[1] |
Xu Y, Fan M, Zhou S, Wang L, Qian H, et al. 2017. Effect of Vaccinium bracteatum Thunb. leaf pigment on the thermal, pasting, and textural properties and microstructure characterization of rice starch. Food chemistry 228:435−40 doi: 10.1016/j.foodchem.2017.02.041 |
[2] |
Wang L, Zhang Y, Xu M, Wang Y, Cheng S, et al. 2013. Anti-diabetic activity of Vaccinium bracteatum Thunb. leaves’ polysaccharide in STZ-induced diabetic mice. International journal of biological macromolecules 61:317−21 doi: 10.1016/j.ijbiomac.2013.07.028 |
[3] |
Wang L, Jiang T, Zhang H, Yao H. 2008. Study on the extraction of black pigment from Vaccinium bracteatum Thunb. leaves by enzyme and its stability. Science and Technology of Food Industry 29:224−226+258 doi: 10.13386/j.issn1002-0306.2008.10.055 |
[4] |
Fan M, Lian W, Li T, Fan Y, Rao Z, et al. 2020. Metabolomics approach reveals discriminatory metabolites associating with the blue pigments from Vaccinium bracteatum thunb. leaves at different growth stages. Industrial Crops and Products 147:112252 doi: 10.1016/j.indcrop.2020.112252 |
[5] |
Zhang J, Chu C, Li X, Yao S, Yan B, et al. 2014. Isolation and identification of antioxidant compounds in Vaccinium bracteatum Thunb. by UHPLC-Q-TOF LC/MS and their kidney damage protection. Journal of Functional Foods 11:62−70 doi: 10.1016/j.jff.2014.09.005 |
[6] |
Ren Y, Ke C, Tang C, Yao S, Ye Y. 2017. Divaccinosides A–D, four rare iridoid glucosidic truxillate esters from the leaves of Vaccinium bracteatum. Tetrahedron Letters 58(24):2385−8 doi: 10.1016/j.tetlet.2017.05.013 |
[7] |
Zhao J, Wu Y, Niu X, Zhang Y, Xu X, et al. 2017. Content determination of vaccinoside in leaves of Vaccinium bracteatum Thunb. by HPLC. Shanghai Journal of Traditional Chinese Medicine 51:100−2 doi: 10.16305/j.1007-1334.2017.10.027 |
[8] |
Fan M, Li T, Li Y, Qian H, Zhang H, et al. 2021. Vaccinium bracteatum Thunb. as a promising resource of bioactive compounds with health benefits: An updated review. Food Chemistry 356:129738 doi: 10.1016/j.foodchem.2021.129738 |
[9] |
Polashock J, Zelzion E, Fajardo D, Zalapa J, Georgi L, et al. 2014. The American cranberry: first insights into the whole genome of a species adapted to bog habitat. BMC Plant Biology 14:165 doi: 10.1186/1471-2229-14-165 |
[10] |
Diaz-Garcia L, Garcia-Ortega LF, González-Rodríguez M, Delaye L, Iorizzo M, et al. 2021. Chromosome-Level Genome Assembly of the American Cranberry (Vaccinium macrocarpon Ait. ) and Its Wild Relative Vaccinium microcarpum. Frontiers in Plant Science 12:633310 doi: 10.3389/fpls.2021.633310 |
[11] |
Wu C, Deng C, Hilario E, Albert NW, Lafferty D, et al. 2022. A chromosome-scale assembly of the bilberry genome identifies a complex locus controlling berry anthocyanin composition. Molecular Ecology Resources 22:345−60 doi: 10.1111/1755-0998.13467 |
[12] |
Tsuda H, Kunitake H, Yamasaki M, Komatsu H, Yoshioka K. 2013. Production of intersectional hybrids between colchicine-induced tetraploid shashanbo (Vaccinium bracteatum) and highbush blueberry ‘Spartan’. Journal of the American Society for Horticultural Science 138:317−24 doi: 10.21273/JASHS.138.4.317 |
[13] |
Costich DE, Ortiz R, Meagher TR, Bruederle LP, Vorsa N. 1993. Determination of ploidy level and nuclear DNA content in blueberry by flow cytometry. Theoretical and Applied Genetics 86:1001−6 doi: 10.1007/BF00211053 |
[14] |
Li X, Sun H, Pei J, Dong Y, Wang F, et al. 2012. De novo sequencing and comparative analysis of the blueberry transcriptome to discover putative genes related to antioxidants. Gene 511:54−61 doi: 10.1016/j.gene.2012.09.021 |
