doi: 10.1073/pnas.1719622115

[32]

Wang P, Yu J, Jin S, Chen S, Yue C, et al. 2021. Genetic basis of high aroma and stress tolerance in the oolong tea cultivar genome. Horticulture research 8:107 doi: 10.1038/s41438-021-00542-x

[33]

Guo W, Chen J, Li J, Huang J, Wang Z, et al. 2020. Portal of Juglandaceae: A comprehensive platform for Juglandaceae study. Horticulture Research 7:35 doi: 10.1038/s41438-020-0256-x

[34]

Zeng C, Hollingsworth PM, Yang J, He Z S, Zhang Z R, et al. 2018. Genome skimming herbarium specimens for DNA barcoding and phylogenomics. Plant Methods 14:43 doi: 10.1186/s13007-018-0300-0

[35]

Dong M, Liu S, Xu Z, Hu Z, Ku W, et al. 2018. The complete chloroplast genome of an economic plant, Camellia sinensis cultivar Anhua, China. Mitochondrial DNA Part B - Resources 3:558−59 doi: 10.1080/23802359.2018.1462124

[36]

Huang H, Shi C, Liu Y, Mao S, Gao L. 2014. Thirteen Camellia chloroplast genome sequences determined by high-throughput sequencing: genome structure and phylogenetic relationships. BMC Evolutionary Biology 14:151 doi: 10.1186/1471-2148-14-151

[37]

Chen S, Li R, Ma Y, Lei S, Ming R, et al. 2021. The complete chloroplast genome sequence of Camellia sinensis var. sinensis cultivar Tieguanyin (Theaceae). Mitochondrial DNA Part B-Resources 6:395−96 doi: 10.1080/23802359.2020.1869615

[38]

Ye X, Zhao Z, Xu Y, Xu H, Sun L. 2015. The Phylogenetic Analysis of Camellia sinensis cv. Longjing 43. Journal of the Korean Tea Society, special 21:63−66

[39]

Li L, Hu Y, He M, Zhang B, Wu W, et al. 2021. Comparative chloroplast genomes: insights into the evolution of the chloroplast genome of Camellia sinensis and the phylogeny of Camellia. BMC genomics 22:138 doi: 10.1186/s12864-021-07427-2

[40]

Li L, Hu Y, Wu L, Chen R, Luo S. 2021. The complete chloroplast genome sequence of Camellia sinensis cv. Dahongpao: a most famous variety of Wuyi tea (Synonym: Thea bohea L.). Mitochondrial DNA Part B - Resources 6:3−5 doi: 10.1080/23802359.2020.1844093

[41]

Hao W, Wang S, Yao M, Ma J, Xu Y, et al. 2019. The complete chloroplast genome of an albino tea, Camellia sinensis cultivar 'Baiye 1'. Mitochondrial DNA Part B - Resources 4:3143−44 doi: 10.1080/23802359.2019.1667889

[42]

Lee DJ, Kim CK, Lee TH, Lee SJ, Moon DG, et al. 2020. The complete chloroplast genome sequence of economical standard tea plant, Camellia sinensis L. cultivar Sangmok, in Korea. Mitochondrial DNA Part B-Resources 5:2841−42 doi: 10.1080/23802359.2020.1790311

[43]

Rawal HC, Kumar PM, Bera B, Singh NK, Mondal TK. 2020. Decoding and analysis of organelle genomes of Indian tea (Camellia assamica) for phylogenetic confirmation. Genomics 112:659−68 doi: 10.1016/j.ygeno.2019.04.018

[44]

Zhang F, Li W, Gao C, Zhang D, Gao L. 2019. Deciphering tea tree chloroplast and mitochondrial genomes of Camellia sinensis var. assamica. Scientific Data 6:209 doi: 10.1038/s41597-019-0201-8

[45]

Jia X, Zhang W, Fernie AR, Wen W. 2019. Camellia sinensis (Tea). Trends in Genetics 37:201−2 doi: 10.1016/j.tig.2020.10.002

[46]

Finn R D, Attwood T K, Babbitt P C, Bateman A, Bork P, et al. 2017. InterPro in 2017—beyond protein family and domain annotations. Nucleic Acids Research 45:D190−D199 doi: 10.1093/nar/gkw1107

[47]

Mistry J, Chuguransky S, Williams L, Qureshi M, Salazar GA, et al. 2021. Pfam: The protein families database in 2021. Nucleic Acids Research 49:D412−D419 doi: 10.1093/nar/gkaa913

[48]

Potter SC, Luciani A, Eddy SR, Park Y, Lopez R, et al. 2018. HMMER web server: 2018 update. Nucleic Acids Research 46:W200−W204 doi: 10.1093/nar/gky448

[49]

Aramaki T, Blanc-Mathieu R, Endo H, Ohkubo K, Kanehisa M, et al. 2020. KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold. Bioinformatics 36:2251−52 doi: 10.1093/bioinformatics/btz859