[15] |
Gupta V, Estrada AD, Blakley I, Reid R, Patel K, et al. 2015. RNA-Seq analysis and annotation of a draft blueberry genome assembly identifies candidate genes involved in fruit ripening, biosynthesis of bioactive compounds, and stage-specific alternative splicing. Gigascience 4:5 doi: 10.1186/s13742-015-0046-9 |
[16] |
Colle M, Leisner CP, Wai CM, Ou S, Bird KA, et al. 2019. Haplotype-phased genome and evolution of phytonutrient pathways of tetraploid blueberry. GigaScience 8:giz012 doi: 10.1093/gigascience/giz012 |
[17] |
Yu J, Hulse-Kemp AM, Babiker E, Staton M. 2021. High-quality reference genome and annotation aids understanding of berry development for evergreen blueberry (Vaccinium darrowii). Horticulture Research 8:228 doi: 10.1038/s41438-021-00641-9 |
[18] |
Wang P, Luo Y, Huang J, Gao S, Zhu G, et al. 2020. The genome evolution and domestication of tropical fruit mango. Genome Biology 21:60 doi: 10.1186/s13059-020-01959-8 |
[19] |
Rose JP, Kleist TJ, Löfstrand SD, Drew BT, Schönenberger J, et al. 2018. Phylogeny, historical biogeography, and diversification of angiosperm order Ericales suggest ancient Neotropical and East Asian connections. Molecular Phylogenetics and Evolution 122:59−79 doi: 10.1016/j.ympev.2018.01.014 |
[20] |
Soza VL, Lindsley D, Waalkes A, Ramage E, Patwardhan RP, et al. 2019. The Rhododendron genome and chromosomal organization provide insight into shared whole-genome duplications across the heath family (Ericaceae). Genome Biology and Evolution 11:3353−71 doi: 10.1093/gbe/evz245 |
[21] |
Peng Y, Lin-Wang K, Cooney JM, Wang T, Espley RV, et al. 2019. Differential regulation of the anthocyanin profile in purple kiwifruit (Actinidia species). Horticulture Research 6:3 doi: 10.1038/s41438-018-0076-4 |
[22] |
Dong J, Cao L, Zhang X, Zhang W, Yang T, et al. 2021. An R2R3-MYB transcription Factor RmMYB108 responds to chilling stress of Rosa multiflora and conferred cold tolerance of Arabidopsis. Frontiers in Plant Science 12:696919 doi: 10.3389/fpls.2021.696919 |
[23] |
Chen Y, Yang X, Li W, Zhao S. 2020. Knockdown of the DUF647 family memberRUS4 impairs stamen development and pollen maturation in Arabidopsis. Plant Science 301:110645 doi: 10.1016/j.plantsci.2020.110645 |
[24] |
Cheng H, Han L, Yang C, Wu X, Zhong N, et al. 2016. The cotton MYB108 forms a positive feedback regulation loop with CML11 and participates in the defense response against Verticillium dahliae infection. Journal of Experimental Botany 67:1935−50 doi: 10.1093/jxb/erw016 |
[25] |
Wei Z, Hu K, Zhao D, Tang J, Huang Z, et al. 2020. MYB44 competitively inhibits the formation of the MYB340-bHLH2-NAC56 complex to regulate anthocyanin biosynthesis in purple-fleshed sweet potato. BMC Plant Biology 20:258 doi: 10.1186/s12870-020-02451-y |
[26] |
El-Sharkawy I, Liang D, Xu K. 2015. Transcriptome analysis of an apple (Malus × domestica) yellow fruit somatic mutation identifies a gene network module highly associated with anthocyanin and epigenetic regulation. Journal of Experimental Botany 66:7359−76 doi: 10.1093/jxb/erv433 |
[27] |
Lin Q, Wang C, Dong W, Jiang Q, Wang D, et al. 2015. Transcriptome and metabolome analyses of sugar and organic acid metabolism in Ponkan (Citrus reticulata) fruit during fruit maturation. Gene 554:64−74 doi: 10.1016/j.gene.2014.10.025 |
[28] |
Guo S, Sun H, Zhang H, Liu J, Ren Y, et al. 2015. Comparative Transcriptome Analysis of Cultivated and Wild Watermelon during Fruit Development. PloS One 10:e0130267 doi: 10.1371/journal.pone.0130267 |
[29] |
Rahim MA, Robin AHK, Natarajan S, Jung HJ, Lee J, et al. 2018. Identification and Characterization of Anthocyanin Biosynthesis-Related Genes in Kohlrabi. Applied Biochemistry and Biotechnology 184:1120−41 doi: 10.1007/s12010-017-2613-2 |
[30] |
Li Y, Nie P, Zhang H, Wang L, Wang H, et al. 2017. Dynamic changes of anthocyanin accumulation and endogenous hormone contents in blueberry. Journal of Beijing Forestry University 39:64−71 doi: 10.13332/j.1000-1522.20160283 |
[31] |
Primetta AK, Karppinen K, Riihinen KR, Jaakola L. 2015. Metabolic and molecular analyses of white mutant Vaccinium berries show down-regulation of MYBPA1-type R2R3 MYB regulatory factor. Planta 242:631−43 doi: 10.1007/s00425-015-2363-8 |
[32] |
Lin Y, Wang Y, Li B, Tan H, Li D, et al. 2018. Comparative transcriptome analysis of genes involved in anthocyanin synthesis in blueberry. Plant Physiology and Biochemistry 127:561−72 doi: 10.1016/j.plaphy.2018.04.034 |
[33] |
Rogers SO, Bendich AJ. 1985. Extraction of DNA from milligram amounts of fresh, herbarium and mummified plant tissues. Plant Molecular Biology 5:69−76 doi: 10.1007/BF00020088 |
[34] |
Jiang S, An H, Xu F, Zhang X. 2020. Chromosome-level genome assembly and annotation of the loquat (Eriobotrya japonica) genome. GigaScience 9:giaa015 doi: 10.1093/gigascience/giaa015 |
[35] |
Li R, Fan W, Tian G, Zhu H, He L, et al. 2010. The sequence and de novo assembly of the giant panda genome. Nature 463:311−17 doi: 10.1038/nature08696 |
[36] |
Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH, et al. 2017. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Research 27:722−36 doi: 10.1101/gr.215087.116 |
[37] |
Vaser R, Sović I, Nagarajan N, Šikić M. 2017. Fast and accurate de novo genome assembly from long uncorrected reads. Genome Res 27:737−46 doi: 10.1101/gr.214270.116 |
[38] |
Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, et al. 2014. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One 9:e112963 doi: 10.1371/journal.pone.0112963 |
[39] |
Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, et al. 2009. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326:289−93 doi: 10.1126/science.1181369 |
[40] |
Rao SSP, Huntley MH, Durand NC, Stamenova EK, Bochkov ID, et al. 2014. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159:1665−80 doi: 10.1016/j.cell.2014.11.021 |
[41] |
Burton JN, Adey A, Patwardhan RP, Qiu R, Kitzman JO, et al. 2013. Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions. Nature Biotechnology 31:1119−25 doi: 10.1038/nbt.2727 |
[42] |
Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754−60 doi: 10.1093/bioinformatics/btp324 |
[43] |
Parra G, Bradnam K, Korf I. 2007. CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics 23:1061−67 doi: 10.1093/bioinformatics/btm071 |
[44] |
Simão FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM. 2015. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31:3210−12 doi: 10.1093/bioinformatics/btv351 |
[45] |
Price AL, Jones NC, Pevzner PA. 2005. De novo identification of repeat families in large genomes. Bioinformatics 21:i351−i358 doi: 10.1093/bioinformatics/bti1018 |
[46] |
Xu Z, Wang H. 2007. LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons. Nucleic Acids Research 35:W265−W268 doi: 10.1093/nar/gkm286 |
[47] |
Hoede C, Arnoux S, Moisset M, Chaumier T, Inizan O, et al. 2014. PASTEC: an automatic transposable element classification tool. PloS One 9:e91929 doi: 10.1371/journal.pone.0091929 |
[48] |
Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, et al. 2005. Repbase Update, a database of eukaryotic repetitive elements. Cytogenetic and Genome Research 110:462−7 doi: 10.1159/000084979 |