[50]

Armenteros JJA, Tsirigos KD, Sønderby, CK, Petersen T N, Winther O, et al. 2019. SignalP 5.0 improves signal peptide predictions using deep neural networks. Nature Biotechnology 37:420−23 doi: 10.1038/s41587-019-0036-z

[51]

Ginestet C. 2011. ggplot2: Elegant Graphics for Data Analysis. Journal of the Royal Statistical Society Series a - Statistics in Society 174:245−46 doi: 10.1111/j.1467-985X.2010.00676_9.x

[52]

Gong X, Zhang D. 2011. Research on Web Server Based on Red5, Tomcat and Apache. Advanced Materials Research 282−283:721−25 doi: 10.4028/www.scientific.net/AMR.282-283.721

[53]

Hoy MB. 2011. HTML5: A new standard for the web. Medical Reference Services Quarterly 30:50−55 doi: 10.1080/02763869.2011.540212

[54]

Prokhorenko V, Choo KKR, Ashman H. 2016. Intent-Based Extensible Real-Time PHP Supervision Framework. IEEE Transactions on Information Forensics and Security 11:2215−26 doi: 10.1109/tifs.2016.2569063

[55]

Di Giacomo M. 2005. MySQL: Lessons learned on a digital library. IEEE Software 22:10−13 doi: 10.1109/MS.2005.71

[56]

Korpela J. 1998. Lurching toward Babel: HTML, CSS and XML. Computer 31:103−4 doi: 10.1109/2.689682

[57]

Wei S, Xhakaj F, Ryder BG. 2016. Empirical study of the dynamic behavior of JavaScript objects. Software-Practice and Experience 46:867−89 doi: 10.1002/spe.2334

[58]

Lee S-U, Moon I-Y. 2011. A study of user interaction using jQuery in Web Application. Journal of Advanced Navigation Technology 15(4):626−31 doi: 10.12673/jant.2011.15.4.626

[59]

Priyam A, Woodcroft BJ, Rai V, Moghul I, Munagala A, et al. 2019. Sequenceserver: a modern graphical user interface for custom BLAST databases. Molecular Biology and Evolution 36:2922−24 doi: 10.1093/molbev/msz185

[60]

Wang H, Ooi BC, Tan KL, Ong TH, Zhou L. 2003. BLAST++: BLASTing queries in batches. Bioinformatics 19:2323−24 doi: 10.1093/bioinformatics/btg310

[61]

Westesson O, Skinner M, Holmes I. 2013. Visualizing next-generation sequencing data with JBrowse. Briefings in Bioinformatics 14:172−77 doi: 10.1093/bib/bbr078

[62]

Seppey M, Manni M, Zdobnov EM. 2019. BUSCO: assessing genome assembly and annotation completeness. In Gene prediction. methods in molecular biology, ed. Kollmar M. vol 1962. New York: Humana. pp. 227−45. https://doi.org/10.1007/978-1-4939-9173-0_14

[63]

Xia EH, Li FD, Tong W, Li PH, Wu Q, et al. 2019. Tea Plant Information Archive: a comprehensive genomics and bioinformatics platform for tea plant. Plant Biotechnology Journal 17:1938−53 doi: 10.1111/pbi.13111

[64]

Yue Y, Chu G, Liu X, Tang X, Wang W, et al. 2014. TMDB: A literature-curated database for small molecular compounds found from tea. BMC Plant Biology 14:243 doi: 10.1186/s12870-014-0243-1

[65]

Zhang R, Ma Y, Hu X, Chen Y, He X, et al. 2020. TeaCoN: a database of gene co-expression network for tea plant (Camellia sinensis). BMC Genomics 21:461 doi: 10.1186/s12864-020-06839-w

[66]

Buels R, Yao E, Diesh CM, Hayes RD, Munoz-Torres M, et al. 2016. JBrowse: a dynamic web platform for genome visualization and analysis. Genome Biology 17:66 doi: 10.1186/s13059-016-0924-1

[67]

Du L, Zhang C, Liu Q, Zhang X, Yue B. 2018. Krait: an ultrafast tool for genome-wide survey of microsatellites and primer design. Bioinformatics 34:681−83 doi: 10.1093/bioinformatics/btx665

[68]

Dubey H, Rawal HC, Rohilla M, Lama U, Kumar PM et al. 2020. TeaMiD: a comprehensive database of simple sequence repeat markers of tea. Database 2020:baaa013 doi: 10.1093/database/baaa013

[69]

Mondal TK, Rawal HC, Bera B, Kumar PM, Choubey M, et al. 2019. Draft genome sequence of a popular Indian tea genotype TV-1 [Camellia assamica L. (O). Kunze]. bioRxiv Preprint doi: 10.1101/762161