[49] |
Tarailo-Graovac M, Chen N. 2009. Using RepeatMasker to identify repetitive elements in genomic sequences. Current Protocols in Bioinformatics 25:4.10.1−4.10.14 doi: 10.1002/0471250953.bi0410s25 |
[50] |
Lowe TM, Eddy SR. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Research 25:955−64 doi: 10.1093/nar/25.5.955 |
[51] |
Kent WJ. 2002. BLAT — the BLAST-like alignment tool. Genome Research 12:656−64 doi: 10.1101/gr.229202 |
[52] |
She R, Chu JS, Wang K, Pei J, Chen N. 2009. GenBlastA: enabling BLAST to identify homologous gene sequences. Genome Research 19:143−49 doi: 10.1101/gr.082081.108 |
[53] |
Birney E, Clamp M, Durbin R. 2004. GeneWise and Genomewise. Genome Research 14:988−95 doi: 10.1101/gr.1865504 |
[54] |
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. Journal of Molecular Biology 215:403−10 doi: 10.1016/S0022-2836(05)80360-2 |
[55] |
Dimmer EC, Huntley RP, Alam-Faruque Y, Sawford T, O'Donovan C, et al. 2012. The UniProt-GO Annotation database in 2011. Nucleic Acids Research 40:D565−D570 doi: 10.1093/nar/gkr1048 |
[56] |
Emms DM, Kelly S. 2019. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biology 20:238 doi: 10.1186/s13059-019-1832-y |
[57] |
Mi H, Muruganujan A, Ebert D, Huang X, Thomas PD. 2019. PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools. Nucleic Acids Research 47:D419−D426 doi: 10.1093/nar/gky1038 |
[58] |
Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ. 2015. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Molecular Biology and Evolution 32:268−74 doi: 10.1093/molbev/msu300 |
[59] |
Katoh K, Asimenos G, Toh H. 2009. Multiple alignment of DNA sequences with MAFFT. In Bioinformatics for DNA Sequence Analysis. Methods in Molecular Biology, eds. Posada D. (eds) vol. 537: XIV, 354. New York: Humana Press. pp. 39−64 https://doi.org/10.1007/978-1-59745-251-9_3 |
[60] |
Talavera G, Castresana J. 2007. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Systematic Biology 56:564−77 doi: 10.1080/10635150701472164 |
[61] |
Kalyaanamoorthy S, Minh BQ, Wong TKF, von Haeseler A, Jermiin LS. 2017. ModelFinder: fast model selection for accurate phylogenetic estimates. Nature Methods 14:587−89 doi: 10.1038/nmeth.4285 |
[62] |
Yang Z. 1997. PAML: a program package for phylogenetic analysis by maximum likelihood. Bioinformatics 13:555−56 doi: 10.1093/bioinformatics/13.5.555 |
[63] |
Han MV, Thomas GW, Lugo-Martinez J, Hahn MW. 2013. Estimating gene gain and loss rates in the presence of error in genome assembly and annotation using CAFE 3. Molecular Biology and Evolution 30:1987−97 doi: 10.1093/molbev/mst100 |
[64] |
Yang Z. 2007. PAML 4: phylogenetic analysis by maximum likelihood. Molecular Biology and Evolution 24:1586−91 doi: 10.1093/molbev/msm088 |
[65] |
Zwaenepoel A, Van de Peer Y. 2019. wgd—simple command line tools for the analysis of ancient whole-genome duplications. Bioinformatics (Oxford, England) 35:2153−55 doi: 10.1093/bioinformatics/bty915 |
[66] |
Buchfink B, Xie C, Huson DH. 2015. Fast and sensitive protein alignment using DIAMOND. Nature Methods 12:59−60 doi: 10.1038/nmeth.3176 |
[67] |
Wang Y, Tang H, Debarry JD, Tan X, Li J, et al. 2012. MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Research 40:e49 doi: 10.1093/nar/gkr1293 |
[68] |
Tang H, Krishnakuar V, Li J. 2015. jcvi: JCVI utility libraries. Zenodo. http://doi.org/10.5281/zenodo.31631 |
[69] |
Xu Y, Bi C, Wu G, Wei S, Dai X, et al. 2016. VGSC: A web-based vector graph toolkit of genome synteny and collinearity. BioMed Research International 2016:7823429 doi: 10.1155/2016/7823429 |